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Zinc in the structure of Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb. (pdb 1xvh)

The binding sites of Zinc atom in the structure of Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb. (pdb code 1xvh). This binding sites where shown with 5.0 Angstroms radius around Zinc atom.
The 1xvh structure was solved by M.CYMBOROWSKI, G.JOACHIMIAK, M.CHRUSZCZ, P.GORNICKI, R.ZHANG, A.JOACHIMIAK, W.MINOR, MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)19.3-2.0
Space groupP21212
a (A)50.783
b (A)59.230
c (A)88.186
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)21.2
Rfree (%)24.4

Zinc Binding Sites:

Zinc binding site 1 out of 16 in 1xvh


Zinc binding site 1 out of 16 in 1xvh
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stereopicture of Zinc binding site 1 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp13, A: Lys69, B: Ser20, B: Asn22, A: Zn1305, A: Hoh1016, A: Hoh1130, A: Hoh1181, B: Hoh1009, B: Hoh1050, B: Hoh1138,

conact list:


AtomAtomDistance (A)
ZnCB A:Asp134.79
ZnOD2 A:Asp132.82
ZnOD1 A:Asp133.49
ZnCG A:Asp133.44
ZnCE A:Lys694.73
ZnNZ A:Lys693.65
ZnCB B:Ser204.41
ZnOG B:Ser204.97
ZnN B:Asn224.78
ZnCB B:Asn224.30
ZnZN A:Zn13052.58
ZnO A:Hoh10164.72
ZnO A:Hoh11303.03
ZnO A:Hoh11812.09
ZnO B:Hoh10094.60
ZnO B:Hoh10504.76
ZnO B:Hoh11381.86

interactive model:


Zinc binding site 2 out of 16 in 1xvh


Zinc binding site 2 out of 16 in 1xvh
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stereopicture of Zinc binding site 2 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp13, A: Gly16, B: Ser20, B: Gln21, A: Zn1302, A: Hoh1008, A: Hoh1067, A: Hoh1130, A: Hoh1181, B: Hoh1009, B: Hoh1138, B: Hoh1161,

conact list:


AtomAtomDistance (A)
ZnO A:Asp134.26
ZnCB A:Asp134.10
ZnOD2 A:Asp133.13
ZnC A:Asp134.84
ZnOD1 A:Asp131.96
ZnCG A:Asp132.82
ZnCA A:Asp134.47
ZnCA A:Gly164.70
ZnCB B:Ser204.22
ZnC B:Ser204.92
ZnCA B:Ser204.49
ZnN B:Gln214.29
ZnCB B:Gln214.86
ZnZN A:Zn13022.58
ZnO A:Hoh10084.38
ZnO A:Hoh10673.54
ZnO A:Hoh11302.08
ZnO A:Hoh11814.66
ZnO B:Hoh10092.32
ZnO B:Hoh11382.41
ZnO B:Hoh11614.73

interactive model:


Zinc binding site 3 out of 16 in 1xvh


Zinc binding site 3 out of 16 in 1xvh
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stereopicture of Zinc binding site 3 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Ser93, A: Asp94, A: Hoh1131,

conact list:


AtomAtomDistance (A)
ZnOG A:Ser934.71
ZnCB A:Asp944.03
ZnOD2 A:Asp941.94
ZnOD1 A:Asp942.44
ZnCG A:Asp942.51
ZnCA A:Asp944.96
ZnO A:Hoh11312.18

interactive model:


Zinc binding site 4 out of 16 in 1xvh


Zinc binding site 4 out of 16 in 1xvh
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stereopicture of Zinc binding site 4 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Ser114, A: Asp118, A: Hoh1043, A: Hoh1063,

conact list:


AtomAtomDistance (A)
ZnO A:Ser1144.17
ZnCB A:Ser1144.48
ZnC A:Ser1144.83
ZnCB A:Asp1184.28
ZnOD2 A:Asp1182.59
ZnOD1 A:Asp1182.22
ZnCG A:Asp1182.75
ZnCA A:Asp1184.98
ZnO A:Hoh10434.28
ZnO A:Hoh10633.20

interactive model:


Zinc binding site 5 out of 16 in 1xvh


Zinc binding site 5 out of 16 in 1xvh
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stereopicture of Zinc binding site 5 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His121, A: Glu125, A: Hoh1035, A: Hoh1065, A: Hoh1201, A: Hoh1205,

conact list:


