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Zinc in PDB 1jpu: Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase

Enzymatic activity of Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase

All present enzymatic activity of Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase:
1.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase, PDB code: 1jpu was solved by S.N.Ruzheinikov, J.Burke, S.Sedelnikova, P.J.Baker, R.Taylor, P.A.Bullough, N.M.Muir, M.G.Gore, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.030, 105.030, 148.200, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase (pdb code 1jpu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase, PDB code: 1jpu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1jpu

Go back to Zinc Binding Sites List in 1jpu
Zinc binding site 1 out of 2 in the Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase


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 Bacillus Stearothermophilus Glycerol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn371

b:23.0
occ:1.00
O A:HOH373 2.0 28.3 1.0
OD1 A:ASP173 2.0 19.8 1.0
NE2 A:HIS256 2.0 19.7 1.0
NE2 A:HIS274 2.1 27.2 1.0
O A:HOH374 2.7 51.4 1.0
CG A:ASP173 2.7 16.8 1.0
OD2 A:ASP173 2.7 23.6 1.0
CE1 A:HIS256 3.0 31.5 1.0
CE1 A:HIS274 3.1 39.6 1.0
CD2 A:HIS274 3.1 29.3 1.0
CD2 A:HIS256 3.1 22.8 1.0
OD1 A:ASP123 3.6 29.5 1.0
O A:HOH391 4.0 64.1 1.0
ND1 A:HIS256 4.1 26.3 1.0
CG2 A:VAL278 4.1 21.1 1.0
CB A:ASP173 4.2 15.7 1.0
ND1 A:HIS274 4.2 27.2 1.0
CG A:HIS256 4.2 28.3 1.0
CG A:HIS274 4.2 30.9 1.0
O A:HOH375 4.3 25.2 1.0
CG A:ASP123 4.4 30.6 1.0
OD2 A:ASP123 4.5 43.7 1.0
CA A:ASP173 4.8 14.7 1.0

Zinc binding site 2 out of 2 in 1jpu

Go back to Zinc Binding Sites List in 1jpu
Zinc binding site 2 out of 2 in the Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase


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 Bacillus Stearothermophilus Glycerol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn372

b:33.7
occ:0.50
OE2 A:GLU268 2.0 34.6 1.0
NE2 A:HIS271 2.2 41.8 1.0
CD A:GLU268 2.8 34.2 1.0
OE1 A:GLU268 2.9 35.9 1.0
CD2 A:HIS271 3.0 29.8 1.0
CE1 A:HIS271 3.2 42.3 1.0
O A:HOH522 3.3 61.0 0.5
CG A:GLU268 4.2 36.2 1.0
CG A:HIS271 4.2 33.7 1.0
ND1 A:HIS271 4.3 36.2 1.0
CA A:GLU268 4.6 27.4 1.0
CB A:GLU268 4.9 29.0 1.0

Reference:

S.N.Ruzheinikov, J.Burke, S.Sedelnikova, P.J.Baker, R.Taylor, P.A.Bullough, N.M.Muir, M.G.Gore, D.W.Rice. Glycerol Dehydrogenase. Structure, Specificity, and Mechanism of A Family III Polyol Dehydrogenase. Structure V. 9 789 2001.
ISSN: ISSN 0969-2126
PubMed: 11566129
DOI: 10.1016/S0969-2126(01)00645-1
Page generated: Wed Dec 16 02:54:07 2020

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