Atomistry » Sodium » PDB 5zo9-5zwy » 5zp5
Atomistry »
  Sodium »
    PDB 5zo9-5zwy »
      5zp5 »

Sodium in PDB 5zp5: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (1)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (1)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (1):
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 (1), PDB code: 5zp5 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) 35.33 / 1.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.724, 64.816, 158.820, 90.00, 117.15, 90.00
R / Rfree (%) 16.7 / 19.8

Other elements in 5zp5:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (1) 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 (1) (pdb code 5zp5). 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 Ethylamine at pH 6 at 277 K (1), PDB code: 5zp5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5zp5

Go back to Sodium Binding Sites List in 5zp5
Sodium binding site 1 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (1)


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 (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:15.2
occ:1.00
OD1 A:ASP440 2.4 19.8 1.0
OD1 A:ASP581 2.5 25.5 1.0
O A:MET441 2.5 19.8 1.0
O A:ILE582 2.5 17.6 1.0
O A:HOH1106 2.9 20.7 1.0
N A:ILE582 3.3 19.8 1.0
C A:ILE582 3.5 15.8 1.0
N A:MET441 3.5 17.6 1.0
C A:MET441 3.6 15.9 1.0
CG A:ASP440 3.6 19.2 1.0
CG A:ASP581 3.7 29.0 1.0
NH2 A:ARG49 3.8 22.1 1.0
C A:ASP581 3.8 20.5 1.0
C A:ASP440 3.9 18.1 1.0
CA A:ILE582 4.0 18.3 1.0
CD1 A:PHE446 4.0 30.7 1.0
CA A:MET441 4.0 19.6 1.0
CA A:ASP581 4.1 21.7 1.0
CA A:ASP440 4.3 14.1 1.0
CE1 A:PHE446 4.4 27.0 1.0
OD2 A:ASP440 4.4 20.3 1.0
CB A:ASP581 4.5 24.5 1.0
O A:ASP440 4.6 15.8 1.0
CB A:MET441 4.6 18.7 1.0
CB A:ASP440 4.6 14.1 1.0
OD2 A:ASP581 4.6 31.4 1.0
O A:ASP581 4.6 18.7 1.0
N A:VAL583 4.6 14.5 1.0
N A:ALA442 4.7 17.7 1.0
CB A:TYR546 4.8 19.6 1.0
CG2 A:VAL583 4.9 17.0 1.0
CG1 A:ILE582 5.0 21.5 1.0

Sodium binding site 2 out of 3 in 5zp5

Go back to Sodium Binding Sites List in 5zp5
Sodium binding site 2 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (1)


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 (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:22.9
occ:1.00
O A:HOH1163 2.5 35.5 1.0
O B:VAL79 2.6 25.7 1.0
O A:ALA94 2.9 22.6 1.0
O A:ALA93 3.0 27.8 1.0
OG A:SER562 3.1 41.3 1.0
O B:THR80 3.1 31.5 1.0
C A:ALA94 3.7 19.3 1.0
C B:THR80 3.7 27.9 1.0
C B:VAL79 3.8 29.0 1.0
CA A:ALA94 3.8 19.0 1.0
CB A:SER562 3.9 40.6 1.0
C A:ALA93 4.1 24.7 1.0
N B:GLY82 4.2 27.0 1.0
CA B:THR80 4.2 23.9 1.0
OE1 B:GLU22 4.3 36.0 1.0
O A:HOH914 4.3 37.0 1.0
N A:ALA94 4.4 22.1 1.0
CG B:GLU22 4.4 31.4 1.0
N B:ASN81 4.4 25.9 1.0
N B:THR80 4.5 24.0 1.0
CA B:GLY82 4.5 28.0 1.0
N A:SER562 4.6 22.5 1.0
CD B:GLU22 4.6 32.0 1.0
C B:ASN81 4.6 29.3 1.0
CA B:ASN81 4.9 25.6 1.0
N A:THR95 4.9 22.0 1.0
CE1 A:HIS561 4.9 31.3 1.0
CA B:VAL79 4.9 24.9 1.0
CA A:SER562 4.9 35.8 1.0

Sodium binding site 3 out of 3 in 5zp5

Go back to Sodium Binding Sites List in 5zp5
Sodium binding site 3 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 6 at 277 K (1)


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 Ethylamine at pH 6 at 277 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:13.4
occ:1.00
OD1 B:ASP581 2.4 22.7 1.0
OD1 B:ASP440 2.5 17.1 1.0
O B:MET441 2.5 15.3 1.0
O B:ILE582 2.5 17.8 1.0
O B:HOH974 2.7 18.0 1.0
N B:ILE582 3.3 15.4 1.0
N B:MET441 3.4 17.7 1.0
C B:ILE582 3.5 14.1 1.0
C B:MET441 3.5 15.4 1.0
CG B:ASP581 3.6 20.6 1.0
CG B:ASP440 3.7 20.2 1.0
NH2 B:ARG49 3.7 22.0 1.0
C B:ASP581 3.8 17.6 1.0
C B:ASP440 3.9 15.4 1.0
CD1 B:PHE446 4.0 28.9 1.0
CA B:ILE582 4.0 15.4 1.0
CA B:MET441 4.0 16.9 1.0
CA B:ASP581 4.1 24.0 1.0
CE1 B:PHE446 4.4 29.9 1.0
CA B:ASP440 4.4 16.7 1.0
CB B:ASP581 4.5 24.6 1.0
OD2 B:ASP440 4.5 22.4 1.0
OD2 B:ASP581 4.5 24.1 1.0
CB B:MET441 4.6 18.9 1.0
O B:ASP440 4.6 15.5 1.0
N B:VAL583 4.6 13.9 1.0
O B:ASP581 4.6 18.3 1.0
CB B:ASP440 4.7 17.7 1.0
N B:ALA442 4.7 14.4 1.0
CB B:TYR546 4.8 17.2 1.0
CG2 B:VAL583 4.8 18.3 1.0
CG1 B:ILE582 4.9 23.5 1.0
O B:PHE446 5.0 29.8 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 01:36:03 2024

Last articles

Cl in 5IJ7
Cl in 5II3
Cl in 5IFM
Cl in 5IJ6
Cl in 5IHG
Cl in 5IHR
Cl in 5IGN
Cl in 5IH5
Cl in 5IG6
Cl in 5IFU
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy