HEADER DNA 14-SEP-99 1VTJ TITLE MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA TITLE 2 CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*TP*AP*TP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.COLL,J.AYMAMI,G.A.VAN DER MAREL,J.H.VAN BOOM,A.RICH,A.H.-J.WANG REVDAT 1 13-JUL-11 1VTJ 0 JRNL AUTH M.COLL,J.AYMAMI,G.A.VAN DER MAREL,J.H.VAN BOOM,A.RICH, JRNL AUTH 2 A.H.-J.WANG JRNL TITL MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) JRNL TITL 2 COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT JRNL REF BIOCHEMISTRY V. 28 310 1989 JRNL REFN ISSN 0006-2960 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.COLL,C.A.FREDERICK,A.H.-J.WANG,A.RICH REMARK 1 TITL A BIFURCATED HYDROGEN-BONDED CONFORMATION IN THE D(A.T) BASE REMARK 1 TITL 2 PAIRS OF THE DNA DODECAMER D(CGCAAATTTGCG) AND ITS COMPLEX REMARK 1 TITL 3 WITH DISTAMYCIN REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 84 8385 1987 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.L.KOPKA,C.YOON,D.GOODSELL,P.PJURA,R.E.DICKERSON REMARK 1 TITL THE MOLECULAR ORIGIN OF DNA-DRUG SPECIFICITY IN NETROPSIN REMARK 1 TITL 2 AND DISTAMYCIN REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 82 1376 1985 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NUCLSQ REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 1848 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 60 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BOND DISTANCE (A) : NULL ; NULL REMARK 3 SUGAR-BASE BOND ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BONDS DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BONDS (A**2) : NULL ; NULL REMARK 3 SUGAR-BASE ANGLES (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BONDS (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VTJ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-11. REMARK 100 THE RCSB ID CODE IS RCSB003043. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 283.00 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : NICOLET P3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1848 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.50, VAPOR DIFFUSION, TEMPERATURE REMARK 280 283.00K 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 12.74000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.44000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.63000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.44000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.74000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.63000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5140 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 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 O3' DG A 12 N2 DG B 22 2664 1.75 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 1 N3 DC A 1 C4 0.062 REMARK 500 DG A 2 P DG A 2 O5' -0.082 REMARK 500 DG A 2 C2' DG A 2 C1' 0.065 REMARK 500 DC A 3 P DC A 3 O5' -0.084 REMARK 500 DC A 3 O4' DC A 3 C1' 0.087 REMARK 500 DG A 4 P DG A 4 OP2 0.160 REMARK 500 DG A 4 P DG A 4 O5' -0.096 REMARK 500 DT A 6 P DT A 6 O5' 0.109 REMARK 500 DA A 5 O3' DT A 6 P -0.139 REMARK 500 DT A 8 P DT A 8 O5' 0.133 REMARK 500 DA A 7 O3' DT A 8 P 0.074 REMARK 500 DC A 9 P DC A 9 OP1 0.110 REMARK 500 DG A 10 P DG A 10 O5' 0.130 REMARK 500 DC A 11 O3' DG A 12 P 0.160 REMARK 500 DG B 16 P DG B 16 OP1 0.141 REMARK 500 DG B 16 P DG B 16 O5' -0.139 REMARK 500 DG B 16 O4' DG B 16 C1' 0.093 REMARK 500 DT B 18 P DT B 18 O5' 0.070 REMARK 500 DA B 17 O3' DT B 18 P 0.084 REMARK 500 DA B 19 O5' DA B 19 C5' 0.097 REMARK 500 DA B 19 C2' DA B 19 C1' -0.079 REMARK 500 DA B 19 O4' DA B 19 C1' 0.085 REMARK 500 DA B 19 N9 DA B 19 C4 -0.051 REMARK 500 DT B 20 P DT B 20 O5' 0.072 REMARK 500 DC B 21 P DC B 21 O5' 0.093 REMARK 500 DC B 21 O5' DC B 21 C5' 0.116 REMARK 500 DG B 22 P DG B 22 OP1 0.132 REMARK 500 DG B 22 P DG B 22 OP2 -0.105 REMARK 500 DG B 22 P DG B 22 O5' 0.082 REMARK 500 DG B 24 P DG B 24 OP1 0.112 REMARK 500 DG B 24 O4' DG B 24 C1' 0.091 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 2 OP1 - P - OP2 ANGL. DEV. = -14.3 DEGREES REMARK 500 DG A 2 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 12.0 DEGREES REMARK 500 DG A 2 N1 - C2 - N3 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 2 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = 8.0 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -9.9 DEGREES REMARK 500 DC A 1 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES REMARK 500 DC A 3 OP1 - P - OP2 