PDB Short entry for 1ZET HEADER REPLICATION/DNA 19-APR-05 1ZET TITLE X-RAY DATA DO NOT SUPPORT HOOGSTEEN BASE-PAIRING DURING REPLICATION BY TITLE 2 HUMAN POLYMERASE IOTA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*AP*GP*GP*GP*(BRU)P*CP*CP*(BRU)P*(BRU) COMPND 3 P*CP*CP*CP*CP*C)-3'; COMPND 4 CHAIN: T; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*(DOC))-3'; COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: POLYMERASE (DNA DIRECTED) IOTA; COMPND 12 CHAIN: A; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: POLI; SOURCE 10 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 11 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS PROTEIN, DNA, DTTP, STATISTICAL DYAD, REPLICATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG REVDAT 7 14-FEB-24 1ZET 1 REMARK LINK REVDAT 6 28-SEP-11 1ZET 1 REMARK VERSN REVDAT 5 23-FEB-11 1ZET 1 REMARK REVDAT 4 16-FEB-10 1ZET 1 JRNL REVDAT 3 24-FEB-09 1ZET 1 VERSN REVDAT 2 11-APR-06 1ZET 1 REMARK REVDAT 1 19-JUL-05 1ZET 0 JRNL AUTH J.WANG JRNL TITL DNA POLYMERASES: HOOGSTEEN BASE-PAIRING IN DNA REPLICATION? JRNL REF NATURE V. 437 E6 2005 JRNL REFN ISSN 0028-0836 JRNL PMID 16163299 JRNL DOI 10.1038/NATURE04199 REMARK 0 REMARK 0 THIS ENTRY 1ZET REFLECTS AN ALTERNATIVE MODELING OF THE REMARK 0 STRUCTURAL DATA IN R1T3NSF ORIGINAL DATA DETERMINED BY REMARK 0 AUTHOR: D.T.NAIR,R.E.JOHNSON,S.PRAKASH,L.PRAKASH,A.K.AGGARWAL REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 1T3N REMARK 0 AUTH D.T.NAIR,R.E.JOHNSON,S.PRAKASH,L.PRAKASH,A.K.AGGARWAL REMARK 0 TITL REPLICATION BY HUMAN DNA POLYMERASE-IOTA OCCURS BY HOOGSTEEN REMARK 0 TITL 2 BASE-PAIRING. REMARK 0 REF NATURE V. 430 377 2004 REMARK 0 REFN ISSN 0028-0836 REMARK 0 PMID 15254543 REMARK 0 DOI 10.1038/NATURE02692 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 559823.990 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 26413 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.261 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1529 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3933 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 252 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3068 REMARK 3 NUCLEIC ACID ATOMS : 550 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.90000 REMARK 3 B22 (A**2) : 6.90000 REMARK 3 B33 (A**2) : -13.81000 REMARK 3 B12 (A**2) : 3.74000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 6.060 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 7.670 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 8.780 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 10.410; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 61.62 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : TTP.PAR REMARK 3 PARAMETER FILE 3 : DNA-RNA_REP-BRU.