10 20 30 40 50 60 70 80 293D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER DNA 09-OCT-96 293D
TITLE INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND POLYAMINE-2: TITLE 2 THE CRYSTAL STRUCTURE OF THE D(CG)3 AND SPERMIDINE COMPLEX
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS Z-DNA, DOUBLE HELIX, COMPLEXED WITH SPERMIDINE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.OHISHI,I.NAKANISHI,K.INUBUSHI,G.A.VAN DER MAREL,J.H.VAN AUTHOR 2 BOOM,A.RICH,A.H.-J.WANG,T.HAKOSHIMA,K.TOMITA
REVDAT 3 24-FEB-09 293D 1 VERSN REVDAT 2 01-APR-03 293D 1 JRNL REVDAT 1 02-DEC-96 293D 0
JRNL AUTH H.OHISHI,I.NAKANISHI,K.INUBUSHI,G.VAN DER MAREL, JRNL AUTH 2 J.H.VAN BOOM,A.RICH,A.H.WANG,T.HAKOSHIMA,K.TOMITA JRNL TITL INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND JRNL TITL 2 POLYAMINE-2. THE CRYSTAL STRUCTURE OF THE D(CG)3 JRNL TITL 3 AND SPERMIDINE COMPLEX. JRNL REF FEBS LETT. V. 391 153 1996 JRNL REFN ISSN 0014-5793 JRNL PMID 8706905 JRNL DOI 10.1016/0014-5793(96)00723-5
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.00 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6301 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) : 0.191 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 : 240 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 74 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 293D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
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 : 7.00 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL 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 <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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: ZDF001 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00, VAPOR DIFFUSION
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 8.96500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.32000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.61500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.32000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 8.96500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.61500 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 58 O HOH A 109 1.93 REMARK 500 OP1 DG A 6 O HOH A 112 2.05 REMARK 500 O HOH A 41 O HOH A 87 2.10 REMARK 500 O HOH A 68 O HOH A 79 2.12 REMARK 500 O HOH A 77 O HOH B 27 2.17 REMARK 500 O HOH A 18 O HOH B 25 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 79 O HOH A 112 1455 1.09 REMARK 500 O HOH A 37 O HOH B 36 4465 1.72 REMARK 500 O HOH A 111 O HOH B 90 3655 2.11 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 C5' DC A 1 C4' 0.068 REMARK 500 DC A 1 C2 DC A 1 O2 -0.070 REMARK 500 DC A 1 C4 DC A 1 N4 0.059 REMARK 500 DC A 1 C4 DC A 1 C5 0.069 REMARK 500 DG A 2 O4' DG A 2 C4' -0.089 REMARK 500 DG A 2 N1 DG A 2 C2 -0.069 REMARK 500 DG A 2 C2 DG A 2 N3 0.082 REMARK 500 DG A 2 C4 DG A 2 C5 -0.062 REMARK 500 DG A 2 C5 DG A 2 C6 0.074 REMARK 500 DG A 2 C8 DG A 2 N9 -0.052 REMARK 500 DG A 2 N9 DG A 2 C4 0.122 REMARK 500 DC A 3 C5' DC A 3 C4' 0.117 REMARK 500 DC A 3 N1 DC A 3 C6 0.055 REMARK 500 DC A 3 N3 DC A 3 C4 0.099 REMARK 500 DC A 3 C5 DC A 3 C6 -0.048 REMARK 500 DG A 4 P DG A 4 OP1 -0.104 REMARK 500 DG A 4 P DG A 4 O5' 0.070 REMARK 500 DG A 4 C4' DG A 4 C3' -0.086 REMARK 500 DG A 4 C2 DG A 4 N3 -0.064 REMARK 500 DG A 4 N3 DG A 4 C4 0.068 REMARK 500 DG A 4 C5 DG A 4 C6 -0.068 REMARK 500 DG A 4 C6 DG A 4 N1 0.077 REMARK 500 DG A 4 C8 DG A 4 N9 0.047 REMARK 500 DC A 5 C2' DC A 5 C1' 0.066 REMARK 500 DC A 5 O4' DC A 5 C4' 0.067 REMARK 500 DC A 5 C1' DC A 5 N1 0.114 REMARK 500 DC A 5 C4 DC A 5 N4 0.072 REMARK 500 DC A 5 N1 DC A 5 C2 -0.073 REMARK 500 DC A 5 C2 DC A 5 N3 0.072 REMARK 500 DC A 5 N3 DC A 5 C4 0.050 REMARK 500 DC A 5 C4 DC A 5 C5 -0.079 REMARK 500 DC A 5 C5 DC A 5 C6 0.071 REMARK 500 DG A 6 P DG A 6 OP2 -0.113 REMARK 500 DG A 6 C2' DG A 6 C1' 0.102 REMARK 500 DG A 6 O4' DG A 6 C4' 0.056 REMARK 500 DG A 6 N3 DG A 6 C4 -0.070 REMARK 500 DG A 6 C6 DG A 6 N1 -0.064 REMARK 500 DG A 6 N7 DG A 6 C8 0.073 REMARK 500 DG A 6 C2 DG A 6 N2 -0.100 REMARK 500 DG A 6 C6 DG A 6 O6 0.065 REMARK 500 DC A 5 O3' DG A 6 P 0.101 REMARK 500 DC B 7 C5' DC B 7 C4' 0.120 REMARK 500 DC B 7 O4' DC B 7 C4' -0.104 REMARK 500 DC B 7 C2 DC B 7 O2 0.057 REMARK 500 DC B 7 N1 DC B 7 C6 0.068 REMARK 500 DC B 7 N3 DC B 7 C4 0.095 REMARK 500 DG B 8 P DG B 8 OP2 0.109 REMARK 500 DG B 8 C2' DG B 8 C1' 0.141 REMARK 500 DG B 8 O4' DG B 8 C1' -0.097 REMARK 500 DG B 8 O4' DG B 8 C4' 0.060 REMARK 500 REMARK 500 THIS ENTRY HAS 83 BOND DEVIATIONS. 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 C3' - C2' - C1' ANGL. DEV. = -6.9 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = -7.2 DEGREES REMARK 500 DC A 1 N1 - C2 - N3 ANGL. DEV. = -7.1 DEGREES REMARK 500 DC A 1 C2 - N3 - C4 ANGL. DEV. = 10.7 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -4.0 DEGREES REMARK 500 DC A 1 C4 - C5 - C6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 1 C5 - C6 - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = 9.5 DEGREES REMARK 500 DC A 1 N3 - C4 - N4 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG A 2 C3' - C2' - C1' ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 2 O4' - C1' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG A 2 C2 - N3 - C4 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG A 2 N3 - C4 - C5 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG A 2 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG A 2 C4 - C5 - N7 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A 2 N3 - C4 - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 2 N3 - C2 - N2 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 3 O5' - P - OP1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC A 3 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 3 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 3 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC A 3 N3 - C4 - C5 ANGL. DEV. = -9.0 DEGREES REMARK 500 DC A 3 C4 - C5 - C6 ANGL. DEV. = 9.5 DEGREES REMARK 500 DC A 3 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DC A 3 C5 - C4 - N4 ANGL. DEV. = 8.0 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG A 4 C6 - N1 - C2 ANGL. DEV. = -10.1 DEGREES REMARK 500 DG A 4 N1 - C2 - N3 ANGL. DEV. = 6.2 DEGREES REMARK 500 DG A 4 N3 - C4 - C5 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 4 C5 - C6 - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 4 C4 - C5 - N7 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG A 4 C5 - N7 - C8 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 4 N9 - C4 - C5 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 4 N1 - C6 - O6 ANGL. DEV. = -9.8 DEGREES REMARK 500 DG A 4 C5 - C6 - O6 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC A 5 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DC A 5 C4' - C3' - C2' ANGL. DEV. = 7.5 DEGREES REMARK 500 DC A 5 C3' - C2' - C1' ANGL. DEV. = -9.3 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = -7.0 DEGREES REMARK 500 DC A 5 C6 - N1 - C2 ANGL. DEV. = 7.4 DEGREES REMARK 500 DC A 5 N1 - C2 - N3 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 5 N3 - C4 - C5 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC A 5 C5 - C6 - N1 ANGL. DEV. = -4.1 DEGREES REMARK 500 DC A 5 N1 - C2 - O2 ANGL. DEV. = 11.