HEADER ANTIBIOTIC/DNA 20-NOV-17 5YTZ TITLE CRYSTAL STRUCTURE OF ECHINOMYCIN-D(ACGTCGT)2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*CP*GP*TP*CP*GP*(UD))-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ECHINOMYCIN; COMPND 7 CHAIN: D, F SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 4 ORGANISM_TAXID: 32644; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: STREPTOMYCES ECHINATUS; SOURCE 7 ORGANISM_TAXID: 67293 KEYWDS ECHINOMYCIN, DNA INTERCALATOR, ANTIBIOTIC, ECHINOMYCIN-DNA COMPLEX, KEYWDS 2 MISMATCHED BASE PAIRS, T-T MISMATCH, PYRIMIDINE-PYRIMIDINE BASE KEYWDS 3 PAIRING, DNA MISMATCH REPAIR (MMR), NON-CANONICAL DUPLEX STRUCTURE, KEYWDS 4 ANTIBIOTIC-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.H.HOU,P.C.WU,Y.F.KAO REVDAT 4 22-NOV-23 5YTZ 1 LINK REVDAT 3 05-SEP-18 5YTZ 1 JRNL REVDAT 2 30-MAY-18 5YTZ 1 DBREF REVDAT 1 23-MAY-18 5YTZ 0 JRNL AUTH P.C.WU,S.L.TZENG,C.K.CHANG,Y.F.KAO,M.J.WARING,M.H.HOU JRNL TITL COOPERATIVE RECOGNITION OF T:T MISMATCH BY ECHINOMYCIN JRNL TITL 2 CAUSES STRUCTURAL DISTORTIONS IN DNA DUPLEX JRNL REF NUCLEIC ACIDS RES. V. 46 7396 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29741655 JRNL DOI 10.1093/NAR/GKY345 REMARK 2 REMARK 2 RESOLUTION. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.383 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 16665 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 : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.895 REMARK 3 FREE R VALUE TEST SET COUNT : 1649 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 27.1635 - 3.5501 1.00 1276 140 0.1884 0.2139 REMARK 3 2 3.5501 - 2.8188 0.99 1260 136 0.1847 0.2222 REMARK 3 3 2.8188 - 2.4627 1.00 1270 139 0.2078 0.2513 REMARK 3 4 2.4627 - 2.2377 1.00 1283 137 0.2118 0.2644 REMARK 3 5 2.2377 - 2.0774 1.00 1264 134 0.2128 0.2186 REMARK 3 6 2.0774 - 1.9549 1.00 1280 143 0.2136 0.2298 REMARK 3 7 1.9549 - 1.8570 1.00 1260 148 0.2166 0.2520 REMARK 3 8 1.8570 - 1.7762 1.00 1270 144 0.2095 0.2307 REMARK 3 9 1.7762 - 1.7078 1.00 1281 131 0.2427 0.2518 REMARK 3 10 1.7078 - 1.6489 1.00 1240 141 0.2111 0.2348 REMARK 3 11 1.6489 - 1.5974 0.95 1220 136 0.2332 0.2886 REMARK 3 12 1.5974 - 1.5517 0.87 1112 120 0.2471 0.2714 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) : 0.139 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.757 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.55 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 : 0.008 482 REMARK 3 ANGLE : 1.344 680 REMARK 3 CHIRALITY : 0.079 68 REMARK 3 PLANARITY : 0.007 30 REMARK 3 DIHEDRAL : 34.649 178 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 5YTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-16 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) : 0.92014 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 : 16665 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 17.30 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : 0.03700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.50 REMARK 200 R MERGE FOR SHELL (I) : 0.14100 REMARK 200 R SYM FOR SHELL (I) : 0.14100 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: PHASER 7.0.005 REMARK 200 STARTING MODEL: 3GO3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM MES (PH 6.0), 10MM MGCL2, 2MM REMARK 280 SPERMINE 4HCL, 2% 2-METHYL-2,4-PENTANEDIOL (MPD), 10MM MNSO4 AND REMARK 280 10MM KBR BY EQUILIBRATING AGAINST 500 UL OF 30% MPD RESERVOIR REMARK 280 SOLUTION., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 20.87950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 20.87950 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.20750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.87950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.60375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.87950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 103.81125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.87950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 103.81125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.87950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.60375 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 20.87950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 20.87950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.20750 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 20.87950 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 20.87950 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 69.20750 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 20.87950 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 103.81125 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 20.87950 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 34.60375 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 20.87950 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 34.60375 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 20.87950 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 103.81125 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 20.87950 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 20.87950 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 69.20750 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: A, B, D, F 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MN MN A 101 LIES ON A SPECIAL POSITION. REMARK 375 MN MN B 101 LIES ON A SPECIAL POSITION. REMARK 375 K K D 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 210 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 221 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 205 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 236 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER REMARK 400 OF THE QUINOXALINE CLASS OF ANTIBIOTICS. REMARK 400 HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE REMARK 400 SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI. REMARK 400 REMARK 400 THE ECHINOMYCIN IS CYCLIC DEPSIPEPTIDE, A MEMBER OF ANTIBIOTIC REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ECHINOMYCIN REMARK 400 CHAIN: D, F REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_3: RESIDUE QUI, 4 COPIES REMARK 400 DESCRIPTION: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. REMARK 400 BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE REMARK 400 C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 REMARK 400 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED REMARK 400 TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. 