ANGL. DEV. = -14.5 DEGREES REMARK 500 DC A 3 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 3 P - O5' - C5' ANGL. DEV. = -11.2 DEGREES REMARK 500 DC A 3 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 3 C1' - O4' - C4' ANGL. DEV. = -8.0 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -7.8 DEGREES REMARK 500 DC A 3 N3 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DC A 3 O3' - P - O5' ANGL. DEV. = 11.8 DEGREES REMARK 500 DG A 4 OP1 - P - OP2 ANGL. DEV. = -16.5 DEGREES REMARK 500 DG A 4 P - O5' - C5' ANGL. DEV. = 15.6 DEGREES REMARK 500 DG A 4 O4' - C4' - C3' ANGL. DEV. = -8.1 DEGREES REMARK 500 DG A 4 C1' - O4' - C4' ANGL. DEV. = -7.1 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 7.8 DEGREES REMARK 500 DG A 4 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC A 3 C3' - O3' - P ANGL. DEV. = -9.6 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 DT A 6 OP1 - P - OP2 ANGL. DEV. = -14.4 DEGREES REMARK 500 DT A 6 O5' - P - OP1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DT A 6 P - O5' - C5' ANGL. DEV. = -11.4 DEGREES REMARK 500 DT A 6 O4' - C4' - C3' ANGL. DEV. = -4.7 DEGREES REMARK 500 DT A 6 C4' - C3' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 DT A 6 N1 - C2 - N3 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 6 N1 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 DA A 5 C3' - O3' - P ANGL. DEV. = 19.0 DEGREES REMARK 500 DT A 6 O3' - P - OP1 ANGL. DEV. = 11.9 DEGREES REMARK 500 DA A 7 OP1 - P - OP2 ANGL. DEV. = -13.3 DEGREES REMARK 500 DA A 7 O5' - P - OP2 ANGL. DEV. = 12.9 DEGREES REMARK 500 DA A 7 O5' - C5' - C4' ANGL. DEV. = -7.9 DEGREES REMARK 500 DA A 7 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 7 C3' - C2' - C1' ANGL. DEV. = -9.2 DEGREES REMARK 500 DA A 7 O4' - C1' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 9.0 DEGREES REMARK 500 DA A 7 N1 - C6 - N6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT A 6 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 DT A 8 P - O5' - C5' ANGL. DEV. = -15.8 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 DT A 8 N1 - C2 - N3 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT A 8 C2 - N3 - C4 ANGL. DEV. = -5.9 DEGREES REMARK 500 DT A 8 N1 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DT A 8 O3' - P - O5' ANGL. DEV. = -13.2 DEGREES REMARK 500 DC A 9 O5' - P - OP2 ANGL. DEV. = 7.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 141 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 DC B 15 -46.5 D D OUTSIDE RANGE 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 A 36 DISTANCE = 7.56 ANGSTROMS REMARK 525 HOH A 37 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH A 44 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A 48 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH A 61 DISTANCE = 7.41 ANGSTROMS REMARK 525 HOH A 65 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A 71 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A 72 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A 77 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH A 82 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A 83 DISTANCE = 5.18 ANGSTROMS REMARK 525 HOH B 31 DISTANCE = 5.50 ANGSTROMS REMARK 525 HOH B 34 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH B 35 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B 39 DISTANCE = 5.39 ANGSTROMS REMARK 525 HOH B 54 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH B 56 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH B 58 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH B 59 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH B 67 DISTANCE = 5.64 ANGSTROMS REMARK 525 HOH B 74 DISTANCE = 6.99 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NT B 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DNE RELATED DB: PDB REMARK 900 1DNE CONTAINS BOTH CONFORMATIONS. DBREF 1VTJ A 1 12 PDB 1VTJ 1VTJ 1 12 DBREF 1VTJ B 13 24 PDB 1VTJ 1VTJ 13 24 SEQRES 1 A 12 DC DG DC DG DA DT DA DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DT DA DT DC DG DC DG HET NT B 25 31 HETNAM NT NETROPSIN FORMUL 3 NT C18 H26 N10 O3 FORMUL 4 HOH *60(H2 O) SITE 1 AC1 13 DG A 4 DA A 5 DT A 6 DA A 7 SITE 2 AC1 13 DT A 8 DC A 9 DG B 16 DA B 17 SITE 3 AC1 13 DT B 18 DA B 19 DT B 20 DC B 21 SITE 4 AC1 13 DG B 22 CRYST1 25.480 41.260 66.880 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 0.039246 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014952 0.00000 MASTER 403 0 1 0 0 0 4 6 0 0 0 2 END