PDB Short entry for 2PFQ HEADER TRANSFERASE, LYASE/DNA 05-APR-07 2PFQ TITLE MANGANESE PROMOTES CATALYSIS IN A DNA POLYMERASE LAMBDA-DNA CRYSTAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: TEMPLATE; COMPND 3 CHAIN: T; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PRIMER; COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DOWNSTREAM PRIMER; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 15 CHAIN: A; COMPND 16 SYNONYM: POL LAMBDA, DNA POLYMERASE KAPPA, DNA POLYMERASE BETA-2, POL COMPND 17 BETA2; COMPND 18 EC: 2.7.7.7, 4.2.99.-; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 MOL_ID: 2; SOURCE 3 SYNTHETIC: YES; SOURCE 4 MOL_ID: 3; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 4; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: POLL; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PET-22B (+) KEYWDS DNA POLYMERASE, DNA REPAIR, PHOSPHORYL TRANSFER REACTION, MANGANESE, KEYWDS 2 TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.GARCIA-DIAZ,K.BEBENEK,J.M.KRAHN,L.C.PEDERSEN,T.A.KUNKEL REVDAT 6 30-AUG-23 2PFQ 1 REMARK REVDAT 5 20-OCT-21 2PFQ 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2PFQ 1 REMARK REVDAT 3 24-FEB-09 2PFQ 1 VERSN REVDAT 2 04-SEP-07 2PFQ 1 JRNL REVDAT 1 15-MAY-07 2PFQ 0 JRNL AUTH M.GARCIA-DIAZ,K.BEBENEK,J.M.KRAHN,L.C.PEDERSEN,T.A.KUNKEL JRNL TITL ROLE OF THE CATALYTIC METAL DURING POLYMERIZATION BY DNA JRNL TITL 2 POLYMERASE LAMBDA. JRNL REF DNA REPAIR V. 6 1333 2007 JRNL REFN ISSN 1568-7864 JRNL PMID 17475573 JRNL DOI 10.1016/J.DNAREP.2007.03.005 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.9 REMARK 3 NUMBER OF REFLECTIONS : 25703 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.256 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1241 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2496 REMARK 3 NUCLEIC ACID ATOMS : 446 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.58300 REMARK 3 B22 (A**2) : -10.71500 REMARK 3 B33 (A**2) : 3.13200 REMARK 3 B12 (A**2) : 0.00000 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.438 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.399 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.944 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.709 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 67.77 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : DCTPSKMN3.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CONFORMATION A IN THE COORDINATES REMARK 3 CORRESPONDS TO THE POST-CATALYTIC STATE, WHILE CONFORMATION B REMARK 3 CORRESPONDS TO THE PRE-CATALYTIC STATE. REMARK 4 REMARK 4 2PFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26491 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1XSN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-20% 2-PROPANOL, 0.2 M SODIUM REMARK 280 CITRATE AND 0.1M SODIUM CACODYLATE , PH 5.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 28.04550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.88750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.74250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.88750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.04550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.74250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, D, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 241 REMARK 465 ALA A 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 