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Nickel in PDB 2j5s: Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid

Enzymatic activity of Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid

All present enzymatic activity of Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid:
3.7.1.7;

Protein crystallography data

The structure of Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid, PDB code: 2j5s was solved by J.P.Bennett, J.L.Whittingham, A.M.Brzozowski, P.M.Leonard, G.Grogan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.19 / 1.57
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 80.387, 80.387, 125.882, 90.00, 90.00, 120.00
R / Rfree (%) 13.8 / 17

Nickel Binding Sites:

The binding sites of Nickel atom in the Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid (pdb code 2j5s). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid, PDB code: 2j5s:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2j5s

Go back to Nickel Binding Sites List in 2j5s
Nickel binding site 1 out of 2 in the Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1254

b:24.0
occ:0.33
 O A:HOH2221 1.5 2.0 0.3
O A:HOH2222 1.8 25.1 0.3
O A:HOH2224 1.9 16.9 0.3
NH2 A:ARG230 3.9 7.9 1.0
NH2 A:ARG227 4.0 12.8 1.0
NH1 A:ARG230 4.0 9.9 1.0
NE A:ARG227 4.1 11.2 1.0
CD2 A:LEU231 4.2 10.1 1.0
CZ A:ARG230 4.5 9.8 1.0
CZ A:ARG227 4.5 11.4 1.0
CD1 A:LEU231 4.9 10.2 1.0

Nickel binding site 2 out of 2 in 2j5s

Go back to Nickel Binding Sites List in 2j5s
Nickel binding site 2 out of 2 in the Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structural of Abdh, A Beta-Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 Bound to (S)-3- Oxocyclohexyl Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1254

b:26.6
occ:0.33
 O B:HOH2219 1.6 2.0 0.3
O B:HOH2221 1.8 32.0 0.3
O B:HOH2222 1.9 19.5 0.3
NH2 B:ARG227 4.0 13.1 1.0
NH2 B:ARG230 4.0 8.8 1.0
NH1 B:ARG230 4.0 11.3 1.0
NE B:ARG227 4.1 10.8 1.0
CD2 B:LEU231 4.2 11.5 1.0
CZ B:ARG230 4.5 10.4 1.0
CZ B:ARG227 4.6 11.1 1.0
CD1 B:LEU231 4.9 12.1 1.0

Reference:

J.P.Bennett, J.L.Whittingham, A.M.Brzozowski, P.M.Leonard, G.Grogan. Structural Characterisation of A Beta Diketone Hydrolase From the Cyanobacterium Anabaena Sp. Pcc 7120 in Native and Product Bound Forms, A Coenzyme A-Independent Member of the Crotonase Suprafamily Biochemistry V. 46 137 2007.
ISSN: ISSN 0006-2960
PubMed: 17198383
DOI: 10.1021/BI061900G
Page generated: Wed Dec 16 01:18:48 2020

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