Atomistry » Sodium » PDB 5zo9-5zwy » 5zpe
Atomistry »
  Sodium »
    PDB 5zo9-5zwy »
      5zpe »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy