HEADER RNA 12-NOV-99 1DDY TITLE MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER CAVEAT 1DDY 6 C3' ATOMS HAVE INCORRECT CHIRALITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN B12 BINDING RNA; COMPND 3 CHAIN: A, C, E, G; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COMPLEXED WITH COBALAMIN, VITAMIN B12 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE RESULTS FROM IN VITRO SELECTION EXPERIMENTS KEYWDS RNA, TRIPLEX, VITAMIN B12, APTAMER EXPDTA X-RAY DIFFRACTION AUTHOR D.SUSSMAN,J.C.NIX,C.WILSON REVDAT 5 07-FEB-24 1DDY 1 REMARK REVDAT 4 24-OCT-12 1DDY 1 FORMUL REVDAT 3 28-DEC-11 1DDY 1 CAVEAT VERSN REVDAT 2 24-FEB-09 1DDY 1 VERSN REVDAT 1 01-JAN-00 1DDY 0 JRNL AUTH D.SUSSMAN,J.C.NIX,C.WILSON JRNL TITL THE STRUCTURAL BASIS FOR MOLECULAR RECOGNITION BY THE JRNL TITL 2 VITAMIN B 12 RNA APTAMER. JRNL REF NAT.STRUCT.BIOL. V. 7 53 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10625428 JRNL DOI 10.1038/71253 REMARK 2 REMARK 2 RESOLUTION. 3.00 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 13252 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) : 0.204 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 663 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1886 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 119 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 3004 REMARK 3 HETEROGEN ATOMS : 372 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 15.23000 REMARK 3 B22 (A**2) : -21.17000 REMARK 3 B33 (A**2) : 5.94000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.30 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) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.54 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 14.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.060 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : DNA-RNA_REP_JHC.PARAM REMARK 3 PARAMETER FILE 2 : B12.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : &_1_TOP_1 REMARK 3 TOPOLOGY FILE 2 : &_1_TOP_2 REMARK 3 TOPOLOGY FILE 3 : &_1_TOP_3 REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FOR CONSISTENCY, SUGARS PUCKERS WERE REMARK 3 RESTRAINED TO THE A-RNA C3'-ENDO CONFORMATION. THIS MIGHT REMARK 3 CONTRIBUTE TO THE HIGH RMSD FROM IDEAL VALUES OF IMPROPER ANGLES REMARK 4 REMARK 4 1DDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000010003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.6047,1.6057,1.5842 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40156 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.850 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.19500 REMARK 200 FOR SHELL : 4.469 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD PHASING 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 (%): 70.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LICL, ISOPROPANOL, MGCL2, PH 7.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.48000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.48000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 45.66500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 80.94000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.66500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 80.94000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.48000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.66500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 80.94000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.48000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.66500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 80.94000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G 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: 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 G A 1 P G A 1 OP3 -0.083 REMARK 500 G C 201 P G C 201 OP3 -0.083 REMARK 500 G E 401 P G E 401 OP3 -0.084 REMARK 500 G G 601 P G G 601 OP3 -0.084 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 G A 12 C2' - C3' - O3' ANGL. DEV. = 10.5 DEGREES REMARK 500 U A 23 C2' - C3' - O3' ANGL. DEV. = 16.6 DEGREES REMARK 500 G C 212 