HEADER DNA 03-JAN-24 8XPA TITLE CRYSTAL STRUCTURE OF D(ACGMCCGT/ACGGCGT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*CP*GP*GP*CP*GP*T)-3'); COMPND 3 CHAIN: A, D, F, H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*AP*CP*GP*(5CM)P*CP*GP*T)-3'); COMPND 7 CHAIN: B, C, E, G; COMPND 8 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 KEYWDS NAKED DNA DUPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.H.HOU,S.M.LIN,S.NEIDLE REVDAT 3 28-AUG-24 8XPA 1 JRNL REVDAT 2 14-AUG-24 8XPA 1 JRNL REVDAT 1 29-MAY-24 8XPA 0 JRNL AUTH S.M.LIN,H.T.HUANG,P.J.FANG,C.F.CHANG,R.SATANGE,C.K.CHANG, JRNL AUTH 2 S.H.CHOU,S.NEIDLE,M.H.HOU JRNL TITL STRUCTURAL BASIS OF WATER-MEDIATED CIS JRNL TITL 2 WATSON-CRICK/HOOGSTEEN BASE-PAIR FORMATION IN NON-CPG JRNL TITL 3 METHYLATION. JRNL REF NUCLEIC ACIDS RES. V. 52 8566 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38989613 JRNL DOI 10.1093/NAR/GKAE594 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 10663 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1056 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 10.0000 - 3.9900 0.97 1214 139 0.1566 0.1679 REMARK 3 2 3.9900 - 3.1700 0.95 1181 118 0.1975 0.2370 REMARK 3 3 3.1700 - 2.7700 0.99 1196 132 0.2726 0.2734 REMARK 3 4 2.7700 - 2.5200 0.99 1229 136 0.2898 0.3348 REMARK 3 5 2.5200 - 2.3400 1.00 1183 134 0.2951 0.3637 REMARK 3 6 2.3400 - 2.2000 0.99 1208 136 0.2829 0.3684 REMARK 3 7 2.2000 - 2.0900 1.00 1211 131 0.2686 0.3448 REMARK 3 8 2.0900 - 2.0000 0.98 1185 130 0.2883 0.3155 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.310 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 : 0.025 NULL REMARK 3 ANGLE : 2.042 NULL REMARK 3 CHIRALITY : 0.186 226 REMARK 3 PLANARITY : 0.013 60 REMARK 3 DIHEDRAL : 33.936 544 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 8XPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300043800. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99984 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10734 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES (PH 6.5), 1MM SPERMINE HCL, REMARK 280 20% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 23.12150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, E 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O5' DA D 1 OP2 DT D 7 2546 1.99 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 DA A 1 C6 DA A 1 N1 -0.053 REMARK 500 DA A 1 C5 DA A 1 N7 -0.041 REMARK 500 DT A 7 O3' DT A 7 C3' -0.040 REMARK 500 DA B 1 O3' DA B 1 C3' -0.046 REMARK 500 DA B 1 N9 DA B 1 C4 0.049 REMARK 500 DT B 7 O3' DT B 7 C3' -0.044 REMARK 500 5CM G 4 O3' DC G 5 P -0.152 REMARK 500 5CM G 4 O3' DC G 5 P -0.156 REMARK 500 DA H 1 O5' DA H 1 C5' -0.162 REMARK 500 DA H 1 C5 DA H 1 C6 0.067 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 DT B 7 O5' - P - OP1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG G 3 O3' - P - OP1 ANGL. DEV. = 10.4 DEGREES REMARK 500 DC G 5 O3' - P - OP1 ANGL. DEV. = 9.5 DEGREES REMARK 500 DC G 5 O3' - P - OP1 ANGL. DEV. = 7.1 DEGREES REMARK 500 DG H 4 N3 - C2 - N2 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG H 4 C8 - N9 - C1' ANGL. DEV. = -8.4 DEGREES REMARK 500 DG H 4 C4 - N9 - C1' ANGL. DEV. = 8.5 DEGREES REMARK 500 DT H 7 O3' - P - OP2 ANGL. DEV. = 6.7 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 MN A 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 N7 REMARK 620 2 HOH A 206 O 87.4 REMARK 620 3 HOH A 207 O 89.8 97.8 REMARK 620 4 HOH A 215 O 90.6 170.7 91.2 REMARK 620 5 DC G 5 OP2 163.6 93.0 73.9 91.4 REMARK 620 6 HOH G 107 O 97.3 101.4 159.7 69.8 98.