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 B 202 O HOH B 234 1.88 REMARK 500 O HOH B 208 O HOH B 239 2.03 REMARK 500 O HOH A 208 O HOH A 226 2.06 REMARK 500 OP1 DG B 6 O HOH B 201 2.14 REMARK 500 O HOH B 225 O HOH B 238 2.18 REMARK 500 O3' DA B 1 O HOH B 202 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 219 O HOH A 219 10565 2.03 REMARK 500 O HOH A 219 O HOH A 233 10565 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 242 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH B 243 DISTANCE = 6.92 ANGSTROMS REMARK 525 HOH D 211 DISTANCE = 7.18 ANGSTROMS 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 DG A 3 N7 0.0 REMARK 620 3 HOH A 205 O 90.0 90.0 REMARK 620 4 HOH A 205 O 90.7 90.7 165.4 REMARK 620 5 HOH A 210 O 92.5 92.5 82.7 82.7 REMARK 620 6 HOH A 210 O 92.5 92.5 82.7 82.7 0.0 REMARK 620 7 HOH A 221 O 87.5 87.5 97.3 97.3 180.0 180.0 REMARK 620 8 HOH A 221 O 87.5 87.5 97.3 97.3 180.0 179.9 0.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 3 N7 REMARK 620 2 DG B 3 N7 0.0 REMARK 620 3 HOH B 214 O 90.7 90.7 REMARK 620 4 HOH B 214 O 86.9 86.9 98.2 REMARK 620 5 HOH F 206 O 87.8 87.8 87.5 172.3 REMARK 620 6 HOH F 206 O 94.9 94.9 172.3 87.4 87.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K D 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 N2C D 3 O REMARK 620 2 N2C D 3 O 0.0 REMARK 620 3 MVA D 4 O 74.1 74.1 REMARK 620 4 MVA D 4 O 74.1 74.1 0.0 REMARK 620 5 HOH D 202 O 125.8 125.8 52.2 52.2 REMARK 620 6 HOH D 202 O 92.5 92.5 154.0 154.0 132.4 REMARK 620 7 HOH D 205 O 92.8 92.8 83.4 83.4 76.2 74.9 REMARK 620 8 HOH D 205 O 156.9 156.9 123.6 123.6 74.9 76.2 103.4 REMARK 620 N 1 2 3 4 5 6 7 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K D 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DSN D 1 and ALA D 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DSN D 1 and MVA D 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ALA D 2 and N2C D 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues N2C D 3 and NCY D 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues N2C D 3 and MVA D 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide MVA D 4 and DSN D 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DSN D 5 and ALA D 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ALA D 6 and NCY D 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues NCY D 7 and MVA D 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide QUI D 101 and DSN D REMARK 800 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide QUI D 102 and DSN D REMARK 800 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DSN F 1 and ALA F 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DSN F 1 and MVA F 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ALA F 2 and N2C F 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues N2C F 3 and NCY F 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues N2C F 3 and MVA F 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide MVA F 4 and DSN F 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DSN F 5 and ALA F 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ALA F 6 and NCY F 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues NCY F 7 and MVA F 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide QUI F 101 and DSN F REMARK 800 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide QUI F 102 and DSN F REMARK 800 5 DBREF 5YTZ A 1 7 PDB 5YTZ 5YTZ 1 7 DBREF 5YTZ B 1 7 PDB 5YTZ 5YTZ 1 7 DBREF 5YTZ D 1 8 NOR 5YTZ 5YTZ 1 8 DBREF 5YTZ F 1 8 NOR 5YTZ 5YTZ 1 8 SEQRES 1 A 7 DA DC DG DT DC DG BRU SEQRES 1 B 7 DA DC DG DT DC DG BRU SEQRES 1 D 8 DSN ALA N2C MVA DSN ALA NCY MVA SEQRES 1 F 8 DSN ALA N2C MVA DSN ALA NCY MVA HET BRU A 7 20 HET BRU B 7 20 HET DSN D 1 6 HET N2C D 3 8 HET MVA D 4 8 HET DSN D 5 6 HET NCY D 7 7 HET MVA D 8 8 HET DSN F 1 6 HET N2C F 3 8 HET MVA F 4 8 HET DSN F 5 6 HET NCY F 7 7 HET MVA F 8 8 HET MN A 101 1 HET MN B 101 1 HET QUI D 101 12 HET QUI D 102 12 HET K D 103 1 HET QUI F 101 12 HET QUI F 102 12 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM DSN D-SERINE HETNAM N2C N,S-DIMETHYLCYSTEINE HETNAM MVA N-METHYLVALINE HETNAM NCY N-METHYLCYSTEINE HETNAM MN MANGANESE (II) ION HETNAM QUI 2-CARBOXYQUINOXALINE HETNAM K POTASSIUM ION FORMUL 1 BRU 2(C9 H12 BR N2 O8 P) FORMUL 3 DSN 4(C3 H7 N O3) FORMUL 3 N2C 2(C5 H11 N O2 S) FORMUL 3 MVA 4(C6 H13 N O2) FORMUL 3 NCY 2(C4 H9 N O2 S) FORMUL 5 MN 2(MN 2+) FORMUL 7 QUI 4(C9 H6 N2 O2) FORMUL 9 K K 1+ FORMUL 12 HOH *100(H2 O) LINK O3' DG A 6 P BRU A 7 1555 1555 1.61 LINK O3' DG B 6 P BRU B 7 1555 1555 1.60 LINK C DSN D 1 N ALA D 2 1555 1555 1.33 LINK OG DSN D 1 C MVA D 8 1555 1555 1.38 LINK N DSN D 1 C QUI D 101 1555 1555 1.43 LINK C ALA D 2 N N2C D 3 1555 1555 1.31 LINK C N2C D 3 N MVA D 4 1555 1555 1.33 LINK CB N2C D 3 SG NCY D 7 1555 1555 1.81 LINK C MVA D 4 OG DSN D 5 1555 1555 1.37 LINK C DSN D 5 N ALA D 6 1555 1555 1.33 LINK N DSN D 5 C QUI D 102 1555 1555 1.43 LINK C ALA D 6 N NCY D 7 1555 1555 1.37 LINK C NCY D 7 N MVA D 8 1555 1555 1.33 LINK C DSN F 1 N ALA F 2 1555 1555 1.33 LINK OG DSN F 1 C MVA F 8 1555 1555 1.37 LINK N DSN F 1 C QUI F 101 1555 1555 1.43 LINK C ALA F 2 N N2C F 3 1555 1555 1.39 LINK C N2C F 3 N MVA F 4 1555 1555 1.34 LINK CB N2C F 3 SG NCY F 7 1555 1555 1.81 LINK C MVA F 4 OG DSN F 5 1555 1555 1.37 LINK C DSN F 5 N ALA F 6 1555 1555 1.33 LINK N DSN F 5 C QUI F 102 1555 1555 1.43 LINK C ALA F 6 N NCY F 7 1555 1555 1.35 LINK C NCY F 7 N MVA F 8 1555 1555 1.33 LINK N7 DG A 3 MN MN A 101 1555 1555 2.30 LINK N7 DG A 3 MN MN A 101 1555 10565 2.30 LINK MN MN A 101 O HOH A 205 1555 1555 2.23 LINK MN MN A 101 O HOH A 205 1555 10565 2.23 LINK MN MN A 101 O HOH A 210 1555 1555 2.18 LINK MN MN A 101 O HOH A 210 1555 10565 2.18 LINK MN MN A 101 O HOH A 221 1555 1555 2.21 LINK MN MN A 101 O HOH A 221 1555 10565 2.21 LINK N7 DG B 3 MN MN B 101 1555 1555 2.24 LINK N7 DG B 3 MN MN B 101 1555 10565 2.24 LINK MN MN B 101 O HOH B 214 1555 1555 2.21 LINK MN MN B 101 O HOH B 214 1555 10565 2.21 LINK MN MN B 101 O HOH F 206 1555 1555 2.27 LINK MN MN B 101 O HOH F 206 1555 10565 2.27 LINK O N2C D 3 K K D 103 1555 1555 2.80 LINK O N2C D 3 K K D 103 1555 8555 2.80 LINK O MVA D 4 K K D 103 1555 1555 2.75 LINK O MVA D 4 K K D 103 1555 8555 2.75 LINK K K D 103 O HOH D 202 1555 1555 3.20 LINK K K D 103 O HOH D 202 1555 8555 3.20 LINK K K D 103 O HOH D 205 1555 1555 2.91 LINK K K D 103 O HOH