PDB Short entry for 3VYQ HEADER HYDROLASE/DNA 02-OCT-12 3VYQ TITLE CRYSTAL STRUCTURE OF THE METHYL CPG BINDING DOMAIN OF MBD4 IN COMPLEX TITLE 2 WITH THE 5MCG/TG SEQUENCE IN SPACE GROUP P1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN PROTEIN 4; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: METHYL CPG BINDING DOMAIN, UNP RESIDUES 63-136; COMPND 5 SYNONYM: METHYL-CPG-BINDING PROTEIN MBD4, MISMATCH-SPECIFIC DNA N- COMPND 6 GLYCOSYLASE; COMPND 7 EC: 3.2.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*AP*TP*GP*T)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MBD4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS METHYL CPG BINDING DOMAIN, PROTEIN-DNA COMPLEX, VERSATILE BASE KEYWDS 2 RECOGNITION, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.OTANI,K.ARITA,T.KATO,M.KINOSHITA,M.ARIYOSHI,M.SHIRAKAWA REVDAT 3 08-NOV-23 3VYQ 1 REMARK LINK REVDAT 2 14-AUG-13 3VYQ 1 JRNL REVDAT 1 16-JAN-13 3VYQ 0 JRNL AUTH J.OTANI,K.ARITA,T.KATO,M.KINOSHITA,H.KIMURA,I.SUETAKE, JRNL AUTH 2 S.TAJIMA,M.ARIYOSHI,M.SHIRAKAWA JRNL TITL STRUCTURAL BASIS OF THE VERSATILE DNA RECOGNITION ABILITY OF JRNL TITL 2 THE METHYL-CPG BINDING DOMAIN OF METHYL-CPG BINDING DOMAIN JRNL TITL 3 PROTEIN 4 JRNL REF J.BIOL.CHEM. V. 288 6351 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23316048 JRNL DOI 10.1074/JBC.M112.431098 REMARK 2 REMARK 2 RESOLUTION. 2.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 7095 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.550 REMARK 3 FREE R VALUE TEST SET COUNT : 323 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 32.9752 - 3.1812 0.98 3679 174 0.1745 0.2057 REMARK 3 2 3.1812 - 2.5253 0.82 3093 149 0.2485 0.3347 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 : 0.31 REMARK 3 B_SOL : 26.54 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.23470 REMARK 3 B22 (A**2) : 5.96930 REMARK 3 B33 (A**2) : -1.73450 REMARK 3 B12 (A**2) : -8.44300 REMARK 3 B13 (A**2) : -4.62720 REMARK 3 B23 (A**2) : 2.77440 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 1542 REMARK 3 ANGLE : 1.161 2158 REMARK 3 CHIRALITY : 0.062 228 REMARK 3 PLANARITY : 0.004 201 REMARK 3 DIHEDRAL : 23.241 605 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 70:132) REMARK 3 ORIGIN FOR THE GROUP (A): 13.0063 -10.4065 9.1365 REMARK 3 T TENSOR REMARK 3 T11: 0.1382 T22: 0.2943 REMARK 3 T33: 0.0735 T12: 0.0286 REMARK 3 T13: 0.0360 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 3.0406 L22: 0.9350 REMARK 3 L33: 2.1090 L12: -0.4356 REMARK 3 L13: 0.5684 L23: -0.2984 REMARK 3 S TENSOR REMARK 3 S11: 0.2038 S12: -0.5951 S13: -0.0653 REMARK 3 S21: -0.0662 S22: 0.0845 S23: 0.1188 REMARK 3 S31: -0.0179 S32: -0.0396 S33: -0.1596 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 2:11) REMARK 3 ORIGIN FOR THE GROUP (A): 11.581 -8.714 -5.848 REMARK 3 