PDB Short entry for 4NY8 HEADER TRANSFERASE, LYASE/DNA 10-DEC-13 4NY8 TITLE DNA POLYMERASE BETA WITH O6MG IN THE TEMPLATE BASE OPPOSITE TO TITLE 2 INCOMING NON-HYDROLYZABLE CTP WITH MANGANESE IN THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 10-335; COMPND 5 EC: 2.7.7.7, 4.2.99.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 9 3'; COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: TEMPLATE; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'; COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: UPSTREAM PRIMER; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: 5'-D(P*GP*TP*CP*GP*G)-3'; COMPND 20 CHAIN: D; COMPND 21 ENGINEERED: YES; COMPND 22 OTHER_DETAILS: DOWNSTREAM PRIMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 4; SOURCE 13 SYNTHETIC: YES KEYWDS DNA BINDING, DNA POLYMERASE FOLD, NUCLEOTIDYL TRANSFER, NUCLEOLUS, KEYWDS 2 TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.-C.KOAG,K.MIN,A.F.MONZINGO,S.LEE REVDAT 3 28-FEB-24 4NY8 1 REMARK LINK REVDAT 2 02-JUL-14 4NY8 1 JRNL REVDAT 1 16-APR-14 4NY8 0 JRNL AUTH M.C.KOAG,S.LEE JRNL TITL METAL-DEPENDENT CONFORMATIONAL ACTIVATION EXPLAINS HIGHLY JRNL TITL 2 PROMUTAGENIC REPLICATION ACROSS O6-METHYLGUANINE BY HUMAN JRNL TITL 3 DNA POLYMERASE BETA. JRNL REF J.AM.CHEM.SOC. V. 136 5709 2014 JRNL REFN ISSN 0002-7863 JRNL PMID 24694247 JRNL DOI 10.1021/JA500172D REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 20960 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.8228 - 4.4775 1.00 2591 138 0.1590 0.1907 REMARK 3 2 4.4775 - 3.5606 1.00 2549 138 0.1728 0.2125 REMARK 3 3 3.5606 - 3.1125 1.00 2550 130 0.2157 0.3013 REMARK 3 4 3.1125 - 2.8288 0.99 2528 130 0.2523 0.3319 REMARK 3 5 2.8288 - 2.6265 0.98 2474 124 0.2484 0.3070 REMARK 3 6 2.6265 - 2.4720 0.97 2471 133 0.2486 0.3196 REMARK 3 7 2.4720 - 2.3484 0.96 2438 127 0.2428 0.3102 REMARK 3 8 2.3484 - 2.2460 0.91 2284 155 0.2324 0.3045 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 3336 REMARK 3 ANGLE : 1.034 4632 REMARK 3 CHIRALITY : 0.077 511 REMARK 3 PLANARITY : 0.003 486 REMARK 3 DIHEDRAL : 19.398 1302 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4NY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083805. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 MICROMAX-007 HF 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21222 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.246 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 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) : 2.25 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14%-23% PEG3400, 350 MM SODIUM REMARK 280 ACETATE, 50 MM IMIDAZOLE, PH 7.5, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.64400 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D 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 THR A 10 REMARK 465 THR A 205 REMARK 465 LYS A 206 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 GLU A 203 CG CD OE1 OE2 REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ASN A 245 CG OD1 ND2 REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 VAL A 303 CG1 CG2 REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 GLN A 324 CG CD OE1 NE2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O3G 0KX A 405 O HOH A 507 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 -0.125 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 DG T 15 O4' - C1' - N9 ANGL. DEV. = 2.2 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 PRO A 50 31.40 -87.53 REMARK 500 CYS A 178 -143.33 -101.29 REMARK 500 PRO A 208 2.36 -66.03 REMARK 500 ASN A 245 -111.93 54.46 REMARK 500 ASN A 294 -168.72 -110.18 REMARK 500 ASP A 332 40.06 -109.44 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 HOH P 101 O 81.4 REMARK 620 3 HOH P 103 O 71.1 86.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 100.2 REMARK 620 3 ILE A 106 O 96.0 89.4 REMARK 620 4 DG P 9 OP1 157.6 97.4 97.9 REMARK 620 5 HOH P 101 O 86.4 93.1 176.2 79.0 REMARK 620 6 HOH P 103 O 74.1 174.0 89.3 88.6 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 90.0 REMARK 620 3 0KX A 405 O1A 108.4 103.6 REMARK 620 4 0KX A 405 O3G 102.3 137.1 110.8 REMARK 620 5 0KX A 405 O2B 164.2 105.2 72.5 63.7 REMARK 620 6 HOH A 507 O 86.3 88.4 160.7 52.4 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 97.7 REMARK 620 3 0KX A 405 O1A 83.9 94.2 REMARK 620 4 HOH A 584 O 63.2 84.0 146.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0KX A 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NXZ RELATED DB: PDB DBREF 4NY8 A 10 335 UNP P06746 DPOLB_HUMAN 10 335 DBREF 4NY8 T 1 16 PDB 4NY8 4NY8 1 16 DBREF 4NY8 P 1 10 PDB 4NY8 4NY8 1 10 DBREF 4NY8 D 1 5 PDB 4NY8 4NY8 1 5 SEQRES 1 A 326 THR LEU ASN GLY GLY ILE THR ASP MET LEU THR GLU LEU SEQRES 2 A 326 ALA ASN PHE GLU LYS ASN VAL SER GLN ALA ILE HIS LYS SEQRES 3 A 326 TYR ASN ALA TYR ARG LYS ALA ALA SER VAL ILE ALA LYS SEQRES 4 A 326 TYR PRO HIS LYS ILE LYS SER GLY ALA GLU ALA LYS LYS SEQRES 5 A 326 LEU PRO GLY VAL GLY THR LYS ILE ALA GLU LYS ILE ASP SEQRES 6 A 326 GLU PHE LEU ALA THR GLY LYS LEU ARG LYS LEU GLU LYS SEQRES 7 A 326 ILE ARG GLN ASP ASP THR SER SER SER ILE ASN PHE LEU SEQRES 8 A 326 THR ARG VAL SER GLY ILE GLY PRO SER ALA ALA ARG LYS SEQRES 9 A 326 PHE VAL ASP GLU GLY ILE LYS THR LEU GLU ASP LEU ARG SEQRES 10 A 326 LYS ASN GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE GLY SEQRES 11 A 326 LEU LYS TYR PHE GLY ASP PHE GLU LYS ARG ILE PRO ARG SEQRES 12 A 326 GLU GLU MET LEU GLN MET GLN ASP ILE VAL LEU ASN GLU SEQRES 13 A 326 VAL LYS LYS VAL ASP SER GLU TYR ILE ALA THR VAL CYS SEQRES 14 A 326 GLY SER PHE ARG ARG GLY ALA GLU SER SER GLY ASP MET SEQRES 15 A 326 ASP VAL LEU LEU THR HIS PRO SER PHE THR SER GLU SER SEQRES 16 A 326 THR LYS GLN PRO LYS LEU LEU HIS GLN VAL VAL GLU GLN SEQRES 17 A 326 LEU GLN LYS VAL HIS PHE ILE THR ASP THR LEU SER LYS SEQRES 18 A 326 GLY GLU THR LYS PHE MET GLY VAL CYS GLN LEU PRO SER SEQRES 19 A 326 LYS ASN ASP GLU LYS GLU TYR PRO HIS ARG ARG ILE ASP SEQRES 20 A 326 ILE ARG LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY VAL SEQRES 21 A 326 LEU TYR PHE THR GLY SER ASP ILE PHE ASN LYS ASN MET SEQRES 22 A 326 ARG ALA HIS ALA LEU GLU LYS GLY PHE THR ILE ASN GLU SEQRES 23 A 326 TYR THR ILE ARG PRO LEU GLY VAL THR