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Arsenic in PDB 1wmb: Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase

Enzymatic activity of Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase

All present enzymatic activity of Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase:
1.1.1.30;

Protein crystallography data

The structure of Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase, PDB code: 1wmb was solved by K.Ito, Y.Nakajima, E.Ichihara, K.Ogawa, T.Yoshimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 64.336, 99.025, 110.229, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 24.7

Other elements in 1wmb:

The structure of Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase (pdb code 1wmb). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase, PDB code: 1wmb:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 1wmb

Go back to Arsenic Binding Sites List in 1wmb
Arsenic binding site 1 out of 2 in the Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1302

b:29.9
occ:1.00
AS A:CAC1302 0.0 29.9 1.0
O2 A:CAC1302 1.6 33.8 1.0
O1 A:CAC1302 1.7 32.5 1.0
C2 A:CAC1302 1.8 33.3 1.0
C1 A:CAC1302 2.0 31.4 1.0
O A:HOH1410 3.3 25.1 1.0
OG A:SER142 3.7 9.6 1.0
OH A:TYR155 3.8 16.1 1.0
O A:HOH1346 3.9 21.6 1.0
O A:GLY186 4.0 12.8 1.0
O A:HOH1418 4.2 31.9 1.0
O A:PRO185 4.4 11.3 1.0
CE1 A:TYR155 4.5 13.6 1.0
CZ A:TYR155 4.5 16.6 1.0
CB A:SER142 4.5 9.8 1.0
O A:HOH1344 4.5 17.6 1.0
NE2 A:GLN94 4.5 35.7 1.0
O A:HOH1513 4.7 43.8 1.0
C A:GLY186 4.7 11.7 1.0
ND1 A:HIS144 4.9 13.7 1.0
O A:HOH1509 4.9 40.4 1.0

Arsenic binding site 2 out of 2 in 1wmb

Go back to Arsenic Binding Sites List in 1wmb
Arsenic binding site 2 out of 2 in the Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Nad Dependent D-3-Hydroxybutylate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As2302

b:28.6
occ:1.00
AS B:CAC2302 0.0 28.6 1.0
O2 B:CAC2302 1.6 29.8 1.0
O1 B:CAC2302 1.7 32.6 1.0
C2 B:CAC2302 1.8 29.3 1.0
C1 B:CAC2302 2.0 28.4 1.0
O B:HOH2342 3.5 18.4 1.0
OH B:TYR155 3.6 13.7 1.0
OG B:SER142 3.7 13.7 1.0
O B:HOH2335 4.0 16.2 1.0
O B:GLY186 4.2 13.4 1.0
CE1 B:TYR155 4.3 14.0 1.0
CZ B:TYR155 4.4 13.6 1.0
NE2 B:GLN94 4.4 27.0 1.0
O B:PRO185 4.4 12.8 1.0
CB B:SER142 4.5 10.1 1.0
O B:HOH2455 4.7 35.6 1.0
ND1 B:HIS144 4.7 9.1 1.0
C B:GLY186 4.9 13.2 1.0

Reference:

K.Ito, Y.Nakajima, E.Ichihara, K.Ogawa, N.Katayama, K.Nakashima, T.Yoshimoto. D-3-Hydroxybutyrate Dehydrogenase From Pseudomonas Fragi: Molecular Cloning of the Enzyme Gene and Crystal Structure of the Enzyme J.Mol.Biol. V. 355 722 2006.
ISSN: ISSN 0022-2836
PubMed: 16325199
DOI: 10.1016/J.JMB.2005.10.072
Page generated: Tue Oct 27 16:47:38 2020

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