HEADER OXIDOREDUCTASE 07-APR-17 5VF9 TITLE NATIVE HUMAN MANGANESE SUPEROXIDE DISMUTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [MN], MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 25-222; COMPND 5 EC: 1.15.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SOD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.AZADMANESH,S.R.TRICKEL,G.E.O.BORGSTAHL REVDAT 6 25-OCT-23 5VF9 1 REMARK REVDAT 5 04-OCT-23 5VF9 1 REMARK REVDAT 4 01-FEB-23 5VF9 1 SPRSDE LINK REVDAT 3 01-JAN-20 5VF9 1 REMARK REVDAT 2 28-JUN-17 5VF9 1 JRNL REVDAT 1 17-MAY-17 5VF9 0 JRNL AUTH J.AZADMANESH,S.R.TRICKEL,G.E.O.BORGSTAHL JRNL TITL SUBSTRATE-ANALOG BINDING AND ELECTROSTATIC SURFACES OF HUMAN JRNL TITL 2 MANGANESE SUPEROXIDE DISMUTASE. JRNL REF J. STRUCT. BIOL. V. 199 68 2017 JRNL REFN ESSN 1095-8657 JRNL PMID 28461152 JRNL DOI 10.1016/J.JSB.2017.04.011 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 36515 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 + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1885 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2434 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3162 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.38000 REMARK 3 B12 (A**2) : -0.06000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.141 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.128 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.526 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3287 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3052 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4449 ; 1.317 ; 1.932 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7025 ; 0.908 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 398 ; 5.515 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;35.115 ;25.031 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 531 ;12.628 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;15.375 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 455 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3770 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 794 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1595 ; 1.392 ; 1.998 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1594 ; 1.391 ; 1.995 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1992 ; 2.315 ; 2.978 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1993 ; 2.315 ; 2.982 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1690 ; 1.747 ; 2.233 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1686 ; 1.712 ; 2.227 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2451 ; 2.834 ; 3.229 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3876 ; 4.248 ;23.714 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3816 ; 4.219 ;23.491 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5VF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227339. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38400 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 67.