GLY VAL ALA GLY SEQRES 24 A 326 GLU PRO LEU PRO VAL ASP SER GLU LYS ASP ILE PHE ASP SEQRES 25 A 326 TYR ILE GLN TRP LYS TYR ARG GLU PRO LYS ASP ARG SER SEQRES 26 A 326 GLU SEQRES 1 T 16 DC DC DG DA DC 6OG DT DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DA SEQRES 1 D 5 DG DT DC DG DG MODRES 4NY8 6OG T 6 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HET 6OG T 6 23 HET MN A 401 1 HET MN A 402 1 HET NA A 403 1 HET NA A 404 1 HET 0KX A 405 28 HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE FORMUL 2 6OG C11 H16 N5 O7 P FORMUL 5 MN 2(MN 2+) FORMUL 7 NA 2(NA 1+) FORMUL 9 0KX C9 H17 N4 O12 P3 FORMUL 10 HOH *120(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 LYS A 48 1 17 HELIX 3 3 SER A 55 LYS A 60 1 6 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 THR A 101 1 11 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 ASN A 128 1 8 HELIX 9 9 GLU A 129 LEU A 132 5 4 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 GLU A 147 1 6 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 CYS A 178 ARG A 183 1 6 HELIX 14 14 LYS A 209 VAL A 221 1 13 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 LYS A 289 1 15 HELIX 18 18 SER A 315 ILE A 323 1 9 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 VAL A 177 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O THR A 196 N ILE A 174 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DC T 5 P 6OG T 6 1555 1555 1.61 LINK O3' 6OG T 6 P DT T 7 1555 1555 1.61 LINK O THR A 101 NA NA A 403 1555 1555 2.55 LINK O THR A 101 NA NA A 404 1555 1555 2.38 LINK O VAL A 103 NA NA A 404 1555 1555 2.40 LINK O ILE A 106 NA NA A 404 1555 1555 2.38 LINK OD1 ASP A 190 MN MN A 401 1555 1555 2.12 LINK OD2 ASP A 190 MN MN A 402 1555 1555 2.72 LINK OD2 ASP A 192 MN MN A 401 1555 1555 2.34 LINK OD1 ASP A 192 MN MN A 402 1555 1555 2.51 LINK MN MN A 401 O1A 0KX A 405 1555 1555 1.74 LINK MN MN A 401 O3G 0KX A 405 1555 1555 2.58 LINK MN MN A 401 O2B 0KX A 405 1555 1555 2.64 LINK MN MN A 401 O HOH A 507 1555 1555 2.27 LINK MN MN A 402 O1A 0KX A 405 1555 1555 2.68 LINK MN MN A 402 O HOH A 584 1555 1555 2.55 LINK NA NA A 403 O HOH P 101 1555 1555 2.87 LINK NA NA A 403 O HOH P 103 1555 1555 2.55 LINK NA NA A 404 OP1 DG P 9 1555 1555 2.38 LINK NA NA A 404 O HOH P 101 1555 1555 2.78 LINK NA NA A 404 O HOH P 103 1555 1555 2.54 CISPEP 1 GLY A 274 SER A 275 0 2.80 SITE 1 AC1 5 ASP A 190 ASP A 192 MN A 402 0KX A 405 SITE 2 AC1 5 HOH A 507 SITE 1 AC2 6 ASP A 190 ASP A 192 MN A 401 0KX A 405 SITE 2 AC2 6 HOH A 584 DA P 10 SITE 1 AC3 4 THR A 101 NA A 404 HOH P 101 HOH P 103 SITE 1 AC4 7 THR A 101 VAL A 103 ILE A 106 NA A 403 SITE 2 AC4 7 DG P 9 HOH P 101 HOH P 103 SITE 1 AC5 16 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC5 16 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC5 16 GLY A 274 SER A 275 ASP A 276 ASN A 279 SITE 4 AC5 16 MN A 401 MN A 402 HOH A 507 HOH A 553 CRYST1 54.625 79.288 54.838 90.00 105.97 90.00 P 1 21 1 2 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 0.018307 0.000000 0.005239 0.00000 SCALE2 0.000000 0.012612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018968 0.00000