PDB Short entry for 5U9H HEADER TRANSFERASE/DNA 16-DEC-16 5U9H TITLE DNA POLYMERASE BETA PRODUCT COMPLEX WITH INSERTED SP-ISOMER OF DCTP- TITLE 2 ALPHA-S COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 3 3'); COMPND 4 CHAIN: T; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(C7R))-3'); COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA POLYMERASE BETA; COMPND 16 CHAIN: A; COMPND 17 EC: 2.7.7.7,4.2.99.-; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: POLB; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, LYASE, DNA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,S.H.WILSON,W.A.BEARD REVDAT 5 04-OCT-23 5U9H 1 LINK REVDAT 4 04-DEC-19 5U9H 1 REMARK REVDAT 3 27-SEP-17 5U9H 1 REMARK REVDAT 2 03-MAY-17 5U9H 1 JRNL REVDAT 1 08-FEB-17 5U9H 0 JRNL AUTH L.PERERA,B.D.FREUDENTHAL,W.A.BEARD,L.G.PEDERSEN,S.H.WILSON JRNL TITL REVEALING THE ROLE OF THE PRODUCT METAL IN DNA POLYMERASE JRNL TITL 2 BETA CATALYSIS. JRNL REF NUCLEIC ACIDS RES. V. 45 2736 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28108654 JRNL DOI 10.1093/NAR/GKW1363 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 67715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 3409 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 26.1844 - 5.3206 0.95 2668 143 0.1731 0.1681 REMARK 3 2 5.3206 - 4.2289 1.00 2761 152 0.1431 0.1621 REMARK 3 3 4.2289 - 3.6960 1.00 2817 145 0.1464 0.1766 REMARK 3 4 3.6960 - 3.3589 1.00 2812 142 0.1600 0.2049 REMARK 3 5 3.3589 - 3.1185 1.00 2793 147 0.1825 0.2109 REMARK 3 6 3.1185 - 2.9349 0.99 2771 153 0.2149 0.2485 REMARK 3 7 2.9349 - 2.7881 0.98 2700 147 0.2079 0.2572 REMARK 3 8 2.7881 - 2.6669 0.98 2755 145 0.2179 0.2652 REMARK 3 9 2.6669 - 2.5643 0.98 2734 132 0.2095 0.2746 REMARK 3 10 2.5643 - 2.4759 0.97 2734 155 0.2160 0.3016 REMARK 3 11 2.4759 - 2.3985 0.97 2691 148 0.2259 0.2576 REMARK 3 12 2.3985 - 2.3300 0.96 2707 127 0.2222 0.2714 REMARK 3 13 2.3300 - 2.2687 0.96 2708 146 0.2254 0.2919 REMARK 3 14 2.2687 - 2.2134 0.96 2584 150 0.2235 0.2655 REMARK 3 15 2.2134 - 2.1631 0.96 2723 149 0.2222 0.2507 REMARK 3 16 2.1631 - 2.1171 0.95 2665 122 0.2237 0.2829 REMARK 3 17 2.1171 - 2.0747 0.95 2682 159 0.2343 0.2954 REMARK 3 18 2.0747 - 2.0356 0.94 2602 126 0.2600 0.3487 REMARK 3 19 2.0356 - 1.9993 0.94 2625 146 0.2546 0.3001 REMARK 3 20 1.9993 - 1.9654 0.93 2585 138 0.2509 0.3009 REMARK 3 21 1.9654 - 1.9337 0.92 2619 131 0.2659 0.3558 REMARK 3 22 1.9337 - 1.9039 0.91 2503 130 0.2801 0.3177 REMARK 3 23 1.9039 - 1.8760 0.90 2542 151 0.3327 0.3863 REMARK 3 24 1.8760 - 1.8495 0.89 2525 125 0.3512 0.4183 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 3374 REMARK 3 ANGLE : 0.880 4696 REMARK 3 CHIRALITY : 0.051 515 REMARK 3 PLANARITY : 0.006 502 REMARK 3 DIHEDRAL : 17.727 1918 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 5U9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67715 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM REMARK 280 CHLORIDE, 17% PEG3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 40.02400 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: 5830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL 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 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 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 LYS A 54 CG CD CE NZ REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 LYS A 127 CD CE NZ REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 GLU A 216 CG CD OE1 OE2 REMARK 470 LYS A 220 CG CD CE NZ REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 ARG A 299 CZ NH1 NH2 REMARK 470 VAL A 303 CG1 CG2 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 O HOH A 555 O HOH A 747 2.09 REMARK 500 O HOH A 669 O HOH A 689 2.10 REMARK 500 O HOH P 102 O HOH P 112 2.13 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 8 O4' - C1' - N1 ANGL. DEV. = 2.4 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 LYS A 120 -6.15 -141.65 REMARK 500 CYS A 178 -137.51 -112.79 REMARK 500 ASP A 246 -2.16 67.43 REMARK 500 ASN A 294 -168.96 -125.31 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 MN T 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH T 240 O REMARK 620 2 HOH T 241 O 102.1 REMARK 620 3 HOH D 106 O 161.5 96.2 REMARK 620 4 HOH A 709 O 99.4 118.5 69.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 105 O 88.1 REMARK 620 3 THR A 101 O 165.8 80.7 REMARK 620 4 VAL A 103 O 97.6 174.3 93.6 REMARK 620 5 ILE A 106 O 95.2 92.3 93.9 87.8 REMARK 620 6 HOH A 714 O 87.9 90.4 83.6 89.2 176.0 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 C7R P 11 OP1 REMARK 620 2 ASP A 190 OD2 115.9 REMARK 620 3 ASP A 192 OD1 89.7 105.5 REMARK 620 4 ASP A 256 OD2 140.3 99.2 98.7 REMARK 620 5 HOH A 551 O 82.1 75.6 171.2 89.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C7R P 11 OP1 REMARK 620 2 ASP A 190 OD1 90.3 REMARK 620 3 ASP A 192 OD2 88.2 93.6 REMARK 620 4 PPV A 401 O11 106.8 96.6 161.7 REMARK 620 5 PPV A 401 O12 74.2 156.9 102.7 72.5 REMARK 620 6 HOH A 509 O 171.6 87.6 83.8 81.5 110.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 404 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 107 O REMARK 620 2 ASP A 145 OD2 167.6 REMARK 620 3 HIS A 252 ND1 96.2 92.6 REMARK 620 4 HOH A 651 O 88.4 83.0 89.5 REMARK 620 5 HOH A 686 O 82.6 88.1 176.1 86.8 REMARK 620 6 HOH A 716 O 82.5 104.5 100.8 166.9 82.8 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 MN T 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 DBREF 5U9H T 1 16 PDB 5U9H 5U9H 1 16 DBREF 5U9H P 1 11 PDB 5U9H 5U9H 1 11 DBREF 5U9H D 1 5 PDB 5U9H 5U9H 1 5 DBREF 5U9H A 1 335 UNP P06746 DPOLB_HUMAN 1 335 SEQRES 1 T 16 DC DC DG DA DC DG DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 11 DG DC DT DG DA DT DG DC DG DC C7R SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU HET C7R P 11 19 HET MN T 101 1 HET PPV A 401 9 HET MN A 402 1 HET MN A 403 1 HET MN A 404 1 HET NA A 405 1 HETNAM C7R 2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE HETNAM MN MANGANESE (II) ION HETNAM PPV PYROPHOSPHATE HETNAM NA SODIUM ION HETSYN C7R 2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE (THIOPHOSPHO HETSYN 2 C7R CONNECTION ISOFORM 1) FORMUL 2 C7R C9 H14 N3 O6 P S FORMUL 5 MN 4(MN 2+) FORMUL 6 PPV H4 O7 P2 FORMUL 10 NA NA 1+ FORMUL 11 HOH *351(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 