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Zinc in PDB 1p0c: Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8)

Enzymatic activity of Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8)

All present enzymatic activity of Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8):
1.1.1.2;

Protein crystallography data

The structure of Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8), PDB code: 1p0c was solved by A.Rosell, E.Valencia, X.Pares, I.Fita, J.Farres, W.F.Ochoa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.551, 79.523, 91.892, 90.00, 113.10, 90.00
R / Rfree (%) 19.8 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) (pdb code 1p0c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8), PDB code: 1p0c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1p0c

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Zinc binding site 1 out of 4 in the Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8)


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 the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:20.7
occ:1.00
SG A:CYS1100 2.3 15.0 1.0
SG A:CYS1103 2.4 19.4 1.0
SG A:CYS1097 2.4 17.8 1.0
SG A:CYS1111 2.5 15.6 1.0
CB A:CYS1103 3.3 18.6 1.0
CB A:CYS1111 3.4 13.3 1.0
CB A:CYS1097 3.5 18.8 1.0
CB A:CYS1100 3.5 17.8 1.0
N A:CYS1097 3.6 19.2 1.0
CA A:CYS1111 3.7 14.0 1.0
N A:CYS1100 3.8 20.2 1.0
N A:GLY1098 3.9 21.7 1.0
CA A:CYS1097 3.9 20.5 1.0
N A:GLU1112 4.0 16.3 1.0
CA A:CYS1100 4.2 18.6 1.0
C A:CYS1111 4.3 16.2 1.0
N A:CYS1103 4.3 16.4 1.0
C A:CYS1097 4.3 21.2 1.0
CA A:CYS1103 4.4 17.9 1.0
N A:SER1099 4.4 24.5 1.0
C A:GLN1096 4.6 18.3 1.0
C A:CYS1100 4.8 18.7 1.0
O A:CYS1100 4.8 19.1 1.0
CA A:GLY1098 4.8 22.9 1.0
N A:LYS1113 4.9 21.6 1.0
CA A:GLN1096 4.9 18.9 1.0
C A:SER1099 4.9 22.6 1.0
N A:CYS1111 5.0 14.7 1.0
C A:GLY1098 5.0 23.8 1.0

Zinc binding site 2 out of 4 in 1p0c

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Zinc binding site 2 out of 4 in the Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8)


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 the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:51.1
occ:0.50
SG A:CYS1173 2.3 31.6 1.0
NE2 A:HIS1067 2.4 31.4 1.0
SG A:CYS1046 2.6 43.7 1.0
O A:HOH232 2.8 32.0 1.0
CD2 A:HIS1067 3.2 28.9 1.0
CB A:CYS1046 3.3 27.8 1.0
CE1 A:HIS1067 3.4 29.9 1.0
OG A:SER1048 3.5 29.0 1.0
CB A:SER1048 3.6 24.5 1.0
CB A:CYS1173 3.7 25.6 1.0
CG A:HIS1067 4.3 28.6 1.0
ND1 A:HIS1067 4.4 30.9 1.0
N A:SER1048 4.7 21.5 1.0
CA A:SER1048 4.8 22.2 1.0
CA A:CYS1046 4.8 26.1 1.0
N A:GLY1174 4.9 24.6 1.0
CA A:CYS1173 4.9 25.4 1.0
OE2 A:GLU1068 4.9 31.2 1.0

Zinc binding site 3 out of 4 in 1p0c

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Zinc binding site 3 out of 4 in the Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8)


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 the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2501

b:22.3
occ:1.00
SG B:CYS2100 2.3 23.2 1.0
SG B:CYS2103 2.4 23.3 1.0
SG B:CYS2111 2.4 18.0 1.0
SG B:CYS2097 2.5 27.6 1.0
CB B:CYS2111 3.2 18.5 1.0
CB B:CYS2103 3.3 25.8 1.0
CB B:CYS2100 3.4 24.4 1.0
CB B:CYS2097 3.5 24.4 1.0
N B:CYS2097 3.5 22.1 1.0
CA B:CYS2111 3.6 21.0 1.0
N B:GLY2098 3.8 27.0 1.0
N B:CYS2100 3.9 27.1 1.0
CA B:CYS2097 3.9 24.2 1.0
N B:GLU2112 4.0 23.4 1.0
CA B:CYS2100 4.2 25.4 1.0
C B:CYS2111 4.2 21.9 1.0
N B:CYS2103 4.2 25.9 1.0
C B:CYS2097 4.3 25.5 1.0
CA B:CYS2103 4.3 26.9 1.0
N B:SER2099 4.5 28.9 1.0
C B:GLN2096 4.5 21.2 1.0
CA B:GLN2096 4.8 22.2 1.0
CA B:GLY2098 4.8 27.0 1.0
C B:CYS2100 4.9 24.8 1.0
N B:CYS2111 4.9 20.1 1.0
N B:LYS2113 4.9 28.5 1.0
O B:CYS2100 5.0 25.2 1.0

Zinc binding site 4 out of 4 in 1p0c

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Zinc binding site 4 out of 4 in the Crystal Structure of the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8)


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 the Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2502

b:51.0
occ:0.50
NE2 B:HIS2067 2.4 32.6 1.0
SG B:CYS2173 2.5 34.4 1.0
SG B:CYS2046 2.6 43.8 1.0
O B:HOH231 2.6 45.0 1.0
OG B:SER2048 3.1 31.9 1.0
CE1 B:HIS2067 3.2 34.3 1.0
CB B:SER2048 3.5 27.9 1.0
CD2 B:HIS2067 3.5 33.1 1.0
CB B:CYS2046 3.6 29.6 1.0
CB B:CYS2173 4.0 25.8 1.0
ND1 B:HIS2067 4.4 32.0 1.0
CG B:HIS2067 4.6 31.4 1.0
N B:SER2048 4.6 27.9 1.0
CA B:SER2048 4.7 28.5 1.0
CE2 B:PHE2093 5.0 28.7 1.0

Reference:

A.Rosell, E.Valencia, X.Pares, I.Fita, J.Farres, W.F.Ochoa. Crystal Structure of the Vertebrate Nadp(H)-Dependent Alcohol Dehydrogenase (ADH8) J.Mol.Biol. V. 330 75 2003.
ISSN: ISSN 0022-2836
PubMed: 12818203
DOI: 10.1016/S0022-2836(03)00431-5
Page generated: Mon Jan 25 16:11:14 2021

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