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA-BRU.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : TTP.TOP REMARK 3 TOPOLOGY FILE 5 : ION.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS ENTRY REFLECTS AN ALTERNATIVE REMARK 3 MODELING OF X-RAY DATA R1T3NSF REMARK 4 REMARK 4 1ZET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 1T3N. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 135.17000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.58500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.37750 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.79250 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 168.96250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 135.17000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 67.58500 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 33.79250 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 101.37750 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 168.96250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC T 18 P DC T 18 OP2 -0.197 REMARK 500 DC T 18 P DC T 18 O5' 0.262 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC T 18 OP1 - P - OP2 ANGL. DEV. = 11.4 DEGREES REMARK 500 DC T 18 O5' - P - OP1 ANGL. DEV. = -10.5 DEGREES REMARK 500 DC T 18 O5' - P - OP2 ANGL. DEV. = -25.0 DEGREES REMARK 500 DC T 18 P - O5' - C5' ANGL. DEV. = -18.2 DEGREES REMARK 500 PRO A 215 C - N - CA ANGL. DEV. = -10.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 37 66.35 18.58 REMARK 500 GLU A 49 23.12 -68.66 REMARK 500 LYS A 51 27.38 -78.06 REMARK 500 VAL A 63 91.28 -68.02 REMARK 500 GLU A 69 23.30 -75.74 REMARK 500 ALA A 70 -17.23 -157.28 REMARK 500 LEU A 73 33.87 -87.20 REMARK 500 MET A 79 -150.80 -71.19 REMARK 500 ASN A 80 94.31 46.53 REMARK 500 ASP A 83 -80.40 -42.82 REMARK 500 LYS A 87 11.37 -66.90 REMARK 500 CYS A 88 82.93 -170.65 REMARK 500 VAL A 92 72.30 33.84 REMARK 500 ASP A 146 -38.09 -137.32 REMARK 500 LYS A 245 -70.96 -64.47 REMARK 500 GLU A 272 -37.19 -135.04 REMARK 500 GLU A 304 81.30 178.17 REMARK 500 GLU A 305 -172.19 -61.84 REMARK 500 SER A 307 -118.26 -82.98 REMARK 500 PHE A 308 52.05 14.35 REMARK 500 LYS A 309 -4.84 -172.68 REMARK 500 ALA A 317 -71.67 -153.77 REMARK 500 LYS A 320 18.99 -66.84 REMARK 500 ILE A 321 -30.15 -138.98 REMARK 500 ALA A 326 -105.06 -66.38 REMARK 500 LEU A 