465 ALA A 249 REMARK 465 THR A 250 REMARK 465 ASN A 251 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 LYS A 259 CE NZ REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 LYS A 273 CG CD CE NZ REMARK 470 LYS A 287 CG CD CE NZ REMARK 470 PHE A 289 CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 VAL A 293 CG1 CG2 REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 SER A 301 OG REMARK 470 ILE A 302 CG1 CG2 CD1 REMARK 470 LYS A 324 CG CD CE NZ REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 GLU A 572 CG CD OE1 OE2 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 DG D 1 P DG D 1 OP3 -0.089 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 LEU A 317 CA - C - N ANGL. DEV. = -13.3 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 ASN A 253 43.71 73.75 REMARK 500 THR A 294 35.80 -149.81 REMARK 500 SER A 319 -81.24 -98.00 REMARK 500 GLU A 330 28.12 -74.60 REMARK 500 ASN A 407 92.65 -168.54 REMARK 500 CYS A 415 -137.44 -104.70 REMARK 500 HIS A 434 116.06 -168.32 REMARK 500 ARG A 438 -36.23 -150.33 REMARK 500 SER A 439 2.48 -61.83 REMARK 500 PHE A 444 -71.45 -33.90 REMARK 500 SER A 463 93.48 -166.44 REMARK 500 LYS A 523 23.41 -75.27 REMARK 500 GLU A 529 -9.65 -53.32 REMARK 500 PRO A 547 -128.74 -59.41 REMARK 500 TYR A 567 151.22 -42.91 REMARK 500 ASP A 574 65.76 -68.74 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 NA A 1 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA P 5 OP1 REMARK 620 2 SER A 339 O 164.8 REMARK 620 3 ILE A 341 O 97.8 96.5 REMARK 620 4 ALA A 344 O 87.2 88.9 85.2 REMARK 620 5 HOH A1452 O 91.5 91.5 98.1 176.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1295 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 6 O3' REMARK 620 2 HOH P 299 O 99.5 REMARK 620 3 ASP A 427 OD2 165.9 79.2 REMARK 620 4 ASP A 429 OD1 96.3 164.1 85.9 REMARK 620 5 ASP A 490 OD1 71.5 88.3 94.4 98.7 REMARK 620 6 DCP A1438 O2A 100.7 85.8 93.2 89.4 169.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1297 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 6 O3' REMARK 620 2 DC P 7 P 41.6 REMARK 620 3 DC P 7 OP1 78.9 39.4 REMARK 620 4 HOH P 299 O 87.8 78.4 89.7 REMARK 620 5 ASP A 427 OD2 176.4 141.5 104.6 91.4 REMARK 620 6 ASP A 429 OD1 96.1 103.9 90.1 176.0 84.7 REMARK 620 7 ASP A 490 OD1 89.8 130.1 168.5 92.1 86.7 88.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1296 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 7 OP1 REMARK 620 2 ASP A 427 OD1 82.6 REMARK 620 3 ASP A 429 OD2 82.8 100.2 REMARK 620 4 PPV A1439 O11 92.6 167.7 90.4 REMARK 620 5 PPV A1439 O12 94.1 80.7 176.6 88.4 REMARK 620 6 HOH A1602 O 175.1 97.6 92.4 88.1 90.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1294 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 91.6 REMARK 620 3 DCP A1438 O2A 98.9 92.1 REMARK 620 4 DCP A1438 O2B 174.7 89.2 86.2 REMARK 620 5 DCP A1438 O2G 88.4 175.0 92.8 90.3 REMARK 620 6 HOH A1602 O 86.2 86.7 174.7 88.6 88.3 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 1294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP A 1438 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPV A 1439 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PFN RELATED DB: PDB REMARK 900 NA IN THE ACTIVE SITE OF DNA POLYMERASE LAMBDA REMARK 900 RELATED ID: 2PFO RELATED DB: PDB REMARK 900 DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND DUPNPP REMARK 900 RELATED ID: 2PFP RELATED DB: PDB REMARK 900 DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND DCTP DBREF 2PFQ A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 2PFQ T 1 11 PDB 2PFQ 2PFQ 1 11 DBREF 2PFQ P 1 7 PDB 2PFQ 2PFQ 1 7 DBREF 2PFQ D 1 4 PDB 2PFQ 2PFQ 1 4 SEQADV 2PFQ MET A 241 UNP Q9UGP5 INITIATING METHIONINE SEQADV 2PFQ ALA A 543 UNP Q9UGP5 CYS 543 ENGINEERED MUTATION SEQRES 1 T 11 DC DG DG DC DG DG DT DA DC DT DG SEQRES 1 P 7 DC DA DG DT DA DC DC SEQRES 1 D 4 DG DC DC DG SEQRES 1 A 335 MET ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN SEQRES 2 A 335 LEU HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA SEQRES 3 A 335 TYR SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR SEQRES 4 A 335 ALA LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO SEQRES 5 A 335 VAL THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE SEQRES 6 A 335 GLY LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SEQRES 7 A 335 SER GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER SEQRES 8 A 335 VAL PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA SEQRES 9 A 335 GLY THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE SEQRES 10 A 335 ARG SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR SEQRES 11 A 335 THR GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE SEQRES 12 A 335 LEU GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU SEQRES 13 A 335 GLN THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY SEQRES 14 A 335 LEU LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS SEQRES 15 A 335 ALA THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO SEQRES 16 A 335 ASP GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU SEQRES 17 A 335 ASP SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU SEQRES 18 A 335 VAL SER GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU SEQRES 19 A 335 GLY VAL CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG SEQRES 20 A 335 ARG LEU ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA SEQRES 21 A 335 CYS ALA LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN SEQRES 22 A 335 ARG SER MET ARG ALA LEU ALA LYS THR LYS GLY MET SER SEQRES 23 A 335 LEU SER GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN SEQRES 24 A 335 THR HIS GLY ALA LYS VAL GLY PRO GLY ARG VAL LEU PRO SEQRES 25 A 335 THR PRO THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU SEQRES 26 A 335 PRO TYR ARG GLU PRO ALA GLU ARG ASP TRP HET MG A1294 1 HET NA A1295 1 HET MN A1296 1 HET MN A1297 1 HET NA A 1 1 HET DCP A1438 28 HET PPV A1439 9 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM MN MANGANESE (II) ION HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM PPV PYROPHOSPHATE FORMUL 5 MG MG 2+ FORMUL 6 NA 2(NA 1+) FORMUL 7 MN 2(MN 2+) FORMUL 10 DCP C9 H16 N3 O13 P3 FORMUL 11 PPV H4 O7 P2 FORMUL 12 HOH *230(H2 O) HELIX 1 1 ILE A 256 GLN A 270 1 15 HELIX 2 2 ASP A 272 LYS A 287 1 16 HELIX 3 3 SER A 295 ILE A 302 1 8 HELIX 4 4 GLY A 306 SER A 319 1 14 HELIX 5 5 LEU A 322 HIS A 327 1 6 HELIX 6 6 SER A 331 ASN A 340 1 10 HELIX 7 7 GLY A 345 GLN A 355 1 11 HELIX 8 8 SER A 359 ALA A 367 1 9 HELIX 9 9 THR A 370 HIS A 379 1 10 HELIX 10 10 SER A 381 GLU A 385 5 5 HELIX 11 11 ARG A 389 ALA A 405 1 17 HELIX 12 12 CYS A 415 ARG A 420 1 6 HELIX 13 13 ILE A 443 GLU A 454 1 12 HELIX 14 14 PRO A 495 SER A 497 5 3 