10 20 30 40 50 60 70 80 1VAQ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 19-FEB-04 1VAQ
TITLE CRYSTAL STRUCTURE OF THE MG2+-(CHROMOMYCIN A3)2-D(TTGGCCAA) TITLE 2 2 COMPLEX REVEALS GGCC BINDING SPECIFICITY OF THE DRUG TITLE 3 DIMER CHELATED BY METAL ION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SYNTHETIC DNA OLIGONUCLEOTIDES WERE SOURCE 4 PURIFIED BY GEL ELECTROPHORESIS.
KEYWDS CHROMOMYCIN A3, X-RAY DIFFRACTION, MAD, DNA DUPLEX, GGCC KEYWDS 2 SITE, DNA KINK, CD SPECTRA
EXPDTA X-RAY DIFFRACTION
AUTHOR M.H.HOU,H.ROBINSON,Y.G.GAO,A.H.-J.WANG
REVDAT 2 24-FEB-09 1VAQ 1 VERSN REVDAT 1 22-JUN-04 1VAQ 0
JRNL AUTH M.H.HOU,H.ROBINSON,Y.G.GAO,A.H.-J.WANG JRNL TITL CRYSTAL STRUCTURE OF THE [MG2+-(CHROMOMYCIN JRNL TITL 2 A3)2]-D(TTGGCCAA)2 COMPLEX REVEALS GGCC BINDING JRNL TITL 3 SPECIFICITY OF THE DRUG DIMER CHELATED BY A METAL JRNL TITL 4 ION JRNL REF NUCLEIC ACIDS RES. V. 32 2214 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 15107489 JRNL DOI 10.1093/NAR/GKH549
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 10.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 7815 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 726 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 735 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 644 REMARK 3 HETEROGEN ATOMS : 338 REMARK 3 SOLVENT ATOMS : 279 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 BOND ANGLES (DEGREES) : 2.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1VAQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-FEB-04. REMARK 100 THE RCSB ID CODE IS RCSB006410.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5432 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : NULL REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.00550 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) : NULL 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM-CACODYLATE, MGCL2, PH 5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 164.07333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 82.03667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 123.05500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 41.01833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 205.09167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 164.07333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 82.03667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 41.01833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 123.05500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 205.09167 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 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 HOH A 268 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 280 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 409 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 345 LIES ON A SPECIAL POSITION.
