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Sodium in PDB 3x42: Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide

Enzymatic activity of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide

All present enzymatic activity of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide:
1.4.3.21;

Protein crystallography data

The structure of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide, PDB code: 3x42 was solved by T.Okajima, S.Nakanishi, T.Murakawa, M.Kataoka, H.Hayashi, A.Hamaguchi, T.Nakai, Y.Kawano, H.Yamaguchi, K.Tanizawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.74 / 1.88
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.684, 63.508, 158.099, 90.00, 117.55, 90.00
R / Rfree (%) 15.8 / 19

Other elements in 3x42:

The structure of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide also contains other interesting chemical elements:

Potassium (K) 2 atoms
Bromine (Br) 8 atoms
Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide (pdb code 3x42). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide, PDB code: 3x42:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3x42

Go back to Sodium Binding Sites List in 3x42
Sodium binding site 1 out of 2 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:11.9
occ:1.00
OD1 A:ASP581 2.4 20.2 1.0
O A:MET441 2.4 15.7 1.0
OD1 A:ASP440 2.4 18.9 1.0
O A:ILE582 2.6 14.8 1.0
O A:HOH831 2.6 15.5 1.0
N A:ILE582 3.2 14.5 1.0
N A:MET441 3.5 11.0 1.0
C A:ILE582 3.5 14.3 1.0
C A:MET441 3.5 12.7 1.0
CG A:ASP581 3.6 19.7 1.0
CG A:ASP440 3.7 15.9 1.0
C A:ASP581 3.7 17.5 1.0
CD1 A:PHE446 3.7 22.9 1.0
NH2 A:ARG49 3.8 15.7 1.0
CA A:ILE582 3.9 13.8 1.0
C A:ASP440 3.9 10.6 1.0
CA A:MET441 4.0 14.4 1.0
CA A:ASP581 4.0 15.8 1.0
CE1 A:PHE446 4.1 21.9 1.0
CA A:ASP440 4.4 11.7 1.0
CB A:ASP581 4.4 17.6 1.0
OD2 A:ASP581 4.5 23.8 1.0
OD2 A:ASP440 4.5 17.2 1.0
O A:ASP581 4.5 16.9 1.0
O A:ASP440 4.6 13.3 1.0
CB A:MET441 4.6 11.8 1.0
N A:VAL583 4.6 13.3 1.0
CB A:ASP440 4.7 11.7 1.0
N A:ALA442 4.7 14.4 1.0
CG2 A:VAL583 4.8 11.7 1.0
CB A:TYR546 4.8 18.1 1.0
O A:PHE446 4.9 19.8 1.0
CG A:PHE446 4.9 26.2 1.0
CG1 A:ILE582 5.0 17.4 1.0

Sodium binding site 2 out of 2 in 3x42

Go back to Sodium Binding Sites List in 3x42
Sodium binding site 2 out of 2 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na706

b:16.8
occ:1.00
OD1 B:ASP581 2.4 25.2 1.0
O B:MET441 2.4 16.2 1.0
OD1 B:ASP440 2.5 20.0 1.0
O B:ILE582 2.5 16.1 1.0
O B:HOH854 2.6 18.5 1.0
N B:ILE582 3.2 19.8 1.0
N B:MET441 3.4 15.2 1.0
C B:ILE582 3.5 18.2 1.0
C B:MET441 3.5 15.6 1.0
CG B:ASP581 3.6 23.3 1.0
CG B:ASP440 3.7 16.6 1.0
CD1 B:PHE446 3.8 24.8 1.0
C B:ASP581 3.8 20.9 1.0
NH2 B:ARG49 3.9 19.5 1.0
CA B:ILE582 3.9 17.4 1.0
C B:ASP440 3.9 17.0 1.0
CA B:MET441 3.9 15.0 1.0
CA B:ASP581 4.1 21.7 1.0
CE1 B:PHE446 4.2 28.6 1.0
CA B:ASP440 4.4 15.8 1.0
CB B:ASP581 4.4 20.4 1.0
OD2 B:ASP581 4.5 23.5 1.0
CB B:MET441 4.5 14.7 1.0
OD2 B:ASP440 4.5 17.2 1.0
O B:ASP440 4.5 16.5 1.0
O B:ASP581 4.6 20.0 1.0
N B:VAL583 4.6 16.8 1.0
N B:ALA442 4.7 18.0 1.0
CB B:ASP440 4.7 16.0 1.0
CB B:TYR546 4.8 22.6 1.0
O B:PHE446 4.8 25.8 1.0
CG2 B:VAL583 4.8 16.9 1.0
CG B:PHE446 4.9 24.1 1.0
CG1 B:ILE582 5.0 22.6 1.0

Reference:

T.Murakawa, A.Hamaguchi, S.Nakanishi, M.Kataoka, T.Nakai, Y.Kawano, H.Yamaguchi, H.Hayashi, K.Tanizawa, T.Okajima. Probing the Catalytic Mechanism of Copper Amine Oxidase From Arthrobacter Globiformis with Halide Ions J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M115.662726
Page generated: Tue Dec 15 06:30:50 2020

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