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Sodium in PDB 3x40: Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Chloride

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

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Chloride:
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 Chloride, PDB code: 3x40 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) 26.22 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 191.812, 63.020, 158.108, 90.00, 117.29, 90.00
R / Rfree (%) 21.2 / 26.4

Other elements in 3x40:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Chloride also contains other interesting chemical elements:

Copper (Cu) 2 atoms
Chlorine (Cl) 5 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 Chloride (pdb code 3x40). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 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 Chloride, PDB code: 3x40:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3x40

Go back to Sodium Binding Sites List in 3x40
Sodium binding site 1 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Chloride


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 Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:18.4
occ:1.00
O A:ALA93 2.8 23.9 1.0
O B:VAL79 2.8 37.4 1.0
O A:ALA94 2.9 23.2 1.0
CB A:SER562 3.1 41.5 1.0
NH1 A:ARG148 3.3 52.6 1.0
O B:THR80 3.4 45.9 1.0
C A:ALA94 3.6 26.1 1.0
CA A:ALA94 3.7 28.4 1.0
C B:THR80 3.8 40.9 1.0
N B:GLY82 3.8 35.0 1.0
C A:ALA93 3.9 26.3 1.0
C B:VAL79 3.9 35.4 1.0
OG A:SER562 4.1 47.9 1.0
N A:SER562 4.1 29.6 1.0
CA B:GLY82 4.2 31.0 1.0
CA A:SER562 4.2 31.4 1.0
N B:ASN81 4.3 36.5 1.0
N A:ALA94 4.3 24.0 1.0
O A:HOH1005 4.3 22.3 1.0
CG B:GLU22 4.3 29.0 1.0
OE1 B:GLU22 4.3 35.3 1.0
C B:ASN81 4.4 40.6 1.0
CA B:THR80 4.4 37.5 1.0
CA B:ASN81 4.6 36.3 1.0
CZ A:ARG148 4.6 50.3 1.0
N B:THR80 4.6 34.5 1.0
CD B:GLU22 4.6 30.5 1.0
N A:THR95 4.8 22.9 1.0
NE2 A:HIS561 4.9 35.8 1.0

Sodium binding site 2 out of 3 in 3x40

Go back to Sodium Binding Sites List in 3x40
Sodium binding site 2 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Chloride


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 Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:22.3
occ:1.00
OD1 A:ASP440 2.3 13.3 1.0
OD1 A:ASP581 2.4 20.7 1.0
O A:MET441 2.5 18.3 1.0
O A:ILE582 2.5 13.0 1.0
O A:HOH831 2.9 21.6 1.0
N A:ILE582 3.2 20.6 1.0
N A:MET441 3.4 18.0 1.0
C A:ILE582 3.5 20.8 1.0
C A:MET441 3.5 17.8 1.0
CG A:ASP440 3.6 23.1 1.0
CD1 A:PHE446 3.6 22.6 1.0
NH2 A:ARG49 3.6 27.2 1.0
CG A:ASP581 3.7 25.1 1.0
C A:ASP581 3.8 22.4 1.0
C A:ASP440 3.8 15.8 1.0
CE1 A:PHE446 3.9 28.4 1.0
CA A:ILE582 3.9 16.6 1.0
CA A:MET441 4.0 15.9 1.0
CA A:ASP581 4.1 22.5 1.0
CA A:ASP440 4.2 16.1 1.0
OD2 A:ASP440 4.4 18.9 1.0
O A:ASP440 4.4 17.5 1.0
CB A:ASP581 4.5 23.2 1.0
CB A:ASP440 4.5 19.4 1.0
OD2 A:ASP581 4.6 21.0 1.0
CB A:MET441 4.6 13.2 1.0
CG2 A:VAL583 4.6 15.0 1.0
N A:VAL583 4.6 19.9 1.0
O A:ASP581 4.7 16.0 1.0
N A:ALA442 4.7 15.2 1.0
CB A:TYR546 4.8 13.1 1.0
CG A:PHE446 4.8 28.6 1.0
CZ A:ARG49 4.9 30.6 1.0

Sodium binding site 3 out of 3 in 3x40

Go back to Sodium Binding Sites List in 3x40
Sodium binding site 3 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Chloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Copper Amine Oxidase From Arthrobacter Globiformis: Product Schiff- Base Form Produced By Anaerobic Reduction in the Presence of Sodium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na705

b:20.7
occ:1.00
OD1 B:ASP581 2.3 22.0 1.0
O B:MET441 2.3 20.5 1.0
OD1 B:ASP440 2.4 13.3 1.0
O B:ILE582 2.5 12.9 1.0
O B:HOH885 2.9 13.0 1.0
N B:ILE582 3.3 18.9 1.0
N B:MET441 3.4 14.0 1.0
C B:MET441 3.4 20.0 1.0
C B:ILE582 3.5 12.4 1.0
CG B:ASP581 3.6 25.4 1.0
CG B:ASP440 3.6 16.6 1.0
CD1 B:PHE446 3.8 25.1 1.0
C B:ASP440 3.8 11.7 1.0
NH2 B:ARG49 3.9 23.7 1.0
CA B:MET441 3.9 18.4 1.0
C B:ASP581 3.9 22.2 1.0
CA B:ILE582 3.9 12.8 1.0
CA B:ASP581 4.2 22.4 1.0
CE1 B:PHE446 4.2 19.0 1.0
CA B:ASP440 4.3 16.0 1.0
OD2 B:ASP581 4.4 32.5 1.0
O B:ASP440 4.5 12.8 1.0
OD2 B:ASP440 4.5 17.1 1.0
CB B:ASP581 4.5 20.7 1.0
CB B:MET441 4.5 19.7 1.0
CB B:ASP440 4.6 11.6 1.0
N B:ALA442 4.6 20.7 1.0
N B:VAL583 4.6 20.2 1.0
CG2 B:VAL583 4.7 12.0 1.0
CB B:TYR546 4.7 16.2 1.0
O B:ASP581 4.8 22.0 1.0
CG B:PHE446 4.9 28.8 1.0
O B:PHE446 4.9 33.9 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: Tue Dec 15 06:30:49 2020

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