HEADER DNA 20-APR-05 1ZF9 TITLE GGG DUPLEX A-DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SOURCE 4 SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL- SOURCE 5 PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN SOURCE 6 DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, SOURCE 7 NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SOURCE 8 SEPHADEX COLUMN. KEYWDS CRYSTALLOGRAPHIC SCREEN, DNA STRUCTURE, HOLLIDAY JUNCTION, MOLECULAR KEYWDS 2 STRUCTURE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR F.A.HAYS,A.T.TEEGARDEN,Z.J.R.JONES,M.HARMS,D.RAUP,J.WATSON, AUTHOR 2 E.CAVALIERE,P.S.HO REVDAT 5 03-APR-24 1ZF9 1 REMARK REVDAT 4 14-FEB-24 1ZF9 1 REMARK LINK REVDAT 3 11-OCT-17 1ZF9 1 REMARK REVDAT 2 24-FEB-09 1ZF9 1 VERSN REVDAT 1 10-MAY-05 1ZF9 0 JRNL AUTH F.A.HAYS,A.TEEGARDEN,Z.J.JONES,M.HARMS,D.RAUP,J.WATSON, JRNL AUTH 2 E.CAVALIERE,P.S.HO JRNL TITL HOW SEQUENCE DEFINES STRUCTURE: A CRYSTALLOGRAPHIC MAP OF JRNL TITL 2 DNA STRUCTURE AND CONFORMATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 7157 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15870206 JRNL DOI 10.1073/PNAS.0409455102 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 53828.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 10051 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) : 0.237 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1034 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.47 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1234 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 124 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.25000 REMARK 3 B22 (A**2) : 0.13900 REMARK 3 B33 (A**2) : 1.11100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.08 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.028 REMARK 3 BOND ANGLES (DEGREES) : 2.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 35.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.740 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.464 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.613 ; 0.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.964 ; 0.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.426 ; 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.74 REMARK 3 BSOL : 80.17 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 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR:DNA-RNA.LINK REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE NOT REFINED TO ITS LOWEST R REMARK 3 AND RFREE VALUES. PLEASE REFER TO CITATION ABOVE FOR MORE REMARK 3 DETAILS. REMARK 4 REMARK 4 1ZF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032652. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-03; 02-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 103; 103 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : APS; ROTATING ANODE REMARK 200 BEAMLINE : 14-ID-B; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.972; 1.542 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10745 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NDB ENTRY ADJ049 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA CACODYLATE, CACL2, SPERMINE, MPD IN REMARK 280 RESEVOIR, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 11.64000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.77500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.65500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.77500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.64000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.65500 REMARK 290 SMTRY3 4 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: 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 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 41 O HOH A 54 1.61 REMARK 500 OP2 DG B 18 O HOH B 49 1.89 REMARK 500 C4' DC A 1 O HOH A 79 2.01 REMARK 500 O HOH A 89 O HOH B 75 2.01 REMARK 500 O HOH A 58 O HOH A 72 2.05 REMARK 500 O HOH A 111 O HOH B 75 2.06 REMARK 500 O HOH A 50 O HOH A 91 2.07 REMARK 500 O HOH A 21 O HOH A 26 2.09 REMARK 500 OP1 DC A 4 O HOH A 116 2.10 REMARK 500 O3' DG B 19 O HOH B 99 2.13 REMARK 500 O HOH A 109 O HOH A 118 2.16 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 O5' DG B 20 O HOH A 63 2555 1.84 REMARK 500 O HOH A 51 O HOH B 99 3546 2.05 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 DC A 3 C2 DC A 3 O2 -0.064 REMARK 500 DC A 4 C2 DC A 4 N3 0.058 REMARK 500 DC A 5 C2 DC A 5 O2 0.063 REMARK 500 DC A 5 N1 DC A 5 C2 -0.076 REMARK 500 DC A 5 C2 DC A 5 N3 0.062 REMARK 500 DG A 6 N3 DG A 6 C4 0.043 REMARK 500 DG A 7 N1 DG A 7 C2 -0.070 REMARK 500 DG A 10 O3' DG A 10 C3' -0.077 REMARK 500 DC B 11 C2 DC B 11 O2 -0.062 REMARK 500 DC B 13 P DC B 13 OP2 -0.116 REMARK 500 DC B 13 O3' DC B 13 C3' -0.037 REMARK 500 DC B 15 C2 DC B 15 O2 -0.120 REMARK 500 DG B 16 O3' DG B 16 C3' -0.041 REMARK 500 DG B 16 C6 DG B 16 O6 -0.056 REMARK 500 DG B 17 N3 DG B 17 C4 0.042 REMARK 500 DG B 18 O3' DG B 18 C3' -0.052 REMARK 500 DG B 18 C8 DG B 18 N9 -0.042 REMARK 500 DG B 19 C4 DG B 19 C5 -0.042 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 A 1 O5' - C5' - C4' ANGL. DEV. = 16.6 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DC A 2 O3' - P - OP2 ANGL. DEV. = -18.9 DEGREES REMARK 500 DC A 2 O3' - P - OP1 ANGL. DEV. = 16.6 DEGREES REMARK 500 DC A 3 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 11 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG B 16 O4' - C1' - C2' ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 17 O3' - P - OP2 ANGL. DEV. = 6.6 DEGREES REMARK 500 DG B 17 O5' - P - OP2 ANGL. DEV. = -8.4 DEGREES REMARK 500 DG B 17 C5' - C4' - C3' ANGL. DEV. = 7.8 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 19 O4' - C4' - C3' ANGL. DEV. = -6.0 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 DC A 5 0.08 SIDE CHAIN REMARK 500 DC B 12 0.08 SIDE CHAIN REMARK 500 DC B 15 0.08 SIDE CHAIN REMARK 500 DG B 16 0.05 SIDE CHAIN 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 NA A 64 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 79 O REMARK 620 2 HOH A 88 O 112.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 35 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 17 O6 REMARK 620 2 HOH B 37 O 73.8 REMARK 620 3 HOH B 47 O 71.0 113.1 REMARK 620 4 HOH B 73 O 159.7 99.7 95.0 REMARK 620 5 HOH B 81 O 107.3 169.7 58.9 75.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 35 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 64 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P4Y RELATED DB: PDB REMARK 900 RELATED ID: 1P4Z RELATED DB: PDB REMARK 900 RELATED ID: 1DCW RELATED DB: PDB REMARK 900 RELATED ID: 1DCV RELATED DB: PDB REMARK 900 RELATED ID: 1ZEW RELATED DB: PDB REMARK 900 RELATED ID: 1ZEX RELATED DB: PDB REMARK 900 RELATED ID: 1ZEY RELATED DB: PDB REMARK 900 RELATED ID: 1ZEZ RELATED DB: PDB REMARK 900 RELATED ID: 1ZF0 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF1 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF2 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF3 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF4 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF5 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF6 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF7 RELATED DB: PDB REMARK 900 RELATED ID: 1ZF8 RELATED DB: PDB REMARK 900 RELATED ID: 1ZFA RELATED DB: PDB REMARK 900 RELATED ID: 1ZFB RELATED DB: PDB REMARK 900 RELATED ID: 1ZFC RELATED DB: PDB REMARK 900 RELATED ID: 1ZFE RELATED DB: PDB REMARK 900 RELATED ID: 1ZFF RELATED DB: PDB REMARK 900 RELATED ID: 1ZFG RELATED DB: PDB REMARK 900 RELATED ID: 1ZFH RELATED DB: PDB REMARK 900 RELATED ID: 1ZFM RELATED DB: PDB DBREF 1ZF9 A 1 10 PDB 1ZF9 1ZF9 1 10 DBREF 1ZF9 B 11 20 PDB 1ZF9 1ZF9 11 20 SEQRES 1 A 10 DC DC DC DC DC DG DG DG DG DG SEQRES 1 B 10 DC DC DC DC DC DG DG DG DG DG HET NA A 64 1 HET NA B 35 1 HETNAM NA SODIUM ION FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *94(H2 O) LINK NA NA A 64 O HOH A 79 1555 1555 2.85 LINK NA NA A 64 O HOH A 88 1555 1555 2.62 LINK O6 DG B 17 NA NA B 35 1555 1555 2.50 LINK NA NA B 35 O HOH B 37 1555 1555 2.28 LINK NA NA B 35 O HOH B 47 1555 1555 2.53 LINK NA NA B 35 O HOH B 73 1555 1555 2.26 LINK NA NA B 35 O HOH B 81 1555 1555 2.49 SITE 1 AC1 5 DG B 17 HOH B 37 HOH B 47 HOH B 73 SITE 2 AC1 5 HOH B 81 SITE 1 AC2 4 DC A 1 DG A 7 HOH A 79 HOH A 88 CRYST1 23.280 45.310 47.550 90.00 90.00 90.00 P 21 21 21 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 0.042955 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021030 0.00000