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Zinc in PDB 1p0f: Crystal Structure of the Binary Complex: Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) with the Cofactor Nadp

Enzymatic activity of Crystal Structure of the Binary Complex: Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) with the Cofactor Nadp

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

Protein crystallography data

The structure of Crystal Structure of the Binary Complex: Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) with the Cofactor Nadp, PDB code: 1p0f 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 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.157, 79.499, 91.837, 90.00, 112.89, 90.00
R / Rfree (%) 19.6 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Binary Complex: Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) with the Cofactor Nadp (pdb code 1p0f). 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 Binary Complex: Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) with the Cofactor Nadp, PDB code: 1p0f:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1p0f

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


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

b:28.5
occ:1.00
 SG A:CYS1173 2.3 19.8 1.0
NE2 A:HIS1067 2.3 21.4 1.0
SG A:CYS1046 2.4 19.5 1.0
O1 A:GOL8001 2.8 43.5 1.0
CD2 A:HIS1067 3.1 20.1 1.0
C5N A:NAP4292 3.1 27.5 1.0
CB A:CYS1046 3.3 16.7 1.0
CE1 A:HIS1067 3.3 19.8 1.0
CB A:CYS1173 3.5 14.9 1.0
C4N A:NAP4292 3.8 27.2 1.0
OG A:SER1048 3.9 18.0 1.0
C6N A:NAP4292 3.9 27.3 1.0
CB A:SER1048 4.0 17.0 1.0
C1 A:GOL8001 4.2 49.0 1.0
CG A:HIS1067 4.3 18.0 1.0
ND1 A:HIS1067 4.4 18.6 1.0
OE2 A:GLU1068 4.6 19.9 1.0
N A:GLY1174 4.7 17.1 1.0
CA A:CYS1173 4.7 16.3 1.0
CA A:CYS1046 4.8 18.3 1.0
NH2 A:ARG1367 4.8 21.5 1.0
N A:SER1048 4.9 16.3 1.0
C A:CYS1173 4.9 16.4 1.0

Zinc binding site 2 out of 4 in 1p0f

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


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

b:17.7
occ:1.00
 SG A:CYS1100 2.3 17.4 1.0
SG A:CYS1097 2.4 18.5 1.0
SG A:CYS1103 2.4 17.6 1.0
SG A:CYS1111 2.4 14.8 1.0
CB A:CYS1111 3.3 18.3 1.0
CB A:CYS1103 3.4 17.3 1.0
CB A:CYS1100 3.4 16.1 1.0
CB A:CYS1097 3.4 17.5 1.0
N A:CYS1097 3.4 17.4 1.0
CA A:CYS1111 3.7 17.8 1.0
N A:GLY1098 3.8 18.2 1.0
N A:CYS1100 3.8 17.1 1.0
CA A:CYS1097 3.9 18.9 1.0
N A:GLU1112 4.0 19.1 1.0
CA A:CYS1100 4.2 16.2 1.0
C A:CYS1111 4.3 19.2 1.0
N A:CYS1103 4.3 18.2 1.0
C A:CYS1097 4.3 19.1 1.0
N A:SER1099 4.4 19.9 1.0
CA A:CYS1103 4.4 18.9 1.0
C A:GLN1096 4.5 17.4 1.0
CA A:GLN1096 4.8 18.5 1.0
CA A:GLY1098 4.8 20.3 1.0
C A:CYS1100 4.8 16.3 1.0
CG A:LYS1113 4.8 27.2 1.0
N A:LYS1113 4.9 19.7 1.0
O A:HOH397 4.9 36.9 1.0
O A:CYS1100 4.9 15.4 1.0
N A:CYS1111 4.9 19.6 1.0
C A:SER1099 5.0 18.8 1.0

Zinc binding site 3 out of 4 in 1p0f

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


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 Binary Complex: Nadp(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) with the Cofactor Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1503

b:33.2
occ:1.00
 SG B:CYS2173 2.3 21.0 1.0
NE2 B:HIS2067 2.3 23.9 1.0
SG B:CYS2046 2.4 21.0 1.0
O1 B:GOL8002 2.6 43.7 1.0
C5N B:NAP3292 3.1 26.9 1.0
CD2 B:HIS2067 3.1 24.4 1.0
CE1 B:HIS2067 3.3 24.8 1.0
CB B:CYS2046 3.3 19.5 1.0
CB B:CYS2173 3.5 19.1 1.0
C1 B:GOL8002 3.6 49.6 1.0
C6N B:NAP3292 3.8 27.4 1.0
C4N B:NAP3292 3.9 27.6 1.0
OG B:SER2048 4.0 22.2 1.0
CB B:SER2048 4.1 20.4 1.0
CG B:HIS2067 4.3 23.0 1.0
ND1 B:HIS2067 4.3 21.8 1.0
OE2 B:GLU2068 4.7 22.8 1.0
N B:GLY2174 4.7 18.3 1.0
NH2 B:ARG2367 4.7 24.7 1.0
CA B:CYS2046 4.8 20.5 1.0
CA B:CYS2173 4.8 18.1 1.0
N B:SER2048 4.9 20.0 1.0
C B:CYS2173 4.9 18.3 1.0
CE2 B:PHE2093 4.9 18.6 1.0

Zinc binding site 4 out of 4 in 1p0f

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


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

b:21.8
occ:1.00
 SG B:CYS2100 2.4 22.3 1.0
SG B:CYS2103 2.4 22.2 1.0
SG B:CYS2111 2.4 19.0 1.0
SG B:CYS2097 2.4 22.0 1.0
CB B:CYS2111 3.2 20.0 1.0
CB B:CYS2103 3.3 23.4 1.0
CB B:CYS2097 3.4 21.9 1.0
N B:CYS2097 3.5 21.0 1.0
CB B:CYS2100 3.5 22.2 1.0
CA B:CYS2111 3.6 19.8 1.0
N B:GLY2098 3.8 23.5 1.0
CA B:CYS2097 3.9 22.0 1.0
N B:CYS2100 3.9 25.3 1.0
N B:GLU2112 4.0 23.2 1.0
C B:CYS2111 4.2 21.9 1.0
N B:CYS2103 4.2 23.6 1.0
CA B:CYS2100 4.3 23.2 1.0
C B:CYS2097 4.3 22.7 1.0
CA B:CYS2103 4.4 25.6 1.0
C B:GLN2096 4.5 20.1 1.0
N B:SER2099 4.5 26.8 1.0
CA B:GLN2096 4.7 20.4 1.0
CA B:GLY2098 4.8 24.4 1.0
N B:LYS2113 4.9 24.3 1.0
N B:CYS2111 4.9 20.4 1.0
C B:CYS2100 4.9 23.1 1.0
CG B:LYS2113 4.9 29.5 1.0
O B:CYS2100 5.0 20.6 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: Wed Oct 16 17:39:58 2024

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