328 -9.57 -55.30 REMARK 500 LEU A 329 -67.33 -108.77 REMARK 500 ASN A 330 -3.78 -58.62 REMARK 500 HIS A 340 19.06 -140.77 REMARK 500 SER A 350 -147.37 -118.52 REMARK 500 GLU A 352 -83.58 58.22 REMARK 500 LYS A 353 -109.53 -140.02 REMARK 500 HIS A 354 41.24 -108.33 REMARK 500 TYR A 355 102.37 -56.27 REMARK 500 ARG A 360 108.53 -174.44 REMARK 500 PRO A 365 147.49 -38.15 REMARK 500 SER A 366 -128.73 -90.26 REMARK 500 HIS A 367 -122.02 32.87 REMARK 500 GLN A 370 53.97 -97.57 REMARK 500 LYS A 371 -162.82 -61.80 REMARK 500 LEU A 372 26.27 -161.54 REMARK 500 MET A 388 47.28 -85.40 REMARK 500 LYS A 389 -38.64 -160.74 REMARK 500 ARG A 392 0.04 -69.08 REMARK 500 VAL A 395 49.33 36.19 REMARK 500 VAL A 397 -36.71 -167.56 REMARK 500 HIS A 402 79.44 27.47 REMARK 500 LEU A 403 45.56 -161.66 REMARK 500 THR A 404 113.50 63.95 REMARK 500 LEU A 405 -145.16 -169.98 REMARK 500 REMARK 500 THIS ENTRY HAS 53 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 461 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 34 OD1 REMARK 620 2 LEU A 35 O 91.9 REMARK 620 3 ASP A 126 OD1 114.3 89.0 REMARK 620 4 TTP A 451 O1A 109.2 158.8 82.3 REMARK 620 5 TTP A 451 O1G 95.4 87.6 150.2 90.4 REMARK 620 6 TTP A 451 O2B 175.7 84.1 67.6 74.7 82.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 461 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP A 451 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T3N RELATED DB: PDB REMARK 900 STRUCTURE OF THE CATALYTIC CORE OF DNA POLYMERASE IOTA IN COMPLEX REMARK 900 WITH DNA AND DTTP DBREF 1ZET A 27 414 GB 21619716 AAH32662 27 414 DBREF 1ZET T 5 18 PDB 1ZET 1ZET 5 18 DBREF 1ZET P 1 13 PDB 1ZET 1ZET 1 13 SEQRES 1 T 14 DA DG DG DG BRU DC DC BRU BRU DC DC DC DC SEQRES 2 T 14 DC SEQRES 1 P 13 DG DG DG DG DG DA DA DG DG DA DC DC DOC SEQRES 1 A 388 SER ARG VAL ILE VAL HIS VAL ASP LEU ASP CYS PHE TYR SEQRES 2 A 388 ALA GLN VAL GLU MET ILE SER ASN PRO GLU LEU LYS ASP SEQRES 3 A 388 LYS PRO LEU GLY VAL GLN GLN LYS TYR LEU VAL VAL THR SEQRES 4 A 388 CYS ASN TYR GLU ALA ARG LYS LEU GLY VAL LYS LYS LEU SEQRES 5 A 388 MET ASN VAL ARG ASP ALA LYS GLU LYS CYS PRO GLN LEU SEQRES 6 A 388 VAL LEU VAL ASN GLY GLU ASP LEU THR ARG TYR ARG GLU SEQRES 7 A 388 MET SER TYR LYS VAL THR GLU LEU LEU GLU GLU PHE SER SEQRES 8 A 388 PRO VAL VAL GLU ARG LEU GLY PHE ASP GLU ASN PHE VAL SEQRES 9 A 388 ASP LEU THR GLU MET VAL GLU LYS ARG LEU GLN GLN LEU SEQRES 10 A 388 GLN SER ASP GLU LEU SER ALA VAL THR VAL SER GLY HIS SEQRES 11 A 388 VAL TYR ASN ASN GLN SER ILE ASN LEU LEU ASP VAL LEU SEQRES 12 A 388 HIS ILE ARG LEU LEU