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Sodium in PDB 3x41: Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Bromide

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Bromide

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Bromide:
1.4.3.21;

Protein crystallography data

The structure of Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Bromide, PDB code: 3x41 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) 31.88 / 1.87
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 191.619, 63.290, 157.851, 90.00, 117.21, 90.00
R / Rfree (%) 15.1 / 18

Other elements in 3x41:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction 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 Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Bromide (pdb code 3x41). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Bromide, PDB code: 3x41:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3x41

Go back to Sodium Binding Sites List in 3x41
Sodium binding site 1 out of 2 in the Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction 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 Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:16.4
occ:1.00
 O A:MET441 2.4 16.6 1.0
OD1 A:ASP581 2.4 20.5 1.0
OD1 A:ASP440 2.5 20.3 1.0
O A:ILE582 2.5 17.7 1.0
O A:HOH845 2.6 17.7 1.0
N A:ILE582 3.2 18.7 1.0
N A:MET441 3.4 14.6 1.0
C A:MET441 3.4 17.1 1.0
C A:ILE582 3.5 17.2 1.0
CG A:ASP581 3.6 23.6 1.0
CG A:ASP440 3.7 20.3 1.0
CD1 A:PHE446 3.7 25.4 1.0
C A:ASP581 3.8 20.8 1.0
C A:ASP440 3.9 14.6 1.0
CA A:MET441 3.9 16.0 1.0
CA A:ILE582 3.9 18.2 1.0
NH2 A:ARG49 3.9 21.8 1.0
CA A:ASP581 4.1 18.3 1.0
CE1 A:PHE446 4.1 28.6 1.0
CA A:ASP440 4.4 14.3 1.0
CB A:ASP581 4.5 20.0 1.0
CB A:MET441 4.5 14.6 1.0
OD2 A:ASP581 4.5 26.0 1.0
OD2 A:ASP440 4.5 19.1 1.0
O A:ASP440 4.5 15.9 1.0
N A:VAL583 4.6 15.8 1.0
N A:ALA442 4.6 15.9 1.0
CB A:ASP440 4.6 14.8 1.0
O A:ASP581 4.7 18.5 1.0
CB A:TYR546 4.8 22.9 1.0
O A:PHE446 4.8 22.4 1.0
CG A:PHE446 4.9 26.3 1.0
CG1 A:ILE582 4.9 22.7 1.0
CG2 A:VAL583 4.9 14.8 1.0

Sodium binding site 2 out of 2 in 3x41

Go back to Sodium Binding Sites List in 3x41
Sodium binding site 2 out of 2 in the Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction 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 Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na707

b:14.8
occ:1.00
 OD1 B:ASP581 2.4 22.0 1.0
O B:MET441 2.4 15.1 1.0
O B:ILE582 2.5 14.9 1.0
OD1 B:ASP440 2.5 17.7 1.0
O B:HOH815 2.5 15.9 1.0
N B:ILE582 3.2 14.9 1.0
N B:MET441 3.4 12.4 1.0
C B:ILE582 3.4 14.4 1.0
C B:MET441 3.5 16.3 1.0
CG B:ASP581 3.6 24.7 1.0
C B:ASP581 3.7 17.9 1.0
CG B:ASP440 3.7 17.1 1.0
CA B:ILE582 3.8 13.6 1.0
CD1 B:PHE446 3.8 27.0 1.0
C B:ASP440 3.9 12.3 1.0
CA B:MET441 3.9 14.2 1.0
NH2 B:ARG49 3.9 16.6 1.0
CA B:ASP581 4.0 15.8 1.0
CE1 B:PHE446 4.2 28.5 1.0
CA B:ASP440 4.4 11.9 1.0
CB B:ASP581 4.4 23.5 1.0
O B:ASP581 4.5 16.9 1.0
OD2 B:ASP581 4.5 27.0 1.0
OD2 B:ASP440 4.5 17.1 1.0
CB B:MET441 4.5 14.8 1.0
N B:VAL583 4.6 12.9 1.0
O B:ASP440 4.6 13.4 1.0
CB B:ASP440 4.7 12.2 1.0
N B:ALA442 4.7 15.3 1.0
CG2 B:VAL583 4.8 12.2 1.0
CB B:TYR546 4.8 18.3 1.0
CG1 B:ILE582 4.9 14.7 1.0
O B:PHE446 5.0 18.1 1.0
CG B:PHE446 5.0 24.9 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: Mon Oct 7 14:05:01 2024

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