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 422 O HOH C 250 2.17 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 A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 10 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC C 45 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG A 3 0.14 SIDE_CHAIN REMARK 500 DG A 4 0.11 SIDE_CHAIN REMARK 500 DT B 10 0.07 SIDE_CHAIN REMARK 500 DG B 11 0.11 SIDE_CHAIN REMARK 500 DG B 12 0.10 SIDE_CHAIN REMARK 500 DG C 44 0.06 SIDE_CHAIN REMARK 500 DC C 45 0.09 SIDE_CHAIN REMARK 500 DG D 51 0.10 SIDE_CHAIN REMARK 500 DC D 53 0.07 SIDE_CHAIN 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 D 257 DISTANCE = 5.07 ANGSTROMS REMARK 525 HOH B 235 DISTANCE = 5.22 ANGSTROMS REMARK 525 HOH D 277 DISTANCE = 10.07 ANGSTROMS REMARK 525 HOH D 278 DISTANCE = 11.39 ANGSTROMS REMARK 525 HOH B 237 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A 390 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH A 418 DISTANCE = 5.58 ANGSTROMS REMARK 525 HOH C 292 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH D 336 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH B 362 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH D 356 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH D 393 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH D 399 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH C 352 DISTANCE = 7.79 ANGSTROMS REMARK 525 HOH C 357 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH D 419 DISTANCE = 10.78 ANGSTROMS REMARK 525 HOH D 464 DISTANCE = 10.14 ANGSTROMS REMARK 525 HOH D 465 DISTANCE = 12.77 ANGSTROMS REMARK 525 HOH C 443 DISTANCE = 7.31 ANGSTROMS REMARK 525 HOH B 394 DISTANCE = 8.85 ANGSTROMS REMARK 525 HOH B 435 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH B 438 DISTANCE = 11.53 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 MG A 81 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 481 O REMARK 620 2 HOH B 480 O 90.2 REMARK 620 3 CPH A 33 O1 99.5 167.5 REMARK 620 4 CPH A 33 O9 105.4 87.9 82.0 REMARK 620 5 CPH B 23 O1 162.6 86.7 86.3 91.7 REMARK 620 6 CPH B 23 O9 81.6 90.5 98.6 172.9 81.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 82 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 483 O REMARK 620 2 HOH D 482 O 93.0 REMARK 620 3 CPH D 63 O9 91.8 85.5 REMARK 620 4 CPH C 73 O1 173.1 82.5 93.1 REMARK 620 5 CPH C 73 O9 93.5 84.8 169.2 80.9 REMARK 620 6 CPH D 63 O1 94.2 166.8 83.3 91.1 105.6 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 1GL B 21 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARI B 22 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDR B 24 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDR B 25 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERI B 26 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1GL A 31 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARI A 32 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDR B 34 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDR B 35 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERI B 36 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1GL D 61 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARI D 62 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDR D 64 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDR D 65 