HELIX 15 15 GLU A 498 GLY A 508 1 11 HELIX 16 16 SER A 509 LYS A 523 1 15 HELIX 17 17 THR A 555 LEU A 563 1 9 HELIX 18 18 GLU A 569 ASP A 574 5 6 SHEET 1 A 2 MET A 387 PRO A 388 0 SHEET 2 A 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 B 5 LEU A 411 ALA A 414 0 SHEET 2 B 5 ASP A 427 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 B 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 428 SHEET 4 B 5 LYS A 472 CYS A 477 -1 N GLY A 475 O LEU A 489 SHEET 5 B 5 LEU A 457 VAL A 462 -1 N THR A 458 O VAL A 476 SHEET 1 C 3 MET A 525 LEU A 527 0 SHEET 2 C 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 C 3 ARG A 549 LEU A 551 -1 O ARG A 549 N THR A 534 SHEET 1 D 2 VAL A 537 ARG A 538 0 SHEET 2 D 2 LYS A 544 GLY A 546 -1 O GLY A 546 N VAL A 537 LINK OP1 DA P 5 NA NA A 1 1555 1555 2.39 LINK O3'B DC P 6 NA B NA A1295 1555 1555 2.49 LINK O3'A DC P 6 MN A MN A1297 1555 1555 2.16 LINK OP1A DC P 7 MN A MN A1296 1555 1555 2.21 LINK P A DC P 7 MN A MN A1297 1555 1555 2.37 LINK OP1A DC P 7 MN A MN A1297 1555 1555 1.88 LINK O HOH P 299 NA B NA A1295 1555 1555 2.30 LINK O HOH P 299 MN A MN A1297 1555 1555 2.23 LINK NA NA A 1 O SER A 339 1555 1555 2.43 LINK NA NA A 1 O ILE A 341 1555 1555 2.45 LINK NA NA A 1 O ALA A 344 1555 1555 2.26 LINK NA NA A 1 O HOH A1452 1555 1555 2.51 LINK OD1BASP A 427 MG B MG A1294 1555 1555 2.06 LINK OD2BASP A 427 NA B NA A1295 1555 1555 2.26 LINK OD1AASP A 427 MN A MN A1296 1555 1555 1.94 LINK OD2AASP A 427 MN A MN A1297 1555 1555 2.25 LINK OD2BASP A 429 MG B MG A1294 1555 1555 2.17 LINK OD1BASP A 429 NA B NA A1295 1555 1555 2.21 LINK OD2AASP A 429 MN A MN A1296 1555 1555 2.04 LINK OD1AASP A 429 MN A MN A1297 1555 1555 2.33 LINK OD1BASP A 490 NA B NA A1295 1555 1555 2.36 LINK OD1AASP A 490 MN A MN A1297 1555 1555 2.01 LINK MG B MG A1294 O2ABDCP A1438 1555 1555 1.98 LINK MG B MG A1294 O2BBDCP A1438 1555 1555 1.87 LINK MG B MG A1294 O2GBDCP A1438 1555 1555 2.00 LINK MG B MG A1294 O HOH A1602 1555 1555 2.05 LINK NA B NA A1295 O2ABDCP A1438 1555 1555 2.45 LINK MN A MN A1296 O11APPV A1439 1555 1555 2.06 LINK MN A MN A1296 O12APPV A1439 1555 1555 2.09 LINK MN A MN A1296 O HOH A1602 1555 1555 2.04 CISPEP 1 GLY A 508 SER A 509 0 0.59 SITE 1 AC1 8 ASP A 427 ASP A 429 NA A1295 MN A1297 SITE 2 AC1 8 DCP A1438 PPV A1439 HOH A1602 DC P 7 SITE 1 AC2 9 ASP A 427 ASP A 429 ASP A 490 MG A1294 SITE 2 AC2 9 MN A1296 DCP A1438 DC P 6 DC P 7 SITE 3 AC2 9 HOH P 299 SITE 1 AC3 8 ASP A 427 ASP A 429 NA A1295 MN A1297 SITE 2 AC3 8 DCP A1438 PPV A1439 HOH A1602 DC P 7 SITE 1 AC4 9 ASP A 427 ASP A 429 ASP A 490 MG A1294 SITE 2 AC4 9 MN A1296 DCP A1438 DC P 6 DC P 7 SITE 3 AC4 9 HOH P 299 SITE 1 AC5 5 SER A 339 ILE A 341 ALA A 344 HOH A1452 SITE 2 AC5 5 DA P 5 SITE 1 AC6 23 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC6 23 GLY A 426 ASP A 427 ASP A 429 TYR A 505 SITE 3 AC6 23 PHE A 506 THR A 507 GLY A 508 ASN A 513 SITE 4 AC6 23 MG A1294 NA A1295 MN A1296 MN A1297 SITE 5 AC6 23 HOH A1449 HOH A1602 DC P 6 DC P 7 SITE 6 AC6 23 HOH P 28 HOH P 84 DG T 5 SITE 1 AC7 12 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC7 12 GLY A 426 ASP A 427 ASP A 429 MG A1294 SITE 3 AC7 12 MN A1296 HOH A1449 HOH A1602 DC P 7 CRYST1 56.091 63.485 139.775 90.00 90.00 90.00 P 21 21 21 4 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 0.017828 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007154 0.00000