TYR A 49 1 18 HELIX 3 AA3 SER A 55 LYS A 61 1 7 HELIX 4 AA4 GLY A 66 GLY A 80 1 15 HELIX 5 AA5 LEU A 82 ASP A 91 1 10 HELIX 6 AA6 ASP A 91 THR A 101 1 11 HELIX 7 AA7 GLY A 107 GLU A 117 1 11 HELIX 8 AA8 THR A 121 ASN A 128 1 8 HELIX 9 AA9 GLU A 129 LEU A 132 5 4 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 GLU A 147 1 6 HELIX 12 AB3 ARG A 152 ASP A 170 1 19 HELIX 13 AB4 CYS A 178 ARG A 183 1 6 HELIX 14 AB5 LYS A 209 VAL A 221 1 13 HELIX 15 AB6 PRO A 261 ASP A 263 5 3 HELIX 16 AB7 GLN A 264 GLY A 274 1 11 HELIX 17 AB8 SER A 275 LYS A 289 1 15 HELIX 18 AB9 SER A 315 ILE A 323 1 9 HELIX 19 AC1 GLU A 329 ARG A 333 5 5 SHEET 1 AA1 2 ILE A 150 PRO A 151 0 SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 AA2 5 ILE A 174 VAL A 177 0 SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ASP A 256 N VAL A 193 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 AA3 2 PHE A 200 THR A 201 0 SHEET 2 AA3 2 SER A 204 THR A 205 -1 O SER A 204 N THR A 201 SHEET 1 AA4 2 PHE A 291 ILE A 293 0 SHEET 2 AA4 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DC P 10 P C7R P 11 1555 1555 1.57 LINK MN MN T 101 O HOH T 240 1555 1555 1.92 LINK MN MN T 101 O HOH T 241 1555 1555 2.33 LINK MN MN T 101 O HOH D 106 1555 1555 2.44 LINK MN MN T 101 O HOH A 709 1555 1555 2.34 LINK OP1 DG P 9 NA NA A 405 1555 1555 2.45 LINK OP1 C7R P 11 MN MN A 402 1555 1555 2.16 LINK OP1 C7R P 11 MN MN A 403 1555 1555 2.10 LINK O HOH P 105 NA NA A 405 1555 1555 2.39 LINK O HOH D 107 MN MN A 404 1556 1555 2.40 LINK O THR A 101 NA NA A 405 1555 1555 2.45 LINK O VAL A 103 NA NA A 405 1555 1555 2.46 LINK O ILE A 106 NA NA A 405 1555 1555 2.44 LINK OD2 ASP A 145 MN MN A 404 1555 1555 2.17 LINK OD2 ASP A 190 MN MN A 402 1555 1555 2.01 LINK OD1 ASP A 190 MN MN A 403 1555 1555 2.10 LINK OD1 ASP A 192 MN MN A 402 1555 1555 2.12 LINK OD2 ASP A 192 MN MN A 403 1555 1555 2.16 LINK ND1 HIS A 252 MN MN A 404 1555 1555 2.38 LINK OD2 ASP A 256 MN MN A 402 1555 1555 2.09 LINK O11 PPV A 401 MN MN A 403 1555 1555 2.27 LINK O12 PPV A 401 MN MN A 403 1555 1555 2.32 LINK MN MN A 402 O HOH A 551 1555 1555 2.25 LINK MN MN A 403 O HOH A 509 1555 1555 2.44 LINK MN MN A 404 O HOH A 651 1555 1555 2.19 LINK MN MN A 404 O HOH A 686 1555 1555 2.20 LINK MN MN A 404 O HOH A 716 1555 1555 2.02 LINK NA NA A 405 O HOH A 714 1555 1555 2.45 CISPEP 1 GLY A 274 SER A 275 0 2.93 SITE 1 AC1 4 HOH A 709 HOH D 106 HOH T 240 HOH T 241 SITE 1 AC2 11 GLY A 179 SER A 180 ARG A 183 GLY A 189 SITE 2 AC2 11 ASP A 190 ASP A 192 MN A 403 HOH A 509 SITE 3 AC2 11 HOH A 523 HOH A 575 C7R P 11 SITE 1 AC3 7 ASP A 190 ASP A 192 ASP A 256 MN A 403 SITE 2 AC3 7 HOH A 551 DC P 10 C7R P 11 SITE 1 AC4 6 ASP A 190 ASP A 192 PPV A 401 MN A 402 SITE 2 AC4 6 HOH A 509 C7R P 11 SITE 1 AC5 6 ASP A 145 HIS A 252 HOH A 651 HOH A 686 SITE 2 AC5 6 HOH A 716 HOH D 107 SITE 1 AC6 6 THR A 101 VAL A 103 ILE A 106 HOH A 714 SITE 2 AC6 6 DG P 9 HOH P 105 CRYST1 50.980 80.048 55.074 90.00 108.05 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 0.019616 0.000000 0.006392 0.00000 SCALE2 0.000000 0.012493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019097 0.00000