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1JA8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M POTASSIUM PHOSPHATE, PH 7.8, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 79.49000 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 158.98000 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 119.23500 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 198.72500 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 39.74500 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 79.49000 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 158.98000 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 198.72500 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 119.23500 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 39.74500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 350 BIOMT1 2 0.500000 -0.866025 0.000000 39.12000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 67.75783 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 198.72500 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 330 O HOH B 444 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 142 -123.02 57.21 REMARK 500 TYR A 165 -18.03 -145.63 REMARK 500 LYS A 170 -133.54 51.39 REMARK 500 LYS B 1 93.52 75.17 REMARK 500 ASN B 142 -125.87 57.77 REMARK 500 TYR B 165 -13.35 -142.61 REMARK 500 LYS B 170 -136.25 52.72 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 K A 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 12 O REMARK 620 2 HOH A 344 O 72.8 REMARK 620 3 HOH A 365 O 92.5 143.0 REMARK 620 4 GLY B 85 O 13.9 64.6 93.3 REMARK 620 5 ASN B 182 O 11.6 66.4 92.6 2.4 REMARK 620 6 HOH B 355 O 57.1 116.8 78.7 70.7 68.3 REMARK 620 7 HOH B 426 O 89.7 73.9 141.3 97.6 96.9 70.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 26 NE2 REMARK 620 2 HIS A 74 NE2 89.4 REMARK 620 3 ASP A 159 OD2 85.0 108.2 REMARK 620 4 HIS A 163 NE2 94.5 128.7 123.1 REMARK 620 5 HOH A 301 O 172.1 94.3 87.2 88.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 26 NE2 REMARK 620 2 HIS B 74 NE2 90.9 REMARK 620 3 ASP B 159 OD2 82.1 108.3 REMARK 620 4 HIS B 163 NE2 93.6 128.7 122.9 REMARK 620 5 HOH B 301 O 172.2 90.1 90.3 91.7 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 MN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 202 DBREF 5VF9 A 1 198 UNP P04179 SODM_HUMAN 25 222 DBREF 5VF9 B 1 198 UNP P04179 SODM_HUMAN 25 222 SEQADV 5VF9 MET A 0 UNP P04179 INITIATING METHIONINE SEQADV 5VF9 MET B 0 UNP P04179 INITIATING METHIONINE SEQRES 1 A 199 MET LYS HIS SER LEU PRO ASP LEU PRO TYR ASP TYR GLY SEQRES 2 A 199 ALA LEU GLU PRO HIS ILE ASN ALA GLN ILE MET GLN LEU SEQRES 3 A 199 HIS HIS SER LYS HIS HIS ALA ALA TYR VAL ASN ASN LEU SEQRES 4 A 199 ASN VAL THR GLU GLU LYS TYR GLN GLU ALA LEU ALA LYS SEQRES 5 A 199 GLY ASP VAL THR ALA GLN ILE ALA LEU GLN PRO ALA LEU SEQRES 6 A 199 LYS PHE ASN GLY GLY GLY HIS ILE ASN HIS SER ILE PHE SEQRES 7 A 199 TRP THR ASN LEU SER PRO ASN GLY GLY GLY GLU PRO LYS SEQRES 8 A 199 GLY GLU LEU LEU GLU ALA ILE LYS ARG ASP PHE GLY SER SEQRES 9 A 199 PHE ASP LYS PHE LYS GLU LYS LEU THR ALA ALA SER VAL SEQRES 10 A 199 GLY VAL GLN GLY SER GLY TRP GLY TRP LEU GLY PHE ASN SEQRES 11 A 199 LYS GLU ARG GLY HIS LEU GLN ILE ALA ALA CYS PRO ASN SEQRES 12 A 199 GLN ASP PRO LEU GLN GLY THR THR GLY LEU ILE PRO LEU SEQRES 13 A 199 LEU GLY ILE ASP VAL TRP GLU HIS ALA TYR TYR LEU GLN SEQRES 14 A 199 TYR LYS ASN VAL ARG PRO ASP TYR LEU LYS ALA ILE TRP SEQRES 15 A 199 ASN VAL ILE ASN TRP GLU ASN VAL THR GLU ARG TYR MET SEQRES 16 A 199 ALA CYS LYS LYS SEQRES 1 B 199 MET LYS HIS SER LEU PRO ASP LEU PRO TYR ASP TYR GLY SEQRES 2 B 199 ALA LEU GLU PRO HIS ILE ASN ALA GLN ILE MET GLN LEU SEQRES 3 B 199 HIS HIS SER LYS HIS HIS ALA ALA TYR VAL ASN ASN LEU SEQRES 4 B 199 ASN VAL THR GLU GLU LYS TYR GLN GLU ALA LEU ALA LYS SEQRES 5 B 199 GLY ASP VAL THR ALA GLN ILE ALA LEU GLN PRO ALA LEU SEQRES 6 B 199 LYS PHE ASN GLY GLY GLY HIS ILE ASN HIS SER ILE PHE SEQRES 7 B 199 TRP THR ASN LEU