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Zinc in PDB 5v9j: Crystal Structure of Catalytic Domain of Glp with MS0105

Enzymatic activity of Crystal Structure of Catalytic Domain of Glp with MS0105

All present enzymatic activity of Crystal Structure of Catalytic Domain of Glp with MS0105:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Glp with MS0105, PDB code: 5v9j was solved by A.Dong, H.Zeng, J.Liu, Y.Xiong, N.Babault, J.Jin, W.Tempel, C.Bountra, C.H.Arrowsmith, A.M.Edwards, H.Wu, P.J.Brown, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.848, 95.891, 102.416, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.7

Other elements in 5v9j:

The structure of Crystal Structure of Catalytic Domain of Glp with MS0105 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Glp with MS0105 (pdb code 5v9j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Catalytic Domain of Glp with MS0105, PDB code: 5v9j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5v9j

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Zinc binding site 1 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Catalytic Domain of Glp with MS0105 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:16.0
occ:1.00
 SG A:CYS1075 2.3 15.2 1.0
SG A:CYS1105 2.3 14.4 1.0
SG A:CYS1109 2.3 15.2 1.0
SG A:CYS1062 2.4 15.5 1.0
CB A:CYS1062 3.3 16.6 1.0
CB A:CYS1105 3.3 14.1 1.0
CB A:CYS1109 3.3 16.4 1.0
CB A:CYS1075 3.4 15.7 1.0
CA A:CYS1105 3.6 13.7 1.0
N A:CYS1062 3.6 15.8 1.0
ZN A:ZN1305 3.8 16.4 1.0
ZN A:ZN1304 3.8 14.9 1.0
CA A:CYS1062 4.0 16.8 1.0
SG A:CYS1111 4.1 16.6 1.0
SG A:CYS1073 4.3 16.2 1.0
N A:ASN1106 4.5 13.8 1.0
N A:CYS1105 4.5 13.3 1.0
CA A:CYS1109 4.6 16.6 1.0
C A:TYR1061 4.6 16.9 1.0
C A:CYS1105 4.6 13.8 1.0
CA A:CYS1075 4.7 15.1 1.0
N A:CYS1075 4.7 15.8 1.0
SG A:CYS1068 4.7 16.1 1.0
CA A:TYR1061 4.8 17.6 1.0
C A:CYS1062 4.8 17.6 1.0
O A:CYS1062 4.9 17.6 1.0
O A:HOH1602 4.9 19.4 1.0

Zinc binding site 2 out of 8 in 5v9j

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Zinc binding site 2 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Catalytic Domain of Glp with MS0105 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1304

b:14.9
occ:1.00
 SG A:CYS1115 2.3 15.5 1.0
SG A:CYS1111 2.3 16.6 1.0
SG A:CYS1068 2.3 16.1 1.0
SG A:CYS1105 2.4 14.4 1.0
CB A:CYS1105 3.2 14.1 1.0
CB A:CYS1111 3.2 16.7 1.0
CB A:CYS1115 3.3 15.2 1.0
CB A:CYS1068 3.3 16.9 1.0
ZN A:ZN1305 3.7 16.4 1.0
ZN A:ZN1303 3.8 16.0 1.0
SG A:CYS1062 4.0 15.5 1.0
NE A:ARG1118 4.3 16.6 1.0
NH2 A:ARG1118 4.4 16.8 1.0
CA A:CYS1105 4.6 13.7 1.0
CB A:ASN1117 4.6 14.2 1.0
CA A:CYS1111 4.6 17.0 1.0
CA A:CYS1068 4.7 18.4 1.0
CA A:CYS1115 4.7 15.9 1.0
CZ A:ARG1118 4.8 17.0 1.0
O A:TRP1112 4.8 18.5 1.0
N A:ASN1117 4.9 14.8 1.0
CB A:CYS1109 5.0 16.4 1.0
SG A:CYS1073 5.0 16.2 1.0