AtomAtomDistance (A)
ZnNE2 A:His1212.26
ZnND1 A:His1214.29
ZnCD2 A:His1213.33
ZnCE1 A:His1213.12
ZnCG A:His1214.42
ZnOE1 A:Glu1252.47
ZnCB A:Glu1254.36
ZnOE2 A:Glu1254.35
ZnCD A:Glu1253.40
ZnCG A:Glu1253.90
ZnO A:Hoh10354.03
ZnO A:Hoh10654.31
ZnO A:Hoh12012.25
ZnO A:Hoh12052.00

interactive model:


Zinc binding site 6 out of 16 in 1xvh


Zinc binding site 6 out of 16 in 1xvh
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stereopicture of Zinc binding site 6 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His121, A: Hoh1141, A: Hoh1143,

conact list:


AtomAtomDistance (A)
ZnO A:His1214.47
ZnNE2 A:His1214.17
ZnN A:His1214.62
ZnCB A:His1213.41
ZnND1 A:His1212.17
ZnCD2 A:His1214.20
ZnC A:His1214.50
ZnCE1 A:His1213.11
ZnCG A:His1213.10
ZnCA A:His1213.59
ZnO A:Hoh11412.21
ZnO A:Hoh11431.88

interactive model:


Zinc binding site 7 out of 16 in 1xvh


Zinc binding site 7 out of 16 in 1xvh
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stereopicture of Zinc binding site 7 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His70, A: Hoh1095, A: Hoh1164,

conact list:


AtomAtomDistance (A)
ZnNE2 A:His703.95
ZnN A:His704.72
ZnCB A:His703.46
ZnND1 A:His701.90
ZnCD2 A:His704.07
ZnCE1 A:His702.79
ZnCG A:His703.01
ZnCA A:His703.92
ZnO A:Hoh10954.26
ZnO A:Hoh11643.88

interactive model:


Zinc binding site 8 out of 16 in 1xvh


Zinc binding site 8 out of 16 in 1xvh
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stereopicture of Zinc binding site 8 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Ser20, A: Gln21, A: Asn22, A: Thr75, B: Asp13, B: Zn1301, A: Hoh1006, A: Hoh1102, B: Hoh1144,

conact list:


AtomAtomDistance (A)
ZnCB A:Ser203.87
ZnOG A:Ser204.25
ZnC A:Ser204.35
ZnCA A:Ser204.46
ZnN A:Gln213.73
ZnOE1 A:Gln214.32
ZnCB A:Gln214.13
ZnC A:Gln214.17
ZnCA A:Gln214.22
ZnN A:Asn223.26
ZnCB A:Asn223.45
ZnCG A:Asn224.74
ZnCA A:Asn223.94
ZnOG1 A:Thr754.48
ZnOD2 B:Asp133.68
ZnOD1 B:Asp133.57
ZnCG B:Asp133.87
ZnZN B:Zn13012.50
ZnO A:Hoh10063.75
ZnO A:Hoh11024.65
ZnO B:Hoh11443.63

interactive model:


Zinc binding site 9 out of 16 in 1xvh


Zinc binding site 9 out of 16 in 1xvh
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stereopicture of Zinc binding site 9 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Ser20, A: Gln21, B: Asp13, B: Gly16, B: Thr17, A: Zn1316, A: Hoh1006, B: Hoh1012, B: Hoh1144,

conact list:


AtomAtomDistance (A)
ZnCB A:Ser204.30
ZnCA A:Ser204.61
ZnN A:Gln214.41
ZnCB A:Gln214.91
ZnO B:Asp134.27
ZnCB B:Asp134.08
ZnOD2 B:Asp133.01
ZnC B:Asp134.82
ZnOD1 B:Asp131.91
ZnCG B:Asp132.74
ZnCA B:Asp134.45
ZnC B:Gly164.92
ZnCA B:Gly164.67
ZnN B:Thr174.94
ZnZN A:Zn13162.50
ZnO A:Hoh10062.33
ZnO B:Hoh10124.27
ZnO B:Hoh11441.94

interactive model:


Zinc binding site 10 out of 16 in 1xvh


Zinc binding site 10 out of 16 in 1xvh
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stereopicture of Zinc binding site 10 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: His121, B: Hoh1044,

conact list:


AtomAtomDistance (A)
ZnNE2 B:His1214.10
ZnCB B:His1213.44
ZnND1 B:His1212.05
ZnCD2 B:His1214.17
ZnCE1 B:His1212.97
ZnCG B:His1213.07
ZnCA B:His1214.10
ZnO B:Hoh10442.52

interactive model:


Zinc binding site 11 out of 16 in 1xvh


Zinc binding site 11 out of 16 in 1xvh
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stereopicture of Zinc binding site 11 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Asn66, B: His70, B: Hoh1147,

conact list:


AtomAtomDistance (A)
ZnO B:Asn664.98
ZnNE2 B:His704.03
ZnN B:His704.65
ZnCB B:His703.29
ZnND1 B:His701.98
ZnCD2 B:His704.06
ZnCE1 B:His702.94
ZnCG B:His702.95
ZnCA B:His703.97
ZnO B:Hoh11473.19

interactive model:


Zinc binding site 12 out of 16 in 1xvh


Zinc binding site 12 out of 16 in 1xvh
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stereopicture of Zinc binding site 12 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Ser114, B: Asp118, B: Hoh1134, B: Hoh1156, B: Hoh1174, B: Hoh1175,

conact list:


AtomAtomDistance (A)
ZnO B:Ser1144.53
ZnN B:Asp1184.99
ZnCB B:Asp1184.27
ZnOD2 B:Asp1183.09
ZnOD1 B:Asp1182.09
ZnCG B:Asp1182.91
ZnCA B:Asp1184.69
ZnO B:Hoh11342.17
ZnO B:Hoh11564.41
ZnO B:Hoh11743.83
ZnO B:Hoh11753.64

interactive model:


Zinc binding site 13 out of 16 in 1xvh


Zinc binding site 13 out of 16 in 1xvh
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stereopicture of Zinc binding site 13 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Glu59, B: Hoh1080, B: Hoh1140,

conact list:


AtomAtomDistance (A)
ZnOE1 B:Glu592.67
ZnCB B:Glu594.76
ZnOE2 B:Glu591.92
ZnCD B:Glu592.61
ZnCG B:Glu594.09
ZnO B:Hoh10803.86
ZnO B:Hoh11402.03

interactive model:


Zinc binding site 14 out of 16 in 1xvh


Zinc binding site 14 out of 16 in 1xvh
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stereopicture of Zinc binding site 14 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: His121, B: Glu125, B: Hoh1066, B: Hoh1184, B: Hoh1197,

conact list:


AtomAtomDistance (A)
ZnNE2 B:His1212.50
ZnND1 B:His1214.58
ZnCD2 B:His1213.43
ZnCE1 B:His1213.47
ZnCG B:His1214.59
ZnOE1 B:Glu1252.46
ZnCB B:Glu1254.29
ZnOE2 B:Glu1254.34
ZnCD B:Glu1253.35
ZnCG B:Glu1253.75
ZnO B:Hoh10664.18
ZnO B:Hoh11844.01
ZnO B:Hoh11972.15

interactive model:


Zinc binding site 15 out of 16 in 1xvh


Zinc binding site 15 out of 16 in 1xvh
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stereopicture of Zinc binding site 15 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Asp27, B: Lys30, B: Asn73, B: Asn77, B: Hoh1110, B: Hoh1142, B: Hoh1167, B: Hoh1183, B: Hoh1191,

conact list:


AtomAtomDistance (A)
ZnCB B:Asp274.31
ZnOD2 B:Asp272.22
ZnOD1 B:Asp273.00
ZnCG B:Asp272.93
ZnNZ B:Lys304.91
ZnND2 B:Asn734.24
ZnOD1 B:Asn774.65
ZnO B:Hoh11102.36
ZnO B:Hoh11422.32
ZnO B:Hoh11673.45
ZnO B:Hoh11832.28
ZnO B:Hoh11913.64

interactive model:


Zinc binding site 16 out of 16 in 1xvh


Zinc binding site 16 out of 16 in 1xvh
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stereopicture of Zinc binding site 16 out of 16 in 1xvh
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Zinc in the PDB 1xvh. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Glu125, B: Hoh1184, B: Hoh1185, B: Hoh1197, B: Hoh1206,

conact list:


AtomAtomDistance (A)
ZnOE1 B:Glu1253.04
ZnOE2 B:Glu1252.44
ZnCD B:Glu1253.09
ZnCG B:Glu1254.55
ZnO B:Hoh11841.75
ZnO B:Hoh11851.85
ZnO B:Hoh11974.94
ZnO B:Hoh12064.40

interactive model:




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