SER PRO ASN GLY GLY GLY GLU PRO LYS SEQRES 8 B 199 GLY GLU LEU LEU GLU ALA ILE LYS ARG ASP PHE GLY SER SEQRES 9 B 199 PHE ASP LYS PHE LYS GLU LYS LEU THR ALA ALA SER VAL SEQRES 10 B 199 GLY VAL GLN GLY SER GLY TRP GLY TRP LEU GLY PHE ASN SEQRES 11 B 199 LYS GLU ARG GLY HIS LEU GLN ILE ALA ALA CYS PRO ASN SEQRES 12 B 199 GLN ASP PRO LEU GLN GLY THR THR GLY LEU ILE PRO LEU SEQRES 13 B 199 LEU GLY ILE ASP VAL TRP GLU HIS ALA TYR TYR LEU GLN SEQRES 14 B 199 TYR LYS ASN VAL ARG PRO ASP TYR LEU LYS ALA ILE TRP SEQRES 15 B 199 ASN VAL ILE ASN TRP GLU ASN VAL THR GLU ARG TYR MET SEQRES 16 B 199 ALA CYS LYS LYS HET MN A 201 1 HET PO4 A 202 5 HET K A 203 1 HET MN B 201 1 HET PO4 B 202 5 HETNAM MN MANGANESE (II) ION HETNAM PO4 PHOSPHATE ION HETNAM K POTASSIUM ION FORMUL 3 MN 2(MN 2+) FORMUL 4 PO4 2(O4 P 3-) FORMUL 5 K K 1+ FORMUL 8 HOH *305(H2 O) HELIX 1 AA1 ASN A 19 LYS A 29 1 11 HELIX 2 AA2 LYS A 29 GLY A 52 1 24 HELIX 3 AA3 ASP A 53 LEU A 60 1 8 HELIX 4 AA4 LEU A 60 LEU A 81 1 22 HELIX 5 AA5 LYS A 90 GLY A 102 1 13 HELIX 6 AA6 SER A 103 GLY A 117 1 15 HELIX 7 AA7 PRO A 145 GLY A 151 1 7 HELIX 8 AA8 TRP A 161 ALA A 164 5 4 HELIX 9 AA9 TYR A 165 LYS A 170 1 6 HELIX 10 AB1 VAL A 172 TRP A 181 1 10 HELIX 11 AB2 ASN A 182 ILE A 184 5 3 HELIX 12 AB3 ASN A 185 LYS A 197 1 13 HELIX 13 AB4 ASN B 19 LYS B 29 1 11 HELIX 14 AB5 LYS B 29 GLY B 52 1 24 HELIX 15 AB6 ASP B 53 LEU B 60 1 8 HELIX 16 AB7 LEU B 60 LEU B 81 1 22 HELIX 17 AB8 LYS B 90 GLY B 102 1 13 HELIX 18 AB9 SER B 103 GLY B 117 1 15 HELIX 19 AC1 PRO B 145 GLY B 151 1 7 HELIX 20 AC2 TRP B 161 ALA B 164 5 4 HELIX 21 AC3 TYR B 165 LYS B 170 1 6 HELIX 22 AC4 VAL B 172 TRP B 181 1 10 HELIX 23 AC5 ASN B 182 ILE B 184 5 3 HELIX 24 AC6 ASN B 185 LYS B 197 1 13 SHEET 1 AA1 3 HIS A 134 PRO A 141 0 SHEET 2 AA1 3 GLY A 122 ASN A 129 -1 N GLY A 127 O GLN A 136 SHEET 3 AA1 3 ILE A 153 ASP A 159 -1 O ILE A 158 N GLY A 124 SHEET 1 AA2 3 HIS B 134 PRO B 141 0 SHEET 2 AA2 3 GLY B 122 ASN B 129 -1 N GLY B 127 O GLN B 136 SHEET 3 AA2 3 ILE B 153 ASP B 159 -1 O ILE B 158 N GLY B 124 LINK O GLY A 12 K K A 203 1555 1555 2.96 LINK NE2 HIS A 26 MN MN A 201 1555 1555 2.25 LINK NE2 HIS A 74 MN MN A 201 1555 1555 2.25 LINK OD2 ASP A 159 MN MN A 201 1555 1555 2.03 LINK NE2 HIS A 163 MN MN A 201 1555 1555 2.25 LINK MN MN A 201 O HOH A 301 1555 1555 2.18 LINK K K A 203 O HOH A 344 1555 1555 2.79 LINK K K A 203 O HOH A 365 1555 1555 3.08 LINK K K A 203 O GLY B 85 1455 1555 3.10 LINK K K A 203 O ASN B 182 1455 1555 2.71 LINK K K A 203 O HOH B 355 1555 1655 3.10 LINK K K A 203 O HOH B 426 1555 1655 2.65 LINK NE2 HIS B 26 MN MN B 201 1555 1555 2.23 LINK NE2 HIS B 74 MN MN B 201 1555 1555 2.25 LINK OD2 ASP B 159 MN MN B 201 1555 1555 2.04 LINK NE2 HIS B 163 MN MN B 201 1555 1555 2.25 LINK MN MN B 201 O HOH B 301 1555 1555 2.15 CISPEP 1 GLU A 15 PRO A 16 0 8.80 CISPEP 2 GLU B 15 PRO B 16 0 -0.69 SITE 1 AC1 5 HIS A 26 HIS A 74 ASP A 159 HIS A 163 SITE 2 AC1 5 HOH A 301 SITE 1 AC2 6 HIS A 2 SER A 3 HIS A 71 HOH A 309 SITE 2 AC2 6 HOH A 352 HOH A 378 SITE 1 AC3 6 GLY A 12 HOH A 344 HOH A 365 GLY B 85 SITE 2 AC3 6 ASN B 182 HOH B 426 SITE 1 AC4 5 HIS B 26 HIS B 74 ASP B 159 HIS B 163 SITE 2 AC4 5 HOH B 301 SITE 1 AC5 5 LYS A 178 HIS B 2 SER B 3 HIS B 71 SITE 2 AC5 5 HOH B 354 CRYST1 78.240 78.240 238.470 90.00 90.00 120.00 P 61 2 2 24 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 0.012781 0.007379 0.000000 0.00000 SCALE2 0.000000 0.014758 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004193 0.00000