VAL GLY SER GLN ILE ALA ALA GLU SEQRES 13 A 388 MET ARG GLU ALA MET TYR ASN GLN LEU GLY LEU THR GLY SEQRES 14 A 388 CYS ALA GLY VAL ALA SER ASN LYS LEU LEU ALA LYS LEU SEQRES 15 A 388 VAL SER GLY VAL PHE LYS PRO ASN GLN GLN THR VAL LEU SEQRES 16 A 388 LEU PRO GLU SER CYS GLN HIS LEU ILE HIS SER LEU ASN SEQRES 17 A 388 HIS ILE LYS GLU ILE PRO GLY ILE GLY TYR LYS THR ALA SEQRES 18 A 388 LYS CYS LEU GLU ALA LEU GLY ILE ASN SER VAL ARG ASP SEQRES 19 A 388 LEU GLN THR PHE SER PRO LYS ILE LEU GLU LYS GLU LEU SEQRES 20 A 388 GLY ILE SER VAL ALA GLN ARG ILE GLN LYS LEU SER PHE SEQRES 21 A 388 GLY GLU ASP ASN SER PRO VAL ILE LEU SER GLY PRO PRO SEQRES 22 A 388 GLN SER PHE SER GLU GLU ASP SER PHE LYS LYS CYS SER SEQRES 23 A 388 SER GLU VAL GLU ALA LYS ASN LYS ILE GLU GLU LEU LEU SEQRES 24 A 388 ALA SER LEU LEU ASN ARG VAL CYS GLN ASP GLY ARG LYS SEQRES 25 A 388 PRO HIS THR VAL ARG LEU ILE ILE ARG ARG TYR SER SER SEQRES 26 A 388 GLU LYS HIS TYR GLY ARG GLU SER ARG GLN CYS PRO ILE SEQRES 27 A 388 PRO SER HIS VAL ILE GLN LYS LEU GLY THR GLY ASN TYR SEQRES 28 A 388 ASP VAL MET THR PRO MET VAL ASP ILE LEU MET LYS LEU SEQRES 29 A 388 PHE ARG ASN MET VAL ASN VAL LYS MET PRO PHE HIS LEU SEQRES 30 A 388 THR LEU LEU SER VAL CYS PHE CYS ASN LEU LYS MODRES 1ZET BRU T 9 DU MODRES 1ZET BRU T 12 DU MODRES 1ZET BRU T 13 DU MODRES 1ZET DOC P 13 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET BRU T 9 20 HET BRU T 12 20 HET BRU T 13 20 HET DOC P 13 18 HET MG A 461 1 HET TTP A 451 29 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE FORMUL 1 BRU 3(C9 H12 BR N2 O8 P) FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 MG MG 2+ FORMUL 5 TTP C10 H17 N2 O14 P3 FORMUL 6 HOH *168(H2 O) HELIX 1 1 CYS A 37 ASN A 47 1 11 HELIX 2 2 PRO A 48 LYS A 51 5 4 HELIX 3 3 ASN A 67 LYS A 72 1 6 HELIX 4 4 VAL A 81 LYS A 87 1 7 HELIX 5 5 LEU A 99 SER A 117 1 19 HELIX 6 6 LEU A 132 LEU A 143 1 12 HELIX 7 7 ASP A 146 VAL A 151 5 6 HELIX 8 8 ASN A 159 GLN A 161 5 3 HELIX 9 9 ASP A 167 GLY A 192 1 26 HELIX 10 10 ASN A 202 GLY A 211 1 10 HELIX 11 11 LEU A 222 GLU A 224 5 3 HELIX 12 12 SER A 225 HIS A 231 1 7 HELIX 13 13 HIS A 235 ILE A 239 5 5 HELIX 14 14 GLY A 243 ALA A 252 1 10 HELIX 15 15 SER A 257 PHE A 264 1 8 HELIX 16 16 SER A 265 PHE A 286 1 22 HELIX 17 17 LYS A 318 GLU A 323 1 6 HELIX 18 18 ALA A 326 ARG A 331 1 6 HELIX 19 19 ASN A 376 ASP A 378 5 3 HELIX 20 20 VAL A 379 PHE A 391 1 13 SHEET 1 A 6 VAL A 120 LEU A 123 0 SHEET 2 A 6 GLU A 127 ASP A 131 -1 O PHE A 129 N GLU A 121 SHEET 3 A 6 ILE A 30 LEU A 35 -1 N VAL A 33 O ASN A 128 SHEET 