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Sodium in PDB 5zp8: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (4)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (4)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (4):
1.4.3.21;

Protein crystallography data

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (4), PDB code: 5zp8 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) 40.36 / 1.66
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.590, 64.297, 158.791, 90.00, 117.20, 90.00
R / Rfree (%) 15.6 / 17.4

Other elements in 5zp8:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (4) 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 277 K (4) (pdb code 5zp8). 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 277 K (4), PDB code: 5zp8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5zp8

Go back to Sodium Binding Sites List in 5zp8
Sodium binding site 1 out of 2 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (4)


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 277 K (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:16.7
occ:1.00
 OD1 A:ASP581 2.4 25.2 1.0
O A:MET441 2.4 21.7 1.0
OD1 A:ASP440 2.5 25.3 1.0
O A:ILE582 2.6 21.5 1.0
O A:HOH1282 2.8 22.2 1.0
N A:ILE582 3.3 19.5 1.0
N A:MET441 3.5 20.3 1.0
C A:MET441 3.5 19.5 1.0
C A:ILE582 3.6 21.3 1.0
CG A:ASP581 3.6 26.5 1.0
CG A:ASP440 3.7 21.2 1.0
NH2 A:ARG49 3.8 29.2 1.0
CD1 A:PHE446 3.8 31.6 1.0
C A:ASP581 3.8 24.0 1.0
C A:ASP440 4.0 20.5 1.0
CA A:MET441 4.0 19.8 1.0
CA A:ILE582 4.0 18.9 1.0
CA A:ASP581 4.1 23.5 1.0
CE1 A:PHE446 4.2 35.6 1.0
CA A:ASP440 4.4 20.4 1.0
CB A:ASP581 4.5 22.7 1.0
OD2 A:ASP440 4.5 23.3 1.0
OD2 A:ASP581 4.5 30.7 1.0
O A:ASP440 4.6 20.3 1.0
CB A:MET441 4.6 22.2 1.0
N A:ALA442 4.7 20.4 1.0
CB A:ASP440 4.7 19.1 1.0
O A:ASP581 4.7 24.3 1.0
N A:VAL583 4.7 18.1 1.0
CB A:TYR546 4.8 22.9 1.0
CG2 A:VAL583 4.9 21.2 1.0
O A:PHE446 5.0 31.0 1.0

Sodium binding site 2 out of 2 in 5zp8

Go back to Sodium Binding Sites List in 5zp8
Sodium binding site 2 out of 2 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (4)


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 277 K (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:15.1
occ:1.00
 OD1 B:ASP581 2.4 21.0 1.0
OD1 B:ASP440 2.5 22.2 1.0
O B:MET441 2.5 19.0 1.0
O B:ILE582 2.6 18.1 1.0
O B:HOH1009 2.8 20.5 1.0
N B:ILE582 3.2 18.4 1.0
C B:ILE582 3.5 17.1 1.0
N B:MET441 3.5 16.1 1.0
C B:MET441 3.6 18.2 1.0
CG B:ASP581 3.6 23.8 1.0
CG B:ASP440 3.7 19.5 1.0
NH2 B:ARG49 3.7 29.5 1.0
C B:ASP581 3.8 19.3 1.0
CD1 B:PHE446 3.9 28.3 1.0
C B:ASP440 4.0 16.2 1.0
CA B:ILE582 4.0 17.0 1.0
CA B:ASP581 4.1 17.8 1.0
CA B:MET441 4.1 15.7 1.0
CE1 B:PHE446 4.3 33.0 1.0
CA B:ASP440 4.4 13.6 1.0
CB B:ASP581 4.4 22.5 1.0
OD2 B:ASP581 4.5 27.9 1.0
OD2 B:ASP440 4.5 19.7 1.0
O B:ASP440 4.6 17.5 1.0
O B:ASP581 4.6 20.2 1.0
N B:VAL583 4.7 14.1 1.0
CB B:MET441 4.7 17.2 1.0
CB B:ASP440 4.7 15.4 1.0
N B:ALA442 4.7 16.2 1.0
CB B:TYR546 4.8 21.0 1.0
CG2 B:VAL583 4.9 18.1 1.0
CG1 B:ILE582 5.0 22.8 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 01:36:40 2024

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