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Sodium in PDB 3x3x: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine:
1.4.3.21;

Protein crystallography data

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine, PDB code: 3x3x 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) 20.41 / 1.57
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 191.658, 62.890, 158.006, 90.00, 117.48, 90.00
R / Rfree (%) 21.5 / 24.3

Other elements in 3x3x:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine (pdb code 3x3x). 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 Anaerobically Reduced By Phenylethylamine, PDB code: 3x3x:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3x3x

Go back to Sodium Binding Sites List in 3x3x
Sodium binding site 1 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine


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 Anaerobically Reduced By Phenylethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:11.7
occ:1.00
 OD1 A:ASP581 2.3 18.2 1.0
OD1 A:ASP440 2.4 12.8 1.0
O A:MET441 2.4 15.7 1.0
O A:ILE582 2.5 9.3 1.0
O A:HOH1136 2.6 13.5 1.0
N A:ILE582 3.2 11.8 1.0
N A:MET441 3.4 12.5 1.0
C A:ILE582 3.4 11.3 1.0
C A:MET441 3.5 14.0 1.0
CG A:ASP581 3.6 24.0 1.0
CG A:ASP440 3.7 20.2 1.0
CD1 A:PHE446 3.7 22.1 1.0
C A:ASP581 3.8 14.9 1.0
CA A:ILE582 3.9 15.7 1.0
NH2 A:ARG49 3.9 20.8 1.0
C A:ASP440 3.9 9.4 1.0
CA A:MET441 4.0 13.2 1.0
CE1 A:PHE446 4.0 26.5 1.0
CA A:ASP581 4.1 13.2 1.0
CA A:ASP440 4.4 7.5 1.0
OD2 A:ASP440 4.4 16.7 1.0
CB A:ASP581 4.4 14.8 1.0
OD2 A:ASP581 4.5 23.0 1.0
CB A:MET441 4.5 12.0 1.0
O A:ASP440 4.5 11.8 1.0
O A:ASP581 4.6 15.3 1.0
N A:VAL583 4.6 12.9 1.0
CB A:ASP440 4.6 9.4 1.0
N A:ALA442 4.7 11.8 1.0
CG2 A:VAL583 4.7 12.7 1.0
CB A:TYR546 4.8 15.7 1.0
CG A:PHE446 4.9 22.3 1.0
CG1 A:ILE582 4.9 12.0 1.0
O A:PHE446 4.9 17.8 1.0

Sodium binding site 2 out of 3 in 3x3x

Go back to Sodium Binding Sites List in 3x3x
Sodium binding site 2 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine


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 Anaerobically Reduced By Phenylethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:13.1
occ:1.00
 O B:VAL79 2.5 16.3 1.0
OG A:SER562 2.6 22.9 1.0
O A:HOH1112 2.6 21.0 1.0
O A:ALA93 2.8 19.2 1.0
OE1 B:GLU22 2.9 21.6 1.0
O A:ALA94 2.9 17.7 1.0
O B:THR80 3.5 20.5 1.0
NH1 A:ARG148 3.6 23.5 1.0
CD B:GLU22 3.7 32.4 1.0
C A:ALA94 3.7 17.7 1.0
C B:VAL79 3.7 21.0 1.0
CB A:SER562 3.8 20.3 1.0
N B:GLY82 3.8 20.9 1.0
C B:THR80 3.9 18.9 1.0
CA A:ALA94 3.9 14.9 1.0
C A:ALA93 3.9 22.0 1.0
O A:HOH1111 4.0 24.7 1.0
CA B:GLY82 4.1 24.0 1.0
CG B:GLU22 4.1 23.4 1.0
C B:ASN81 4.3 20.6 1.0
N B:ASN81 4.4 20.3 1.0
N A:ALA94 4.4 16.3 1.0
CA B:THR80 4.5 20.6 1.0
OE2 B:GLU22 4.5 31.1 1.0
N A:SER562 4.5 17.8 1.0
N B:THR80 4.6 18.9 1.0
O A:HOH969 4.6 17.6 1.0
CA B:ASN81 4.7 15.5 1.0
CA B:VAL79 4.7 16.2 1.0
CZ A:ARG148 4.8 27.1 1.0
CA A:SER562 4.8 22.4 1.0
N A:THR95 4.9 18.4 1.0
O B:ASN81 5.0 24.4 1.0

Sodium binding site 3 out of 3 in 3x3x

Go back to Sodium Binding Sites List in 3x3x
Sodium binding site 3 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine


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 Anaerobically Reduced By Phenylethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:11.6
occ:1.00
 OD1 B:ASP581 2.4 13.4 1.0
OD1 B:ASP440 2.4 13.9 1.0
O B:MET441 2.4 14.7 1.0
O B:ILE582 2.5 11.2 1.0
O B:HOH847 2.7 12.7 1.0
N B:ILE582 3.2 11.3 1.0
N B:MET441 3.4 13.3 1.0
C B:ILE582 3.5 10.3 1.0
C B:MET441 3.5 14.1 1.0
CG B:ASP581 3.6 16.0 1.0
CG B:ASP440 3.6 11.8 1.0
CD1 B:PHE446 3.8 19.6 1.0
C B:ASP581 3.8 18.3 1.0
NH2 B:ARG49 3.9 16.1 1.0
C B:ASP440 3.9 11.6 1.0
CA B:ILE582 3.9 16.2 1.0
CA B:MET441 4.0 14.7 1.0
CA B:ASP581 4.1 15.3 1.0
CE1 B:PHE446 4.1 15.5 1.0
CA B:ASP440 4.3 13.4 1.0
OD2 B:ASP440 4.4 12.4 1.0
CB B:ASP581 4.5 16.1 1.0
OD2 B:ASP581 4.5 21.8 1.0
CB B:MET441 4.5 15.9 1.0
O B:ASP440 4.5 12.3 1.0
CB B:ASP440 4.6 9.1 1.0
N B:VAL583 4.6 12.4 1.0
N B:ALA442 4.7 10.5 1.0
O B:ASP581 4.7 15.6 1.0
CG2 B:VAL583 4.7 16.4 1.0
CB B:TYR546 4.8 13.3 1.0
CG B:PHE446 4.9 22.2 1.0
CG1 B:ILE582 4.9 16.2 1.0
O B:PHE446 5.0 20.3 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 14:03:36 2024

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