4 A 6 GLY A 195 ALA A 200 -1 O CYS A 196 N ASP A 34 SHEET 5 A 6 GLN A 218 VAL A 220 1 O THR A 219 N VAL A 199 SHEET 6 A 6 HIS A 156 VAL A 157 1 N HIS A 156 O GLN A 218 SHEET 1 B 3 VAL A 63 CYS A 66 0 SHEET 2 B 3 GLY A 56 GLN A 58 -1 N VAL A 57 O THR A 65 SHEET 3 B 3 VAL A 94 ASN A 95 1 O VAL A 94 N GLN A 58 SHEET 1 C 2 LYS A 338 PRO A 339 0 SHEET 2 C 2 LEU A 413 LYS A 414 -1 O LYS A 414 N LYS A 338 SHEET 1 D 3 GLN A 361 PRO A 363 0 SHEET 2 D 3 THR A 341 LEU A 344 -1 N VAL A 342 O CYS A 362 SHEET 3 D 3 VAL A 408 CYS A 409 -1 O CYS A 409 N ARG A 343 LINK O3' DG T 8 P BRU T 9 1555 1555 1.61 LINK O3' BRU T 9 P DC T 10 1555 1555 1.60 LINK C4 BRU T 9 C8 DG P 3 1555 12554 1.86 LINK C5 BRU T 9 N7 DG P 3 1555 12554 1.68 LINK C5 BRU T 9 C8 DG P 3 1555 12554 1.58 LINK O2 BRU T 9 C5 DG P 3 1555 12554 1.87 LINK O2 BRU T 9 N9 DG P 3 1555 12554 1.57 LINK O4 BRU T 9 N7 DG P 3 1555 12554 1.93 LINK C1' BRU T 9 C4' DG P 3 1555 12554 2.03 LINK C1' BRU T 9 O4' DG P 3 1555 12554 1.49 LINK C1' BRU T 9 C3' DG P 3 1555 12554 1.98 LINK C1' BRU T 9 C2' DG P 3 1555 12554 1.11 LINK C1' BRU T 9 N9 DG P 3 1555 12554 1.66 LINK C2' BRU T 9 C5' DG P 3 1555 12554 1.91 LINK C2' BRU T 9 C4' DG P 3 1555 12554 1.67 LINK C2' BRU T 9 C3' DG P 3 1555 12554 1.31 LINK C2' BRU T 9 C2' DG P 3 1555 12554 1.40 LINK C3' BRU T 9 C4' DG P 3 1555 12554 1.38 LINK C3' BRU T 9 O3' DG P 3 1555 12554 1.48 LINK C3' BRU T 9 C2' DG P 3 1555 12554 2.01 LINK C4' BRU T 9 O4' DG P 3 1555 12554 1.64 LINK C4' BRU T 9 C3' DG P 3 1555 12554 1.62 LINK C4' BRU T 9 O3' DG P 3 1555 12554 1.78 LINK O3' BRU T 9 C3' DG P 3 1555 12554 1.30 LINK O4' BRU T 9 C4' DG P 3 1555 12554 1.68 LINK O4' BRU T 9 C1' DG P 3 1555 12554 1.12 LINK C5' BRU T 9 C4' DG P 3 1555 12554 1.50 LINK O5' BRU T 9 P DG P 3 1555 12554 1.72 LINK O5' BRU T 9 OP1 DG P 3 1555 12554 1.76 LINK O5' BRU T 9 O5' DG P 3 1555 12554 1.20 LINK O5' BRU T 9 C5' DG P 3 1555 12554 1.21 LINK O5' BRU T 9 C4' DG P 3 1555 12554 1.64 LINK C4 BRU T 9 C5 DG P 3 1555 12554 2.02 LINK P BRU T 9 OP1 DG P 3 1555 12554 1.29 LINK P BRU T 9 OP2 DG P 3 1555 12554 1.49 LINK P BRU T 9 O5' DG P 3 1555 12554 1.61 LINK OP1 BRU T 9 P DG P 3 1555 12554 1.86 LINK OP1 BRU T 9 OP1 DG P 3 1555 12554 1.13 LINK OP2 BRU T 9 P DG P 3 1555 12554 1.61 LINK OP2 BRU T 9 OP2 DG P 3 1555 12554 1.14 LINK OP2 BRU T 9 O5' DG P 3 1555 12554 1.74 LINK N3 BRU T 9 C8 DG P 3 1555 12554 1.68 LINK N1 BRU T 9 C1' DG P 3 1555 12554 1.66 LINK N3 BRU T 9 C4 DG P 3 1555 12554 1.77 LINK N3 BRU T 9 C6 DG P 3 1555 12554 1.89 LINK C2 BRU T 9 C8 DG P 3 1555 12554 1.41 LINK C2 