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERI D 66 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1GL C 71 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARI C 72 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDR C 74 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDR C 75 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERI C 76 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 81 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 82 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPH B 23 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPH A 33 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPH D 63 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPH C 73
DBREF 1VAQ A 1 8 PDB 1VAQ 1VAQ 1 8 DBREF 1VAQ B 9 16 PDB 1VAQ 1VAQ 9 16 DBREF 1VAQ C 41 48 PDB 1VAQ 1VAQ 41 48 DBREF 1VAQ D 49 56 PDB 1VAQ 1VAQ 49 56
SEQRES 1 A 8 DT DT DG DG DC DC DA DA SEQRES 1 B 8 DT DT DG DG DC DC DA DA SEQRES 1 C 8 DT DT DG DG DC DC DA DA SEQRES 1 D 8 DT DT DG DG DC DC DA DA
HET 1GL B 21 11 HET ARI B 22 12 HET CDR B 24 9 HET CDR B 25 9 HET ERI B 26 14 HET 1GL A 31 11 HET ARI A 32 12 HET CDR B 34 9 HET CDR B 35 9 HET ERI B 36 14 HET 1GL D 61 11 HET ARI D 62 12 HET CDR D 64 9 HET CDR D 65 9 HET ERI D 66 14 HET 1GL C 71 11 HET ARI C 72 12 HET CDR C 74 9 HET CDR C 75 9 HET ERI C 76 14 HET MG A 81 1 HET MG D 82 1 HET CPH B 23 28 HET CPH A 33 28 HET CPH D 63 28 HET CPH C 73 28
HETNAM 1GL 4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE HETNAM ARI [O4]-ACETOXY-2,3-DIDEOXYFUCOSE HETNAM CDR 2,3-DIDEOXYFUCOSE HETNAM ERI 4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO- HETNAM 2 ERI HEXOPYRANOSE HETNAM MG MAGNESIUM ION HETNAM CPH 1,8-DIHYDROXY-7-METHYL-3-(1,3,4-TRIHYDROXY-2-OXO- HETNAM 2 CPH PENTYL)-3,10-DIHYDRO-2H-ANTHRACEN-9-ONE
FORMUL 5 1GL 4(C7 H14 O4) FORMUL 5 ARI 4(C8 H14 O4) FORMUL 6 CDR 8(C6 H12 O3) FORMUL 6 ERI 4(C9 H16 O5) FORMUL 13 MG 2(MG 2+) FORMUL 15 CPH 4(C21 H24 O7) FORMUL 19 HOH *283(H2 O)
LINK OGL ARI B 22 C6 CPH B 23 1555 1555 1.38 LINK C2 CPH B 23 OGL CDR B 24 1555 1555 1.38 LINK OGL ARI A 32 C6 CPH A 33 1555 1555 1.38 LINK C2 CPH A 33 OGL CDR B 34 1555 1555 1.39 LINK OGL ARI D 62 C6 CPH D 63 1555 1555 1.38 LINK C2 CPH D 63 OGL CDR D 64 1555 1555 1.38 LINK OGL ARI C 72 C6 CPH C 73 1555 1555 1.37 LINK C2 CPH C 73 OGL CDR C 74 1555 1555 1.39 LINK O1 1GL B 21 C3 ARI B 22 1555 1555 1.39 LINK C3 CDR B 24 OGL CDR B 25 1555 1555 1.39 LINK C3 CDR B 25 OGL ERI B 26 1555 1555 1.39 LINK O1 1GL A 31 C3 ARI A 32 1555 1555 1.38 LINK C3 CDR B 34 OGL CDR B 35 1555 1555 1.39 LINK C3 CDR B 35 OGL ERI B 36 1555 1555 1.39 LINK O1 1GL D 61 C3 ARI D 62 1555 1555 1.40 LINK C3 CDR D 64 OGL CDR D 65 1555 1555 1.40 LINK C3 CDR D 65 OGL ERI D 66 1555 1555 1.37 LINK O1 1GL C 71 C3 ARI C 72 1555 1555 1.39 LINK C3 CDR C 74 OGL CDR C 75 1555 1555 1.39 LINK C3 CDR C 75 OGL ERI C 76 1555 1555 1.38 LINK MG MG A 81 O HOH A 481 1555 1555 2.06 LINK MG MG A 81 O HOH B 480 1555 1555 2.07 LINK MG MG D 82 O HOH D 483 1555 1555 2.01 LINK MG MG D 82 O HOH D 482 1555 1555 2.07 LINK O1 CPH A 33 MG MG A 81 1555 1555 2.04 LINK O9 CPH A 33 MG MG A 81 1555 1555 1.87 LINK MG MG A 81 O1 CPH B 23 1555 1555 2.00 LINK MG MG A 81 O9 CPH B 23 1555 1555 1.81 LINK O9 CPH D 63 MG MG D 82 1555 1555 1.84 LINK MG MG D 82 O1 CPH C 73 1555 1555 2.07 LINK MG MG D 82 O9 CPH C 73 1555 1555 1.88 LINK MG MG D 82 O1 CPH D 63 1555 1555 2.11
