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Nickel in PDB 1wmo: Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion

Enzymatic activity of Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion

All present enzymatic activity of Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion:
1.4.3.6;

Protein crystallography data

The structure of Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion, PDB code: 1wmo was solved by T.Okajima, S.Kishishita, Y.C.Chiu, T.Murakawa, M.Kim, H.Yamaguchi, S.Hirota, S.Kuroda, K.Tanizawa, 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 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.679, 62.993, 183.670, 90.00, 111.83, 90.00
R / Rfree (%) 22.3 / 26.6

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion (pdb code 1wmo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion, PDB code: 1wmo:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1wmo

Go back to Nickel Binding Sites List in 1wmo
Nickel binding site 1 out of 2 in the Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1001

b:13.2
occ:1.00
O A:HOH1418 1.8 6.0 1.0
NE2 A:HIS431 2.1 9.9 1.0
O A:HOH1276 2.1 11.7 1.0
O A:HOH1269 2.2 9.0 1.0
NE2 A:HIS433 2.3 16.6 1.0
ND1 A:HIS592 2.3 8.3 1.0
CE1 A:HIS431 3.0 8.9 1.0
CD2 A:HIS431 3.1 5.8 1.0
CD2 A:HIS433 3.1 14.6 1.0
CE1 A:HIS592 3.1 12.7 1.0
CE1 A:HIS433 3.3 15.8 1.0
CG A:HIS592 3.3 9.4 1.0
CB A:HIS592 3.7 8.4 1.0
ND1 A:HIS431 4.1 9.8 1.0
O A:HOH1273 4.2 19.3 1.0
CG A:HIS431 4.2 8.3 1.0
O A:HOH1302 4.2 12.9 1.0
NE2 A:HIS592 4.3 6.0 1.0
O A:HOH1182 4.3 10.4 1.0
CG A:HIS433 4.3 14.7 1.0
ND1 A:HIS433 4.4 12.1 1.0
CD2 A:HIS592 4.4 6.7 1.0
O2 A:TPQ382 4.5 17.7 1.0
SD A:MET602 4.5 18.2 1.0
O A:HOH1272 4.6 15.0 1.0
CE A:MET602 4.6 18.0 1.0

Nickel binding site 2 out of 2 in 1wmo

Go back to Nickel Binding Sites List in 1wmo
Nickel binding site 2 out of 2 in the Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Topaquinone-Containing Amine Oxidase Activated By Nickel Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1002

b:10.6
occ:1.00
O B:HOH1526 1.7 5.0 1.0
NE2 B:HIS431 2.0 7.4 1.0
O B:HOH1320 2.2 11.9 1.0
NE2 B:HIS433 2.2 13.5 1.0
ND1 B:HIS592 2.2 6.5 1.0
O B:HOH1317 2.3 11.2 1.0
CE1 B:HIS431 3.0 6.8 1.0
CD2 B:HIS431 3.0 5.1 1.0
CD2 B:HIS433 3.1 11.8 1.0
CE1 B:HIS592 3.1 12.0 1.0
CE1 B:HIS433 3.3 13.3 1.0
CG B:HIS592 3.3 10.8 1.0
CB B:HIS592 3.7 8.2 1.0
ND1 B:HIS431 4.1 7.1 1.0
CG B:HIS431 4.2 6.1 1.0
O B:HOH1176 4.3 17.1 1.0
O B:HOH1331 4.3 9.3 1.0
NE2 B:HIS592 4.3 5.1 1.0
CG B:HIS433 4.3 11.7 1.0
O B:HOH1104 4.3 9.2 1.0
ND1 B:HIS433 4.3 12.8 1.0
SD B:MET602 4.4 17.5 1.0
O2 B:TPQ382 4.4 15.4 1.0
CD2 B:HIS592 4.4 4.9 1.0
O B:HOH1322 4.7 13.2 1.0
CE B:MET602 4.9 13.2 1.0

Reference:

T.Okajima, S.Kishishita, Y.C.Chiu, T.Murakawa, M.Kim, H.Yamaguchi, S.Hirota, S.Kuroda, K.Tanizawa. Reinvestigation of Metal Ion Specificity For Quinone Cofactor Biogenesis in Bacterial Copper Amine Oxidase Biochemistry V. 44 12041 2005.
ISSN: ISSN 0006-2960
PubMed: 16142901
DOI: 10.1021/BI051070R
Page generated: Fri Sep 25 08:03:15 2020
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