Sodium in PDB 5zph: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at PH6 at 293K (2)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at PH6 at 293K (2):
1.4.3.21;

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at PH6 at 293K (2), PDB code: 5zph 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)	40.44 / 1.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	193.464, 64.505, 158.895, 90.00, 117.06, 90.00
R / Rfree (%)	15.3 / 17.9

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at PH6 at 293K (2) also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Sodium atom in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at PH6 at 293K (2) (pdb code 5zph). 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 PH6 at 293K (2), PDB code: 5zph:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at PH6 at 293K (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 PH6 at 293K (2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:15.6 occ:1.00 OD1 A:ASP581 2.4 24.4 1.0 OD1 A:ASP440 2.4 21.2 1.0 O A:MET441 2.4 19.8 1.0 O A:ILE582 2.5 20.2 1.0 O A:HOH1303 2.8 18.4 1.0 N A:ILE582 3.2 18.7 1.0 C A:ILE582 3.5 21.1 1.0 N A:MET441 3.5 15.1 1.0 C A:MET441 3.5 16.5 1.0 CG A:ASP581 3.6 27.3 1.0 CG A:ASP440 3.7 20.5 1.0 NH2 A:ARG49 3.8 36.6 1.0 C A:ASP581 3.8 20.0 1.0 C A:ASP440 3.9 17.8 1.0 CD1 A:PHE446 3.9 33.0 1.0 CA A:ILE582 4.0 20.9 1.0 CA A:MET441 4.0 16.1 1.0 CA A:ASP581 4.1 20.8 1.0 CE1 A:PHE446 4.3 32.0 1.0 CA A:ASP440 4.4 15.8 1.0 CB A:ASP581 4.4 23.1 1.0 OD2 A:ASP440 4.5 21.1 1.0 OD2 A:ASP581 4.5 30.0 1.0 O A:ASP440 4.5 17.3 1.0 N A:VAL583 4.6 17.2 1.0 O A:ASP581 4.6 22.4 1.0 CB A:ASP440 4.6 16.9 1.0 CB A:MET441 4.7 16.3 1.0 N A:ALA442 4.7 19.0 1.0 CB A:TYR546 4.8 22.8 1.0 CG2 A:VAL583 4.8 20.7 1.0 CG1 A:ILE582 4.9 27.6 1.0 O A:PHE446 5.0 31.6 1.0

Sodium binding site 2 out of 2 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at PH6 at 293K (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 PH6 at 293K (2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:12.8 occ:1.00 OD1 B:ASP440 2.4 19.4 1.0 OD1 B:ASP581 2.4 18.8 1.0 O B:MET441 2.4 16.5 1.0 O B:ILE582 2.5 15.4 1.0 O B:HOH1060 2.8 18.1 1.0 N B:ILE582 3.2 13.0 1.0 C B:ILE582 3.5 14.3 1.0 N B:MET441 3.5 14.6 1.0 C B:MET441 3.5 14.8 1.0 CG B:ASP581 3.7 25.0 1.0 CG B:ASP440 3.7 15.7 1.0 NH2 B:ARG49 3.7 39.7 1.0 C B:ASP581 3.8 16.1 1.0 C B:ASP440 3.9 11.5 1.0 CD1 B:PHE446 3.9 25.6 1.0 CA B:ILE582 4.0 13.9 1.0 CA B:MET441 4.0 14.8 1.0 CA B:ASP581 4.1 15.8 1.0 CE1 B:PHE446 4.3 31.2 1.0 CA B:ASP440 4.3 11.3 1.0 OD2 B:ASP440 4.5 16.4 1.0 CB B:ASP581 4.5 19.1 1.0 O B:ASP440 4.5 14.7 1.0 OD2 B:ASP581 4.5 24.9 1.0 N B:VAL583 4.6 11.7 1.0 CB B:ASP440 4.6 12.5 1.0 CB B:MET441 4.6 13.2 1.0 O B:ASP581 4.6 18.1 1.0 N B:ALA442 4.7 14.1 1.0 CB B:TYR546 4.8 17.9 1.0 CG2 B:VAL583 4.9 15.9 1.0 CG1 B:ILE582 5.0 21.8 1.0 CZ B:ARG49 5.0 39.2 1.0

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