SITE 1 AC1 5 DG B 12 DC B 13 ARI B 22 DA C 48 SITE 2 AC1 5 HOH C 358 SITE 1 AC2 4 1GL B 21 CPH B 23 CDR B 35 ERI B 36 SITE 1 AC3 5 DC B 14 CPH B 23 CDR B 25 HOH B 404 SITE 2 AC3 5 CPH C 73 SITE 1 AC4 6 ARI A 32 CPH A 33 DA B 15 CDR B 24 SITE 2 AC4 6 ERI B 26 CPH C 73 SITE 1 AC5 7 DG A 3 DG A 4 ARI A 32 CPH A 33 SITE 2 AC5 7 DA B 15 CDR B 25 HOH B 236 SITE 1 AC6 3 DG A 4 ARI A 32 HOH A 417 SITE 1 AC7 6 DC A 5 1GL A 31 CPH A 33 HOH A 240 SITE 2 AC7 6 CDR B 25 ERI B 26 SITE 1 AC8 7 DC A 6 CPH A 33 CDR B 35 HOH B 359 SITE 2 AC8 7 HOH B 467 CDR C 74 CPH D 63 SITE 1 AC9 5 ARI B 22 CPH B 23 CDR B 34 ERI B 36 SITE 2 AC9 5 ARI D 62 SITE 1 BC1 7 DA A 7 DG B 11 ARI B 22 CPH B 23 SITE 2 BC1 7 CDR B 35 HOH B 383 HOH B 384 SITE 1 BC2 4 DG D 52 DC D 53 ARI D 62 HOH D 323 SITE 1 BC3 5 CDR B 35 CDR C 75 ERI C 76 1GL D 61 SITE 2 BC3 5 CPH D 63 SITE 1 BC4 7 DT B 9 DC D 54 CPH D 63 CDR D 65 SITE 2 BC4 7 HOH D 283 HOH D 448 HOH D 449 SITE 1 BC5 6 ARI C 72 CPH C 73 DA D 55 CDR D 64 SITE 2 BC5 6 ERI D 66 HOH D 449 SITE 1 BC6 9 DG C 43 DG C 44 1GL C 71 ARI C 72 SITE 2 BC6 9 CPH C 73 DA D 55 DA D 56 CDR D 65 SITE 3 BC6 9 HOH D 211 SITE 1 BC7 5 DT A 1 DG C 44 DC C 45 ARI C 72 SITE 2 BC7 5 ERI D 66 SITE 1 BC8 5 DT C 41 1GL C 71 CPH C 73 CDR D 65 SITE 2 BC8 5 ERI D 66 SITE 1 BC9 5 CPH A 33 CDR B 34 DC C 46 CPH C 73 SITE 2 BC9 5 CDR C 75 SITE 1 CC1 5 CPH B 23 CDR C 74 ERI C 76 ARI D 62 SITE 2 CC1 5 CPH D 63 SITE 1 CC2 8 HOH B 463 DA C 48 CDR C 75 HOH C 259 SITE 2 CC2 8 DG D 51 DG D 52 ARI D 62 CPH D 63 SITE 1 CC3 4 CPH A 33 HOH A 481 CPH B 23 HOH B 480 SITE 1 CC4 4 CPH C 73 CPH D 63 HOH D 482 HOH D 483 SITE 1 CC5 23 DC A 6 CPH A 33 MG A 81 HOH A 481 SITE 2 CC5 23 DG B 11 DG B 12 DC B 13 DC B 14 SITE 3 CC5 23 DA B 15 ARI B 22 CDR B 24 CDR B 35 SITE 4 CC5 23 ERI B 36 HOH B 251 HOH B 350 HOH B 351 SITE 5 CC5 23 HOH B 431 HOH B 456 HOH B 480 DA C 47 SITE 6 CC5 23 DA C 48 CDR C 75 HOH C 455 SITE 1 CC6 15 DG A 3 DG A 4 DC A 5 DC A 6 SITE 2 CC6 15 ARI A 32 MG A 81 DC B 14 CPH B 23 SITE 3 CC6 15 CDR B 25 ERI B 26 CDR B 34 HOH B 314 SITE 4 CC6 15 HOH B 359 HOH B 480 CDR C 74 SITE 1 CC7 17 DA A 8 CDR B 34 DC C 46 CPH C 73 SITE 2 CC7 17 CDR C 75 ERI C 76 DG D 52 DC D 53 SITE 3 CC7 17 DC D 54 DA D 55 ARI D 62 CDR D 64 SITE 4 CC7 17 MG D 82 HOH D 283 HOH D 315 HOH D 482 SITE 5 CC7 17 HOH D 483 SITE 1 CC8 19 CDR B 24 CDR B 25 DG C 43 DG C 44 SITE 2 CC8 19 DC C 45 DC C 46 ARI C 72 CDR C 74 SITE 3 CC8 19 HOH C 227 HOH C 230 HOH C 298 HOH C 427 SITE 4 CC8 19 DC D 54 CPH D 63 CDR D 65 ERI D 66 SITE 5 CC8 19 MG D 82 HOH D 482 HOH D 483
CRYST1 42.230 42.230 246.110 90.00 90.00 120.00 P 65 2 2 48
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 0.023680 0.013672 0.000000 0.00000
SCALE2 0.000000 0.027343 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004063 0.00000