BRU T 9 C5 DG P 3 1555 12554 1.34 LINK C2 BRU T 9 N7 DG P 3 1555 12554 1.67 LINK O3' BRU T 9 P DG P 4 1555 12554 1.36 LINK O3' BRU T 9 O5' DG P 4 1555 12554 2.03 LINK O3' BRU T 9 OP2 DG P 4 1555 12554 1.87 LINK O3' DC T 11 P BRU T 12 1555 1555 1.61 LINK O3' BRU T 12 P BRU T 13 1555 1555 1.60 LINK C4 BRU T 12 O4 BRU T 13 1555 12554 1.71 LINK O2 BRU T 12 C2 BRU T 13 1555 12554 1.80 LINK O2 BRU T 12 N3 BRU T 13 1555 12554 1.43 LINK O2 BRU T 12 O2 BRU T 13 1555 12554 1.81 LINK O4 BRU T 12 O4 BRU T 13 1555 12554 1.82 LINK N3 BRU T 12 O4 BRU T 13 1555 12554 1.42 LINK N3 BRU T 12 C4 BRU T 13 1555 12554 1.72 LINK N3 BRU T 12 N3 BRU T 13 1555 12554 1.78 LINK O2 BRU T 12 C2 BRU T 13 12554 1555 1.80 LINK C2 BRU T 12 N3 BRU T 13 12554 1555 1.74 LINK N3 BRU T 12 N3 BRU T 13 12554 1555 1.78 LINK O2 BRU T 12 N3 BRU T 13 12554 1555 1.43 LINK N3 BRU T 12 C4 BRU T 13 12554 1555 1.72 LINK C2 BRU T 12 N3 BRU T 13 1555 12554 1.74 LINK O4 BRU T 12 O4 BRU T 13 12554 1555 1.82 LINK C4 BRU T 12 O4 BRU T 13 12554 1555 1.71 LINK O2 BRU T 12 O2 BRU T 13 12554 1555 1.81 LINK N3 BRU T 12 O4 BRU T 13 12554 1555 1.42 LINK O5' BRU T 12 N9 DA P 6 1555 12554 1.45 LINK C4 BRU T 12 N6 DA P 6 1555 12554 1.40 LINK C5 BRU T 12 C6 DA P 6 1555 12554 1.72 LINK C6 BRU T 12 N1 DA P 6 1555 12554 1.84 LINK C6 BRU T 12 C5 DA P 6 1555 12554 1.39 LINK O2 BRU T 12 N1 DA P 6 1555 12554 1.88 LINK C1' BRU T 12 N1 DA P 6 1555 12554 1.38 LINK C1' BRU T 12 C4 DA P 6 1555 12554 1.68 LINK C1' BRU T 12 C6 DA P 6 1555 12554 2.03 LINK C2' BRU T 12 C2 DA P 6 1555 12554 1.82 LINK C2' BRU T 12 N3 DA P 6 1555 12554 1.34 LINK C2' BRU T 12 C4 DA P 6 1555 12554 1.59 LINK C3' BRU T 12 N3 DA P 6 1555 12554 1.47 LINK C3' BRU T 12 C4 DA P 6 1555 12554 1.67 LINK C3' BRU T 12 C1' DA P 6 1555 12554 2.04 LINK C3' BRU T 12 N9 DA P 6 1555 12554 1.90 LINK C4' BRU T 12 N3 DA P 6 1555 12554 1.56 LINK C4' BRU T 12 C4 DA P 6 1555 12554 1.28 LINK C4' BRU T 12 C1' DA P 6 1555 12554 1.81 LINK C4' BRU T 12 N9 DA P 6 1555 12554 1.39 LINK O4' BRU T 12 C2 DA P 6 1555 12554 1.76 LINK O4' BRU T 12 N3 DA P 6 1555 12554 1.24 LINK O4' BRU T 12 C4 DA P 6 1555 12554 1.43 LINK C5' BRU T 12 C4 DA P 6 1555 12554 1.68 LINK C5' BRU T 12 C1' DA P 6 1555 12554 1.80 LINK C5' BRU T 12 C8 DA P 6 1555 12554 1.31 LINK O5' BRU T 12 C1' DA P 6 1555 12554 1.30 LINK O5' BRU T 12 C8 DA P 6 1555 12554 1.73 LINK P BRU T 12 O5' DA P 6 1555 12554 1.61 LINK P BRU T 12 O4' DA P 6 1555 12554 1.78 LINK OP1 BRU T 12 P DA P 6 1555 12554 1.83 LINK OP1 BRU T 12 O5' DA P 6 1555 12554 1.28 LINK OP1 BRU T 12 C5' DA P 6 1555 12554 1.81 