T TENSOR REMARK 3 T11: 0.3294 T22: 0.1360 REMARK 3 T33: 0.2122 T12: 0.0826 REMARK 3 T13: 0.0176 T23: -0.0588 REMARK 3 L TENSOR REMARK 3 L11: 4.7090 L22: 7.7506 REMARK 3 L33: 5.4614 L12: -4.0205 REMARK 3 L13: 3.8515 L23: -3.1737 REMARK 3 S TENSOR REMARK 3 S11: 0.2764 S12: 0.3929 S13: 0.6010 REMARK 3 S21: 0.1410 S22: -0.8930 S23: 0.1245 REMARK 3 S31: -0.9129 S32: 0.3172 S33: -0.2417 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN C AND RESID 1:11) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8095 -10.5140 -5.3296 REMARK 3 T TENSOR REMARK 3 T11: 0.3276 T22: 0.1257 REMARK 3 T33: 0.1544 T12: 0.0295 REMARK 3 T13: -0.0316 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 2.5678 L22: 0.5355 REMARK 3 L33: 2.8119 L12: -0.5116 REMARK 3 L13: -0.9572 L23: -0.8178 REMARK 3 S TENSOR REMARK 3 S11: 0.2461 S12: -0.0240 S13: -0.0368 REMARK 3 S21: -0.3666 S22: -0.4822 S23: -0.0210 REMARK 3 S31: -0.1797 S32: -0.2425 S33: 0.1551 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN D AND RESID 70:132) REMARK 3 ORIGIN FOR THE GROUP (A): 10.3282 -26.2174 -22.2785 REMARK 3 T TENSOR REMARK 3 T11: 0.1750 T22: 0.4176 REMARK 3 T33: 0.0829 T12: 0.1229 REMARK 3 T13: 0.0639 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 2.2885 L22: 1.0114 REMARK 3 L33: 1.0790 L12: -0.0977 REMARK 3 L13: 0.4555 L23: -0.1188 REMARK 3 S TENSOR REMARK 3 S11: -0.1358 S12: 0.0607 S13: -0.3282 REMARK 3 S21: 0.0522 S22: 0.2831 S23: -0.0335 REMARK 3 S31: -0.0555 S32: 0.0083 S33: -0.1095 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 71:83 OR RESSEQ 85:87 REMARK 3 OR RESSEQ 97:105 OR RESSEQ 110:116 OR REMARK 3 RESSEQ 118:132 ) REMARK 3 SELECTION : CHAIN D AND (RESSEQ 71:83 OR RESSEQ 85:87 REMARK 3 OR RESSEQ 97:105 OR RESSEQ 110:116 OR REMARK 3 RESSEQ 118:132 ) REMARK 3 ATOM PAIRS NUMBER : 376 REMARK 3 RMSD : 0.037 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3VYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000095667. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7225 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.12500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.400 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: PDB ENTRY 3VXV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2MM ZINC ACETATE, 100MM SODIUM REMARK 280 CACODYLATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 4150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 SER A 63 REMARK 465 THR A 64 REMARK 465 THR A 65 REMARK 465 ALA A 66 REMARK 465 THR A 67 REMARK 465 GLU A 68 REMARK 465 GLY A 69 REMARK 465 LEU A 133 REMARK 465 PRO A 134 REMARK 465 LYS A 135 REMARK 465 GLY A 136 REMARK 465 DA B 1 REMARK 465 SER D 63 REMARK 465 THR D 64 REMARK 465 THR D 65 REMARK 465 ALA D 66 REMARK 465 THR D 67 REMARK 465 GLU D 68 REMARK 465 GLY D 69 REMARK 465 LEU D 133 REMARK 465 PRO D 134 REMARK 465 LYS D 135 REMARK 465 GLY D 136 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 C 7 C3' - C2' - C1' ANGL. DEV. = -7.4 DEGREES REMARK 500 DG C 7 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT C 11 O4' - C1' - N1 ANGL. DEV. = -5.7 DEGREES 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 75 SG REMARK 620 2 HOH A 311 O 129.