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 102 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 OP2 REMARK 620 2 HOH A 209 O 78.4 REMARK 620 3 HOH A 213 O 95.1 170.7 REMARK 620 4 HOH A 216 O 98.8 106.1 68.0 REMARK 620 5 HOH G 103 O 165.2 87.3 99.5 88.6 REMARK 620 6 HOH G 105 O 94.8 86.2 101.1 163.2 80.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 3 N7 REMARK 620 2 HOH D 203 O 81.5 REMARK 620 3 DC E 5 OP2 159.7 93.9 REMARK 620 4 HOH E 106 O 88.5 95.1 72.2 REMARK 620 5 HOH E 110 O 91.5 171.7 94.2 89.2 REMARK 620 6 HOH E 112 O 97.8 97.3 102.4 166.8 79.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 3 OP2 REMARK 620 2 HOH D 211 O 88.2 REMARK 620 3 HOH D 213 O 83.1 89.0 REMARK 620 4 HOH D 218 O 96.9 164.4 77.0 REMARK 620 5 HOH E 104 O 165.1 77.2 93.4 96.4 REMARK 620 6 HOH E 108 O 94.7 94.8 175.6 99.5 89.7 REMARK 620 N 1 2 3 4 5 DBREF 8XPA A 1 7 PDB 8XPA 8XPA 1 7 DBREF 8XPA B 1 7 PDB 8XPA 8XPA 1 7 DBREF 8XPA C 1 7 PDB 8XPA 8XPA 1 7 DBREF 8XPA D 1 7 PDB 8XPA 8XPA 1 7 DBREF 8XPA F 1 7 PDB 8XPA 8XPA 1 7 DBREF 8XPA E 1 7 PDB 8XPA 8XPA 1 7 DBREF 8XPA G 1 7 PDB 8XPA 8XPA 1 7 DBREF 8XPA H 1 7 PDB 8XPA 8XPA 1 7 SEQRES 1 A 7 DA DC DG DG DC DG DT SEQRES 1 B 7 DA DC DG 5CM DC DG DT SEQRES 1 C 7 DA DC DG 5CM DC DG DT SEQRES 1 D 7 DA DC DG DG DC DG DT SEQRES 1 F 7 DA DC DG DG DC DG DT SEQRES 1 E 7 DA DC DG 5CM DC DG DT SEQRES 1 G 7 DA DC DG 5CM DC DG DT SEQRES 1 H 7 DA DC DG DG DC DG DT HET 5CM B 4 20 HET 5CM C 4 20 HET 5CM E 4 40 HET 5CM G 4 40 HET MN A 101 1 HET MN A 102 1 HET MN D 101 1 HET MG D 102 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION FORMUL 2 5CM 4(C10 H16 N3 O7 P) FORMUL 9 MN 3(MN 2+) FORMUL 12 MG MG 2+ FORMUL 13 HOH *102(H2 O) LINK O3' DG B 3 P 5CM B 4 1555 1555 1.61 LINK O3' 5CM B 4 P DC B 5 1555 1555 1.61 LINK O3' DG C 3 P 5CM C 4 1555 1555 1.62 LINK O3' 5CM C 4 P DC C 5 1555 1555 1.61 LINK O3' DG E 3 P A5CM E 4 1555 1555 1.61 LINK O3' DG E 3 P B5CM E 4 1555 1555 1.61 LINK O3'A5CM E 4 P DC E 5 1555 1555 1.61 LINK O3'B5CM E 4 P DC E 5 1555 1555 1.61 LINK O3' DG G 3 P A5CM G 4 1555 1555 1.61 LINK O3' DG G 3 P B5CM G 4 1555 1555 1.60 LINK O3'A5CM G 4 P DC G 5 1555 1555 1.46 LINK O3'B5CM G 4 P DC G 5 1555 1555 1.45 LINK N7 DG A 3 MN MN A 101 1555 1555 2.41 LINK OP2 DG A 3 MN MN A 102 1555 1555 1.99 LINK MN MN A 101 O HOH A 206 1555 1555 2.23 LINK MN MN A 101 O HOH A 207 1555 1555 2.14 LINK MN MN A 101 O HOH A 215 1555 1555 2.07 LINK MN MN A 101 OP2 DC G 5 1555 1555 2.38 LINK MN MN A 101 O HOH G 107 1555 1555 2.03 LINK MN MN A 102 O HOH A 209 1555 1555 2.37 LINK MN MN A 102 O HOH A 213 1555 1555 2.12 LINK MN MN A 102 O HOH A 216 1555 1555 2.21 LINK MN MN A 102 O HOH G 103 1555 1555 2.17 LINK MN MN A 102 O HOH G 105 1555 1555 2.27 LINK N7 DG D 3 MN MN D 101 1555 1555 2.47 LINK OP2 DG D 3 MG MG D 102 1555 1555 2.10 LINK MN MN D 101 O HOH D 203 1555 1555 2.32 LINK MN MN D 101 OP2 DC E 5 1555 1555 2.18 LINK MN MN D 101 O HOH E 106 1555 1555 2.27 LINK MN MN D 101 O HOH E 110 1555 1555 2.03 LINK MN MN D 101 O HOH E 112 1555 1555 2.04 LINK MG MG D 102 O HOH D 211 1555 1555 2.06 LINK MG MG D 102 O HOH D 213 1555 1555 2.35 LINK MG MG D 102 O HOH D 218 1555 1555 2.23 LINK MG MG D 102 O HOH E 104 1555 1555 2.07 LINK MG MG D 102 O HOH E 108 1555 1555 2.16 CRYST1 39.432 46.243 47.061 90.00 110.92 90.00 P 1 21 1 8 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 0.025360 0.000000 0.009694 0.00000 SCALE2 0.000000 0.021625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022749 0.00000