LINK OP1 BRU T 12 C4' DA P 6 1555 12554 1.83 LINK OP1 BRU T 12 O4' DA P 6 1555 12554 1.96 LINK OP2 BRU T 12 O5' DA P 6 1555 12554 1.80 LINK C2 BRU T 12 C6 DA P 6 1555 12554 2.04 LINK C2 BRU T 12 N1 DA P 6 1555 12554 1.15 LINK N1 BRU T 12 N6 DA P 6 1555 12554 1.95 LINK N1 BRU T 12 C5 DA P 6 1555 12554 1.96 LINK N1 BRU T 12 C2 DA P 6 1555 12554 1.59 LINK O3' BRU T 13 P DC T 14 1555 1555 1.61 LINK C6 BRU T 13 C4 DA P 7 1555 12554 1.64 LINK BR BRU T 13 C5 DA P 7 1555 12554 1.69 LINK C1' BRU T 13 N3 DA P 7 1555 12554 1.76 LINK C4' BRU T 13 C1' DA P 7 1555 12554 2.03 LINK O4' BRU T 13 N3 DA P 7 1555 12554 1.69 LINK C5' BRU T 13 N9 DA P 7 1555 12554 1.65 LINK C5' BRU T 13 O4' DA P 7 1555 12554 1.80 LINK C5' BRU T 13 C2' DA P 7 1555 12554 1.80 LINK O5' BRU T 13 N9 DA P 7 1555 12554 1.14 LINK O5' BRU T 13 O4' DA P 7 1555 12554 1.39 LINK O5' BRU T 13 C1' DA P 7 1555 12554 1.17 LINK O5' BRU T 13 C4 DA P 7 1555 12554 2.04 LINK C6 BRU T 13 N1 DA P 7 1555 12554 1.42 LINK OP1 BRU T 13 C4' DA P 7 1555 12554 2.01 LINK OP1 BRU T 13 O4' DA P 7 1555 12554 1.48 LINK OP2 BRU T 13 O5' DA P 7 1555 12554 1.59 LINK OP2 BRU T 13 C5' DA P 7 1555 12554 1.54 LINK OP2 BRU T 13 O4' DA P 7 1555 12554 1.90 LINK C6 BRU T 13 C6 DA P 7 1555 12554 1.97 LINK C6 BRU T 13 N3 DA P 7 1555 12554 1.14 LINK C5 BRU T 13 C5 DA P 7 1555 12554 2.04 LINK C5 BRU T 13 C2 DA P 7 1555 12554 1.60 LINK C4 BRU T 13 N1 DA P 7 1555 12554 1.23 LINK N3 BRU T 13 N1 DA P 7 1555 12554 2.00 LINK C2 BRU T 13 C2 DA P 7 1555 12554 1.77 LINK N1 BRU T 13 N3 DA P 7 1555 12554 1.42 LINK C2' BRU T 13 C1' DG P 8 1555 12554 1.90 LINK C2' BRU T 13 O4' DG P 8 1555 12554 1.68 LINK C3' BRU T 13 C4' DG P 8 1555 12554 2.04 LINK C3' BRU T 13 O4' DG P 8 1555 12554 1.55 LINK O3' DC P 12 P DOC P 13 1555 1555 1.60 LINK OD1 ASP A 34 MG MG A 461 1555 1555 2.18 LINK O LEU A 35 MG MG A 461 1555 1555 2.39 LINK OD1 ASP A 126 MG MG A 461 1555 1555 2.39 LINK O1A TTP A 451 MG MG A 461 1555 1555 2.58 LINK O1G TTP A 451 MG MG A 461 1555 1555 2.50 LINK O2B TTP A 451 MG MG A 461 1555 1555 2.51 SITE 1 AC1 4 ASP A 34 LEU A 35 ASP A 126 TTP A 451 SITE 1 AC2 18 ASP A 34 LEU A 35 ASP A 36 CYS A 37 SITE 2 AC2 18 PHE A 38 TYR A 39 THR A 65 TYR A 68 SITE 3 AC2 18 ARG A 71 LYS A 77 ASP A 126 LYS A 214 SITE 4 AC2 18 MG A 461 HOH A 510 HOH A 550 HOH A 607 SITE 5 AC2 18 DOC P 13 DA T 5 CRYST1 98.831 98.831 202.755 90.00 90.00 120.00 P 65 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010118 0.005842 0.000000 0.00000 SCALE2 0.000000 0.011684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004932 0.00000