Zinc binding site 3 out of 8 in 5v9j

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Zinc binding site 3 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Catalytic Domain of Glp with MS0105 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1305

b:16.4
occ:1.00
 SG A:CYS1073 2.3 16.2 1.0
SG A:CYS1064 2.3 17.6 1.0
SG A:CYS1068 2.3 16.1 1.0
SG A:CYS1062 2.4 15.5 1.0
CB A:CYS1062 3.1 16.6 1.0
CB A:CYS1064 3.2 19.9 1.0
CB A:CYS1068 3.3 16.9 1.0
CB A:CYS1073 3.3 17.4 1.0
ZN A:ZN1304 3.7 14.9 1.0
ZN A:ZN1303 3.8 16.0 1.0
CA A:CYS1068 3.9 18.4 1.0
CA A:CYS1073 3.9 18.5 1.0
SG A:CYS1105 4.0 14.4 1.0
N A:CYS1064 4.4 21.1 1.0
CA A:CYS1064 4.5 20.9 1.0
O A:HOH1495 4.5 19.7 1.0
CA A:CYS1062 4.6 16.8 1.0
C A:CYS1073 4.7 18.4 1.0
SG A:CYS1111 4.7 16.6 1.0
N A:CYS1068 4.8 18.0 1.0
O A:HOH1538 4.8 17.3 1.0
CB A:CYS1111 4.8 16.7 1.0
N A:MET1074 4.8 17.6 1.0

Zinc binding site 4 out of 8 in 5v9j

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Zinc binding site 4 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Catalytic Domain of Glp with MS0105 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1306

b:24.2
occ:1.00
 SG A:CYS1258 2.3 24.4 1.0
SG A:CYS1256 2.3 31.1 1.0
SG A:CYS1263 2.3 24.4 1.0
SG A:CYS1203 2.3 23.4 1.0
CB A:CYS1263 3.3 27.1 1.0
CB A:CYS1256 3.4 28.9 1.0
CB A:CYS1258 3.4 23.8 1.0
CB A:CYS1203 3.4 22.0 1.0
CA A:CYS1263 3.7 28.3 1.0
O A:HOH1596 4.0 23.4 1.0
N A:CYS1203 4.1 20.1 1.0
N A:CYS1258 4.1 24.8 1.0
N A:ARG1264 4.2 28.8 1.0
NE2 A:HIS1201 4.2 19.7 1.0
CA A:CYS1258 4.3 24.8 1.0
CD2 A:HIS1201 4.3 20.0 1.0
CA A:CYS1203 4.4 20.5 1.0
C A:CYS1263 4.4 30.1 1.0
N A:HIS1265 4.6 29.0 1.0
CA A:CYS1256 4.6 30.0 1.0
C A:CYS1256 4.7 29.4 1.0
O A:CYS1256 4.8 32.1 1.0
N A:GLY1259 4.8 26.7 1.0
C A:CYS1258 4.9 25.5 1.0
N A:CYS1263 5.0 29.4 1.0

Zinc binding site 5 out of 8 in 5v9j

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Zinc binding site 5 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Catalytic Domain of Glp with MS0105 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1303

b:15.9
occ:1.00
 SG B:CYS1109 2.3 14.2 1.0
SG B:CYS1105 2.3 15.3 1.0
SG B:CYS1075 2.3 15.5 1.0
SG B:CYS1062 2.4 14.7 1.0
CB B:CYS1062 3.2 15.8 1.0
CB B:CYS1105 3.3 14.5 1.0
CB B:CYS1109 3.3 14.6 1.0
CB B:CYS1075 3.4 16.7 1.0
N B:CYS1062 3.6 16.2 1.0
CA B:CYS1105 3.6 14.2 1.0
ZN B:ZN1304 3.8 15.8 1.0
ZN B:ZN1305 3.8 16.0 1.0
CA B:CYS1062 4.0 16.3 1.0
SG B:CYS1111 4.2 15.5 1.0
SG B:CYS1073 4.3 15.1 1.0
N B:CYS1105 4.5 14.0 1.0
C B:TYR1061 4.5 18.3 1.0
N B:ASN1106 4.5 14.6 1.0
CA B:CYS1109 4.6 15.5 1.0
CA B:CYS1075 4.6 17.1 1.0
C B:CYS1105 4.7 14.4 1.0
N B:CYS1075 4.7 17.2 1.0
SG B:CYS1068 4.7 14.8 1.0
C B:CYS1062 4.8 16.6 1.0
CA B:TYR1061 4.8 18.9 1.0
O B:CYS1062 4.9 16.3 1.0
O B:HOH1622 4.9 19.0 1.0

Zinc binding site 6 out of 8 in 5v9j

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Zinc binding site 6 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Catalytic Domain of Glp with MS0105 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1304

b:15.8
occ:1.00
 SG B:CYS1115 2.3 15.5 1.0
SG B:CYS1111 2.3 15.5 1.0
SG B:CYS1068 2.3 14.8 1.0
SG B:CYS1105 2.3 15.3 1.0
CB B:CYS1105 3.2 14.5 1.0
CB B:CYS1115 3.2 15.8 1.0
CB B:CYS1111 3.3 16.0 1.0
CB B:CYS1068 3.4 15.8 1.0
ZN B:ZN1305 3.8 16.0 1.0
ZN B:ZN1303 3.8 15.9 1.0
SG B:CYS1062 3.9 14.7 1.0
NH2 B:ARG1118 4.3 17.0 1.0
NE B:ARG1118 4.3 15.9 1.0
CA B:CYS1105 4.6 14.2 1.0
CB B:ASN1117 4.6 16.6 1.0
CA B:CYS1111 4.7 15.7 1.0
CA B:CYS1115 4.7 16.6 1.0
CA B:CYS1068 4.7 17.2 1.0
CZ B:ARG1118 4.7 16.3 1.0
O B:TRP1112 4.8 15.9 1.0
N B:ASN1117 5.0 17.1 1.0
CB B:CYS1109 5.0 14.6 1.0

Zinc binding site 7 out of 8 in 5v9j

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Zinc binding site 7 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Catalytic Domain of Glp with MS0105 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1305

b:16.0
occ:1.00
 SG B:CYS1064 2.3 14.5 1.0
SG B:CYS1073 2.3 15.1 1.0
SG B:CYS1068 2.3 14.8 1.0
SG B:CYS1062 2.3 14.7 1.0
CB B:CYS1062 3.2 15.8 1.0
CB B:CYS1073 3.2 16.4 1.0
CB B:CYS1064 3.2 16.5 1.0
CB B:CYS1068 3.3 15.8 1.0
ZN B:ZN1304 3.8 15.8 1.0
ZN B:ZN1303 3.8 15.9 1.0
CA B:CYS1073 3.9 16.6 1.0
CA B:CYS1068 3.9 17.2 1.0
SG B:CYS1105 4.1 15.3 1.0
N B:CYS1064 4.4 17.3 1.0
CA B:CYS1064 4.4 17.4 1.0
O B:HOH1452 4.6 18.2 1.0
CA B:CYS1062 4.6 16.3 1.0
C B:CYS1073 4.6 16.8 1.0
N B:MET1074 4.7 16.7 0.5
O B:HOH1607 4.7 17.7 1.0
N B:MET1074 4.7 17.3 0.5
N B:CYS1068 4.7 17.2 1.0
SG B:CYS1111 4.8 15.5 1.0
CB B:CYS1111 4.9 16.0 1.0
O B:HOH1567 4.9 26.9 1.0

Zinc binding site 8 out of 8 in 5v9j

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Zinc binding site 8 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Catalytic Domain of Glp with MS0105 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1306

b:18.3
occ:1.00
 SG B:CYS1256 2.3 17.4 1.0
SG B:CYS1258 2.3 18.5 1.0
SG B:CYS1263 2.3 17.6 1.0
SG B:CYS1203 2.3 17.5 1.0
CB B:CYS1263 3.3 18.1 1.0
CB B:CYS1256 3.4 20.4 1.0
CB B:CYS1258 3.4 19.3 1.0
CB B:CYS1203 3.4 17.2 1.0
CA B:CYS1263 3.8 18.4 1.0
O B:HOH1540 4.0 19.7 1.0
N B:CYS1203 4.1 16.0 1.0
NE2 B:HIS1201 4.1 17.2 1.0
N B:CYS1258 4.2 20.1 1.0
CD2 B:HIS1201 4.3 17.2 1.0
N B:ARG1264 4.3 19.0 1.0
CA B:CYS1258 4.3 19.4 1.0
CA B:CYS1203 4.4 17.0 1.0
C B:CYS1263 4.5 18.7 1.0
N B:HIS1265 4.6 19.9 1.0
CA B:CYS1256 4.6 20.9 1.0
C B:CYS1256 4.7 21.7 1.0
N B:GLY1259 4.8 18.8 1.0
CB B:HIS1265 4.9 20.6 1.0
C B:CYS1258 4.9 18.7 1.0
O B:CYS1256 5.0 21.9 1.0
CB B:SER1260 5.0 19.5 1.0

Reference:

H.Zeng, A.Dong, J.Liu, Y.Xiong, N.Babault, J.Jin, W.Tempel, C.Bountra, C.H.Arrowsmith, A.M.Edwards, H.Wu, P.J.Brown, Structural Genomics Consortium (Sgc). Crystal Structure of Catalytic Domain of Glp with MS0105 To Be Published.
Page generated: Thu Aug 21 09:50:05 2025

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