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Zinc in PDB 1u3u: Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution

Enzymatic activity of Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution:
1.1.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution, PDB code: 1u3u was solved by B.J.Gibbons, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.080, 52.510, 90.120, 79.76, 89.67, 68.97
R / Rfree (%) 16.9 / 19

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution (pdb code 1u3u). 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 Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution, PDB code: 1u3u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1u3u

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution


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 Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:12.8
occ:1.00
 SG A:CYS103 2.3 11.7 1.0
SG A:CYS111 2.3 9.4 1.0
SG A:CYS97 2.3 11.8 1.0
SG A:CYS100 2.4 11.3 1.0
CB A:CYS111 3.4 7.8 1.0
CB A:CYS103 3.4 9.2 1.0
CB A:CYS97 3.4 9.8 1.0
CB A:CYS100 3.5 12.0 1.0
N A:CYS97 3.5 7.7 1.0
CA A:CYS111 3.8 9.5 1.0
CA A:CYS97 3.9 9.4 1.0
N A:CYS100 3.9 12.2 1.0
N A:GLY98 3.9 9.3 1.0
N A:LEU112 3.9 8.7 1.0
N A:CYS103 4.2 9.3 1.0
CA A:CYS100 4.2 12.1 1.0
C A:CYS97 4.3 11.8 1.0
C A:CYS111 4.3 8.4 1.0
CA A:CYS103 4.3 12.9 1.0
N A:LYS99 4.4 14.9 1.0
C A:GLN96 4.6 9.4 1.0
CA A:GLN96 4.9 7.4 1.0
CA A:GLY98 4.9 10.8 1.0
N A:LYS113 4.9 11.9 1.0
C A:CYS100 4.9 10.2 1.0
O A:HOH1690 5.0 25.2 1.0
O A:CYS100 5.0 9.3 1.0

Zinc binding site 2 out of 4 in 1u3u

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution


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 Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:14.3
occ:1.00
 NE2 A:HIS67 2.0 8.0 1.0
O16 A:BNF1378 2.2 11.4 1.0
SG A:CYS174 2.3 10.3 1.0
SG A:CYS46 2.3 9.5 1.0
CD2 A:HIS67 3.0 10.9 1.0
C14 A:BNF1378 3.0 10.5 1.0
CE1 A:HIS67 3.1 11.0 1.0
CB A:CYS46 3.2 10.5 1.0
CB A:CYS174 3.4 9.3 1.0
C5N A:NAD1377 3.5 7.7 1.0
OG1 A:THR48 4.0 6.9 1.0
CB A:THR48 4.0 6.8 1.0
C6N A:NAD1377 4.1 6.3 1.0
CG A:HIS67 4.1 9.3 1.0
ND1 A:HIS67 4.2 7.3 1.0
N13 A:BNF1378 4.3 12.9 1.0
C4N A:NAD1377 4.3 9.7 1.0
NH2 A:ARG369 4.5 8.4 1.0
OE2 A:GLU68 4.6 8.4 1.0
CA A:CYS46 4.7 9.1 1.0
CA A:CYS174 4.7 6.0 1.0
N A:GLY175 4.8 9.1 1.0
CG2 A:THR48 4.8 8.1 1.0
C A:CYS174 4.9 9.2 1.0
N A:THR48 5.0 7.5 1.0

Zinc binding site 3 out of 4 in 1u3u

Go back to Zinc Binding Sites List in 1u3u
Zinc binding site 3 out of 4 in the Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution


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 Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:8.4
occ:1.00
 SG B:CYS100 2.3 9.9 1.0
SG B:CYS111 2.3 9.5 1.0
SG B:CYS97 2.4 12.4 1.0
SG B:CYS103 2.4 9.3 1.0
CB B:CYS111 3.4 10.0 1.0
CB B:CYS103 3.4 10.1 1.0
CB B:CYS100 3.4 11.6 1.0
CB B:CYS97 3.4 10.6 1.0
N B:CYS97 3.6 9.7 1.0
CA B:CYS111 3.7 8.5 1.0
N B:CYS100 3.8 8.7 1.0
CA B:CYS97 3.9 9.4 1.0
N B:GLY98 3.9 8.6 1.0
N B:LEU112 3.9 8.2 1.0
N B:CYS103 4.2 12.0 1.0
CA B:CYS100 4.2 10.3 1.0
C B:CYS111 4.3 9.6 1.0
C B:CYS97 4.3 12.3 1.0
CA B:CYS103 4.3 12.8 1.0
N B:LYS99 4.5 13.9 1.0
C B:GLN96 4.6 9.2 1.0
C B:CYS100 4.9 9.1 1.0
N B:LYS113 4.9 10.8 1.0
CA B:GLY98 4.9 11.1 1.0
CA B:GLN96 4.9 8.2 1.0
CG B:LYS113 5.0 14.4 1.0
O B:CYS100 5.0 9.5 1.0

Zinc binding site 4 out of 4 in 1u3u

Go back to Zinc Binding Sites List in 1u3u
Zinc binding site 4 out of 4 in the Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution


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 Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:10.8
occ:1.00
 NE2 B:HIS67 2.1 8.5 1.0
O16 B:BNF2378 2.2 9.6 1.0
SG B:CYS174 2.2 9.6 1.0
SG B:CYS46 2.3 10.2 1.0
C14 B:BNF2378 3.0 13.3 1.0
CD2 B:HIS67 3.0 11.8 1.0
CE1 B:HIS67 3.1 10.5 1.0
CB B:CYS46 3.2 10.3 1.0
CB B:CYS174 3.4 8.1 1.0
C5N B:NAD2377 3.4 7.8 1.0
OG1 B:THR48 3.9 7.8 1.0
CB B:THR48 4.0 7.3 1.0
C6N B:NAD2377 4.1 8.5 1.0
CG B:HIS67 4.2 12.3 1.0
ND1 B:HIS67 4.2 9.0 1.0
C4N B:NAD2377 4.2 9.6 1.0
N13 B:BNF2378 4.2 12.7 1.0
OE2 B:GLU68 4.5 8.6 1.0
NH2 B:ARG369 4.5 9.1 1.0
CA B:CYS174 4.7 6.6 1.0
CA B:CYS46 4.7 8.6 1.0
N B:GLY175 4.8 9.3 1.0
CG2 B:THR48 4.8 10.9 1.0
C B:CYS174 4.9 8.8 1.0

Reference:

B.J.Gibbons, T.D.Hurley. Structure of Three Class I Human Alcohol Dehydrogenases Complexed with Isoenzyme Specific Formamide Inhibitors Biochemistry V. 43 12555 2004.
ISSN: ISSN 0006-2960
PubMed: 15449945
DOI: 10.1021/BI0489107
Page generated: Wed Oct 16 19:25:57 2024

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