C2' - C3' - O3' ANGL. DEV. = 13.5 DEGREES REMARK 500 G E 412 C2' - C3' - O3' ANGL. DEV. = 12.1 DEGREES REMARK 500 G G 612 C2' - C3' - O3' ANGL. DEV. = 11.9 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 A C 214 0.06 SIDE CHAIN REMARK 500 G C 226 0.05 SIDE CHAIN REMARK 500 A E 414 0.05 SIDE CHAIN REMARK 500 A G 614 0.06 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 B12 A 101 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NME A 102 C REMARK 620 2 B12 A 101 N21 89.7 REMARK 620 3 B12 A 101 N22 89.0 90.6 REMARK 620 4 B12 A 101 N23 90.5 173.3 96.1 REMARK 620 5 B12 A 101 N24 88.2 83.4 173.4 89.9 REMARK 620 6 NME A 102 N 1.0 88.8 88.5 91.4 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 B12 C 301 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NME C 302 N REMARK 620 2 B12 C 301 N21 89.2 REMARK 620 3 B12 C 301 N22 86.1 90.7 REMARK 620 4 B12 C 301 N23 90.9 173.5 95.7 REMARK 620 5 B12 C 301 N24 91.0 84.2 174.2 89.3 REMARK 620 6 NME C 302 C 1.1 89.8 87.1 90.2 90.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 B12 E 501 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NME E 502 C REMARK 620 2 B12 E 501 N21 89.3 REMARK 620 3 B12 E 501 N22 88.9 90.8 REMARK 620 4 B12 E 501 N23 90.1 172.6 96.5 REMARK 620 5 B12 E 501 N24 88.4 84.1 174.3 88.5 REMARK 620 6 NME E 502 N 1.0 88.4 88.6 91.1 88.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 B12 G 701 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NME G 702 N REMARK 620 2 B12 G 701 N21 90.7 REMARK 620 3 B12 G 701 N22 87.7 90.9 REMARK 620 4 B12 G 701 N23 89.7 172.9 96.2 REMARK 620 5 B12 G 701 N24 90.1 84.1 174.5 88.9 REMARK 620 6 NME G 702 C 0.6 90.7 88.3 89.6 89.5 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 B12 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B12 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B12 E 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B12 G 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NME A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NME C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NME E 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NME G 702 DBREF 1DDY A 1 35 PDB 1DDY 1DDY 1 35 DBREF 1DDY C 201 235 PDB 1DDY 1DDY 201 235 DBREF 1DDY E 401 435 PDB 1DDY 1DDY 401 435 DBREF 1DDY G 601 635 PDB 1DDY 1DDY 601 635 SEQRES 1 A 35 G G A A C C G G U G C G C SEQRES 2 A 35 A U A A C C A C C U C A G SEQRES 3 A 35 U G C G A G C A A SEQRES 1 C 35 G G A A C C G G U G C G C SEQRES 2 C 35 A U A A C C A C C U C A G SEQRES 3 C 35 U G C G A G C A A SEQRES 1 E 35 G G A A C C G G U G C G C SEQRES 2 E 35 A U A A C C A C C U C A G SEQRES 3 E 35 U G C G A G C A A SEQRES 1 G 35 G G A A C C G G U G C G C SEQRES 2 G 35 A U A A C C A C C U C A G SEQRES 3 G 35 U G C G A G C A A HET B12 A 101 91 HET NME A 102 2 HET B12 C 301 91 HET NME C 302 2 HET B12 E 501 91 HET NME E 502 2 HET B12 G 701 91 HET NME G 702 2 HETNAM B12 COBALAMIN HETNAM NME METHYLAMINE FORMUL 5 B12 4(C62 H89 CO N13 O14 P 2+) FORMUL 6 NME 4(C H5 N) LINK CO B12 A 101 C NME A 102 1555 1555 1.85 LINK CO B12 A 101 N NME A 102 1555 1555 2.99 LINK CO B12 C 301 N NME C 302 1555 1555 2.99 LINK CO B12 C 301 C NME C 302 1555 1555 1.85 LINK CO B12 E 501 C NME E 502 1555 1555 1.85 LINK CO B12 E 501 N NME E 502 1555 1555 3.00 LINK CO B12 G 701 N NME G 702 1555 1555 3.00 LINK CO B12 G 701 C NME G 702 1555 1555 1.85 SITE 1 AC1 6 A A 14 A A 16 C A 29 G A 30 SITE 2 AC1 6 A A 31 NME A 102 SITE 1 AC2 7 A C 214 A C 216 C C 229 G C 230 SITE 2 AC2 7 A C 231 NME C 302 A E 416 SITE 1 AC3 8 A C 217 A E 414 A E 416 C E 429 SITE 2 AC3 8 G E 430 A E 431 NME E 502 B12 G 701 SITE 1 AC4 8 B12 E 501 A G 614 A G 616 A G 617 SITE 2 AC4 8 C G 629 G G 630 A G 631 NME G 702 SITE 1 AC5 3 C A 11 A A 16 B12 A 101 SITE 1 AC6 3 C C 211 A C 216 B12 C 301 SITE 1 AC7 4 C E 411 A E 416 G E 430 B12 E 501 SITE 1 AC8 3 C G 611 A G 616 B12 G 701 CRYST1 91.330 161.880 100.960 90.00 90.00 90.00 C 2 2 21 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 0.010949 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009905 0.00000