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Sodium in PDB 5zpe: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 288 K (2)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 288 K (2)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 288 K (2):
1.4.3.21;

Protein crystallography data

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 288 K (2), PDB code: 5zpe was solved by T.Murakawa, S.Baba, Y.Kawano, H.Hayashi, T.Yano, K.Tanizawa, T.Kumasaka, M.Yamamoto, T.Okajima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.41 / 1.69
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.558, 64.465, 158.831, 90.00, 117.12, 90.00
R / Rfree (%) 15.1 / 17.3

Other elements in 5zpe:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 288 K (2) 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 Ethylamine at pH 6 at 288 K (2) (pdb code 5zpe). 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 Anaerobically Reduced By Ethylamine at pH 6 at 288 K (2), PDB code: 5zpe:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5zpe

Go back to Sodium Binding Sites List in 5zpe
Sodium binding site 1 out of 2 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 288 K (2)


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 Ethylamine at pH 6 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1003

b:14.3
occ:1.00
 OD1 A:ASP581 2.4 24.6 1.0
O A:MET441 2.4 19.0 1.0
OD1 A:ASP440 2.5 21.8 1.0
O A:ILE582 2.6 16.3 1.0
O A:HOH1296 2.8 18.2 1.0
N A:ILE582 3.2 16.8 1.0
N A:MET441 3.5 16.2 1.0
C A:ILE582 3.5 18.1 1.0
C A:MET441 3.5 15.8 1.0
CG A:ASP581 3.6 26.6 1.0
CG A:ASP440 3.7 19.5 1.0
NH2 A:ARG49 3.8 30.1 1.0
C A:ASP581 3.8 19.3 1.0
CD1 A:PHE446 3.9 32.2 1.0
C A:ASP440 3.9 18.9 1.0
CA A:ILE582 4.0 16.3 1.0
CA A:MET441 4.0 15.6 1.0
CA A:ASP581 4.1 19.3 1.0
CE1 A:PHE446 4.3 31.7 1.0
CA A:ASP440 4.4 15.2 1.0
CB A:ASP581 4.5 20.9 1.0
OD2 A:ASP440 4.5 20.1 1.0
OD2 A:ASP581 4.5 27.3 1.0
O A:ASP440 4.6 15.7 1.0
N A:VAL583 4.6 15.3 1.0
CB A:MET441 4.6 16.2 1.0
CB A:ASP440 4.7 16.4 1.0
O A:ASP581 4.7 19.8 1.0
N A:ALA442 4.7 17.1 1.0
CB A:TYR546 4.8 20.8 1.0
CG2 A:VAL583 4.9 15.9 1.0
CG1 A:ILE582 4.9 22.1 1.0
O A:PHE446 5.0 27.8 1.0

Sodium binding site 2 out of 2 in 5zpe

Go back to Sodium Binding Sites List in 5zpe
Sodium binding site 2 out of 2 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 288 K (2)


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 Ethylamine at pH 6 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:11.7
occ:1.00
 OD1 B:ASP581 2.4 18.3 1.0
O B:MET441 2.5 15.1 1.0
OD1 B:ASP440 2.5 19.2 1.0
O B:ILE582 2.5 12.9 1.0
O B:HOH1063 2.8 15.6 1.0
N B:ILE582 3.2 13.8 1.0
C B:ILE582 3.5 13.6 1.0
N B:MET441 3.5 14.1 1.0
C B:MET441 3.6 14.1 1.0
CG B:ASP581 3.6 23.9 1.0
CG B:ASP440 3.7 17.5 1.0
C B:ASP581 3.8 16.4 1.0
NH2 B:ARG49 3.8 29.7 1.0
CA B:ILE582 3.9 13.3 1.0
C B:ASP440 3.9 11.0 1.0
CD1 B:PHE446 4.0 26.6 1.0
CA B:MET441 4.1 13.4 1.0
CA B:ASP581 4.1 14.9 1.0
CE1 B:PHE446 4.4 28.9 1.0
CA B:ASP440 4.4 10.5 1.0
CB B:ASP581 4.5 17.6 1.0
OD2 B:ASP581 4.5 22.8 1.0
OD2 B:ASP440 4.5 16.3 1.0
O B:ASP440 4.6 13.7 1.0
O B:ASP581 4.6 16.3 1.0
CB B:MET441 4.6 12.0 1.0
N B:VAL583 4.6 10.9 1.0
CB B:ASP440 4.7 12.2 1.0
N B:ALA442 4.7 12.8 1.0
CB B:TYR546 4.8 18.0 1.0
CG2 B:VAL583 4.9 14.7 1.0
CG1 B:ILE582 4.9 18.0 1.0

Reference:

T.Murakawa, S.Baba, Y.Kawano, H.Hayashi, T.Yano, T.Kumasaka, M.Yamamoto, K.Tanizawa, T.Okajima. In Crystallothermodynamic Analysis of Conformational Change of the Topaquinone Cofactor in Bacterial Copper Amine Oxidase Proc. Natl. Acad. Sci. V. 116 135 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30563857
DOI: 10.1073/PNAS.1811837116
Page generated: Tue Oct 8 01:37:28 2024

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