D 205 1555 8555 2.91 SITE 1 AC1 4 DG A 3 HOH A 205 HOH A 210 HOH A 221 SITE 1 AC2 3 DG B 3 HOH B 214 HOH F 206 SITE 1 AC3 3 N2C D 3 MVA D 4 HOH D 205 SITE 1 AC4 10 DG B 6 BRU B 7 N2C D 3 MVA D 4 SITE 2 AC4 10 ALA D 6 NCY D 7 MVA D 8 QUI D 101 SITE 3 AC4 10 HOH D 206 N2C F 3 SITE 1 AC5 10 DC A 2 DG B 6 BRU B 7 ALA D 2 SITE 2 AC5 10 N2C D 3 ALA D 6 NCY D 7 QUI D 101 SITE 3 AC5 10 HOH D 206 N2C F 3 SITE 1 AC6 12 DG B 6 DSN D 1 MVA D 4 DSN D 5 SITE 2 AC6 12 ALA D 6 NCY D 7 MVA D 8 QUI D 101 SITE 3 AC6 12 K D 103 DSN F 1 NCY F 7 MVA F 8 SITE 1 AC7 11 DSN D 1 ALA D 2 MVA D 4 DSN D 5 SITE 2 AC7 11 ALA D 6 MVA D 8 K D 103 HOH D 201 SITE 3 AC7 11 DSN F 1 NCY F 7 MVA F 8 SITE 1 AC8 11 DT B 4 DSN D 1 ALA D 2 DSN D 5 SITE 2 AC8 11 ALA D 6 NCY D 7 K D 103 HOH D 202 SITE 3 AC8 11 DSN F 1 NCY F 7 MVA F 8 SITE 1 AC9 11 DG A 3 DT A 4 DT B 4 ALA D 2 SITE 2 AC9 11 N2C D 3 ALA D 6 QUI D 102 K D 103 SITE 3 AC9 11 HOH D 202 HOH D 205 MVA F 8 SITE 1 AD1 10 DG A 3 DT A 4 ALA D 2 N2C D 3 SITE 2 AD1 10 MVA D 4 NCY D 7 MVA D 8 QUI D 102 SITE 3 AD1 10 HOH D 205 MVA F 8 SITE 1 AD2 10 DG A 3 DSN D 1 ALA D 2 N2C D 3 SITE 2 AD2 10 MVA D 4 DSN D 5 MVA D 8 QUI D 102 SITE 3 AD2 10 HOH D 201 NCY F 7 SITE 1 AD3 8 DC A 2 DG B 6 DSN D 1 ALA D 2 SITE 2 AD3 8 N2C D 3 ALA D 6 HOH D 201 NCY F 7 SITE 1 AD4 11 DA A 1 DC A 2 DG B 6 BRU B 7 SITE 2 AD4 11 ALA D 2 N2C D 3 NCY D 7 MVA D 8 SITE 3 AD4 11 HOH D 203 HOH D 206 N2C F 3 SITE 1 AD5 10 DG A 3 DT A 4 DT B 4 DC B 5 SITE 2 AD5 10 N2C D 3 MVA D 4 ALA D 6 HOH D 204 SITE 3 AD5 10 HOH D 205 MVA F 8 SITE 1 AD6 11 DC B 2 DG B 3 DT B 4 N2C D 3 SITE 2 AD6 11 N2C F 3 MVA F 4 ALA F 6 NCY F 7 SITE 3 AD6 11 MVA F 8 QUI F 101 HOH F 204 SITE 1 AD7 13 DT A 4 DC A 5 DG B 3 DT B 4 SITE 2 AD7 13 N2C D 3 MVA D 4 DSN D 5 HOH D 202 SITE 3 AD7 13 ALA F 2 ALA F 6 NCY F 7 QUI F 101 SITE 4 AD7 13 HOH F 204 SITE 1 AD8 10 DC B 2 DG B 3 DSN D 1 DSN F 1 SITE 2 AD8 10 MVA F 4 DSN F 5 ALA F 6 NCY F 7 SITE 3 AD8 10 MVA F 8 QUI F 101 SITE 1 AD9 10 DSN D 1 N2C D 3 NCY D 7 DSN F 1 SITE 2 AD9 10 ALA F 2 MVA F 4 DSN F 5 ALA F 6 SITE 3 AD9 10 MVA F 8 HOH F 202 SITE 1 AE1 8 DG A 6 DA B 1 DC B 2 DSN D 1 SITE 2 AE1 8 ALA F 2 DSN F 5 ALA F 6 NCY F 7 SITE 1 AE2 10 DG A 6 BRU A 7 DA B 1 DC B 2 SITE 2 AE2 10 ALA F 2 N2C F 3 ALA F 6 QUI F 102 SITE 3 AE2 10 HOH F 201 HOH F 205 SITE 1 AE3 11 DC A 5 DG A 6 BRU A 7 ALA F 2 SITE 2 AE3 11 N2C F 3 MVA F 4 NCY F 7 MVA F 8 SITE 3 AE3 11 QUI F 102 HOH F 201 HOH F 205 SITE 1 AE4 12 DC A 5 DG A 6 N2C D 3 NCY D 7 SITE 2 AE4 12 DSN F 1 ALA F 2 N2C F 3 MVA F 4 SITE 3 AE4 12 DSN F 5 MVA F 8 QUI F 102 HOH F 202 SITE 1 AE5 13 DT A 4 DC A 5 DG B 3 N2C D 3 SITE 2 AE5 13 MVA D 4 DSN D 5 NCY D 7 HOH D 202 SITE 3 AE5 13 DSN F 1 ALA F 2 N2C F 3 ALA F 6 SITE 4 AE5 13 HOH F 202 SITE 1 AE6 10 DT A 4 DC A 5 DG B 3 DT B 4 SITE 2 AE6 10 N2C D 3 ALA F 2 NCY F 7 MVA F 8 SITE 3 AE6 10 HOH F 204 HOH F 206 SITE 1 AE7 10 DG A 6 BRU A 7 DA B 1 DC B 2 SITE 2 AE7 10 N2C F 3 MVA F 4 ALA F 6 HOH F 201 SITE 3 AE7 10 HOH F 203 HOH F 205 CRYST1 41.759 41.759 138.415 90.00 90.00 90.00 I 41 2 2 32 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 0.023947 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023947 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007225 0.00000