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VXV RELATED DB: PDB REMARK 900 RELATED ID: 3VXX RELATED DB: PDB REMARK 900 RELATED ID: 3VYB RELATED DB: PDB DBREF 3VYQ A 63 136 UNP Q9Z2D7 MBD4_MOUSE 63 136 DBREF 3VYQ D 63 136 UNP Q9Z2D7 MBD4_MOUSE 63 136 DBREF 3VYQ B 1 11 PDB 3VYQ 3VYQ 1 11 DBREF 3VYQ C 1 11 PDB 3VYQ 3VYQ 1 11 SEQRES 1 A 74 SER THR THR ALA THR GLU GLY HIS LYS PRO VAL PRO CYS SEQRES 2 A 74 GLY TRP GLU ARG VAL VAL LYS GLN ARG LEU SER GLY LYS SEQRES 3 A 74 THR ALA GLY LYS PHE ASP VAL TYR PHE ILE SER PRO GLN SEQRES 4 A 74 GLY LEU LYS PHE ARG SER LYS ARG SER LEU ALA ASN TYR SEQRES 5 A 74 LEU LEU LYS ASN GLY GLU THR PHE LEU LYS PRO GLU ASP SEQRES 6 A 74 PHE ASN PHE THR VAL LEU PRO LYS GLY SEQRES 1 B 11 DA DC DA DT DC 5CM DG DG DT DG DA SEQRES 1 C 11 DT DC DA DC DT DG DG DA DT DG DT SEQRES 1 D 74 SER THR THR ALA THR GLU GLY HIS LYS PRO VAL PRO CYS SEQRES 2 D 74 GLY TRP GLU ARG VAL VAL LYS GLN ARG LEU SER GLY LYS SEQRES 3 D 74 THR ALA GLY LYS PHE ASP VAL TYR PHE ILE SER PRO GLN SEQRES 4 D 74 GLY LEU LYS PHE ARG SER LYS ARG SER LEU ALA ASN TYR SEQRES 5 D 74 LEU LEU LYS ASN GLY GLU THR PHE LEU LYS PRO GLU ASP SEQRES 6 D 74 PHE ASN PHE THR VAL LEU PRO LYS GLY MODRES 3VYQ 5CM B 6 DC HET 5CM B 6 20 HET ZN A 201 1 HET EDO B 101 4 HET ZN D 201 1 HET ZN D 202 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 5 ZN 3(ZN 2+) FORMUL 6 EDO C2 H6 O2 FORMUL 9 HOH *55(H2 O) HELIX 1 1 SER A 107 ASN A 118 1 12 HELIX 2 2 LYS A 124 PHE A 128 5 5 HELIX 3 3 SER D 107 ASN D 118 1 12 HELIX 4 4 LYS D 124 PHE D 128 5 5 SHEET 1 A 3 GLU A 78 GLN A 83 0 SHEET 2 A 3 PHE A 93 ILE A 98 -1 O ASP A 94 N LYS A 82 SHEET 3 A 3 LYS A 104 PHE A 105 -1 O PHE A 105 N PHE A 97 SHEET 1 B 3 GLU D 78 GLN D 83 0 SHEET 2 B 3 PHE D 93 ILE D 98 -1 O TYR D 96 N VAL D 80 SHEET 3 B 3 LYS D 104 PHE D 105 -1 O PHE D 105 N PHE D 97 LINK O3' DC B 5 P 5CM B 6 1555 1555 1.60 LINK O3' 5CM B 6 P DG B 7 1555 1555 1.61 LINK SG CYS A 75 ZN ZN A 201 1555 1555 2.40 LINK ZN ZN A 201 O HOH A 311 1555 1555 2.09 LINK ND1 HIS D 70 ZN ZN D 202 1555 1555 2.17 LINK SG CYS D 75 ZN ZN D 201 1555 1555 2.50 SITE 1 AC1 4 CYS A 75 HOH A 311 GLU D 120 HOH D 303 SITE 1 AC2 2 DG B 10 ARG D 106 SITE 1 AC3 3 GLU A 120 HOH A 320 CYS D 75 SITE 1 AC4 2 HIS A 70 HIS D 70 CRYST1 30.604 34.093 61.165 75.28 77.76 87.31 P 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 0.032675 -0.001538 -0.006922 0.00000 SCALE2 0.000000 0.029364 -0.007587 0.00000 SCALE3 0.000000 0.000000 0.017279 0.00000