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 127 ANGLE DEVIATIONS. 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 40 DISTANCE = 7.41 ANGSTROMS REMARK 525 HOH A 88 DISTANCE = 8.27 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 B 14 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 95 O REMARK 620 2 HOH A 93 O 87.5 REMARK 620 3 HOH B 96 O 94.9 97.1 REMARK 620 4 HOH B 94 O 176.9 95.0 86.6 REMARK 620 5 HOH B 92 O 98.7 172.2 87.0 78.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 15 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 99 O REMARK 620 2 HOH A 95 O 75.7 REMARK 620 3 HOH B 96 O 152.5 89.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 16 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 105 O REMARK 620 2 HOH B 103 O 102.4 REMARK 620 3 HOH B 102 O 101.0 80.4 REMARK 620 4 HOH A 101 O 79.5 97.2 177.6 REMARK 620 5 HOH A 104 O 79.4 177.1 101.6 80.8 REMARK 620 6 HOH B 106 O 172.7 70.9 80.8 98.4 107.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 17 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 112 O REMARK 620 2 HOH A 109 O 73.8 REMARK 620 3 HOH A 108 O 107.2 89.6 REMARK 620 4 HOH A 110 O 107.1 174.0 95.7 REMARK 620 5 HOH A 107 O 85.4 86.5 165.2 87.6 REMARK 620 6 HOH A 111 O 156.4 83.2 77.5 95.2 87.9 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 SPD A 13 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 14 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 15 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 16 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 17
DBREF 293D A 1 6 PDB 293D 293D 1 6 DBREF 293D B 7 12 PDB 293D 293D 7 12
SEQRES 1 A 6 DC DG DC DG DC DG SEQRES 1 B 6 DC DG DC DG DC DG
HET SPD A 13 10 HET MG B 14 1 HET MG A 15 1 HET MG B 16 1 HET NA A 17 1
HETNAM SPD SPERMIDINE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION
HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
FORMUL 3 SPD C7 H19 N3 FORMUL 4 MG 3(MG 2+) FORMUL 7 NA NA 1+ FORMUL 8 HOH *95(H2 O)
LINK MG MG B 14 O HOH A 95 1555 1555 2.03 LINK MG MG B 14 O HOH A 93 1555 1555 2.34 LINK MG MG B 14 O HOH B 96 1555 1555 2.18 LINK MG MG B 14 O HOH B 94 1555 1555 2.37 LINK MG MG B 14 O HOH B 92 1555 1555 2.18 LINK MG MG A 15 O HOH A 99 1555 1555 2.41 LINK MG MG A 15 O HOH A 95 1555 1555 2.00 LINK MG MG A 15 O HOH B 96 1555 1555 2.39 LINK MG MG B 16 O HOH A 105 1555 1555 2.26 LINK MG MG B 16 O HOH B 103 1555 1555 2.22 LINK MG MG B 16 O HOH B 102 1555 1555 2.31 LINK MG MG B 16 O HOH A 101 1555 1555 2.22 LINK MG MG B 16 O HOH A 104 1555 1555 2.17 LINK MG MG B 16 O HOH B 106 1555 1555 2.33 LINK NA NA A 17 O HOH A 112 1555 1555 2.19 LINK NA NA A 17 O HOH A 109 1555 1555 2.22 LINK NA NA A 17 O HOH A 108 1555 1555 2.14 LINK NA NA A 17 O HOH A 110 1555 1555 2.29 LINK NA NA A 17 O HOH A 107 1555 1555 2.41 LINK NA NA A 17 O HOH A 111 1555 1555 2.54
SITE 1 AC1 12 DC A 3 HOH A 18 HOH A 28 HOH A 34 SITE 2 AC1 12 HOH A 35 HOH A 43 HOH A 68 HOH A 82 SITE 3 AC1 12 HOH A 83 HOH A 88 DG B 8 HOH B 36 SITE 1 AC2 7 DG A 6 MG A 15 HOH A 93 HOH A 95 SITE 2 AC2 7 HOH B 92 HOH B 94 HOH B 96 SITE 1 AC3 7 HOH A 95 HOH A 97 HOH A 98 HOH A 99 SITE 2 AC3 7 MG B 14 HOH B 96 HOH B 100 SITE 1 AC4 6 HOH A 101 HOH A 104 HOH A 105 HOH B 102 SITE 2 AC4 6 HOH B 103 HOH B 106 SITE 1 AC5 7 HOH A 79 HOH A 107 HOH A 108 HOH A 109 SITE 2 AC5 7 HOH A 110 HOH A 111 HOH A 112
CRYST1 17.930 31.230 44.640 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 0.055772 0.000000 0.000000 0.00000
SCALE2 0.000000 0.032020 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022401 0.00000