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

Sodium in PDB 5zpl: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 K (1)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 K (1)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 K (1):
1.4.3.21;

Protein crystallography data

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 K (1), PDB code: 5zpl 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) 39.70 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.923, 64.472, 158.944, 90.00, 116.91, 90.00
R / Rfree (%) 15.2 / 17.1

Other elements in 5zpl:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 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 Phenylethylamine at pH 7 at 288 K (1) (pdb code 5zpl). 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 Phenylethylamine at pH 7 at 288 K (1), PDB code: 5zpl:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5zpl

Go back to Sodium Binding Sites List in 5zpl
Sodium binding site 1 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 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 Phenylethylamine at pH 7 at 288 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:14.0
occ:1.00
 OD1 A:ASP581 2.4 22.2 1.0
OD1 A:ASP440 2.4 19.9 1.0
O A:MET441 2.5 18.6 1.0
O A:ILE582 2.6 16.7 1.0
O A:HOH1006 2.8 16.9 1.0
N A:ILE582 3.3 16.4 1.0
N A:MET441 3.5 15.1 1.0
C A:MET441 3.5 17.0 1.0
C A:ILE582 3.5 18.2 1.0
CG A:ASP581 3.6 24.2 1.0
CG A:ASP440 3.7 20.4 1.0
NH2 A:ARG49 3.8 34.5 1.0
C A:ASP581 3.8 21.5 1.0
CD1 A:PHE446 3.9 31.7 1.0
C A:ASP440 3.9 15.7 1.0
CA A:ILE582 4.0 16.4 1.0
CA A:MET441 4.0 15.0 1.0
CA A:ASP581 4.1 18.3 1.0
CE1 A:PHE446 4.2 32.6 1.0
CA A:ASP440 4.4 15.8 1.0
CB A:ASP581 4.4 18.9 1.0
OD2 A:ASP440 4.4 21.2 1.0
OD2 A:ASP581 4.5 28.4 1.0
O A:ASP440 4.5 17.4 1.0
CB A:MET441 4.6 17.8 1.0
CB A:ASP440 4.6 15.3 1.0
O A:ASP581 4.6 20.3 1.0
N A:VAL583 4.7 15.2 1.0
N A:ALA442 4.7 16.1 1.0
CG2 A:VAL583 4.8 18.6 1.0
CB A:TYR546 4.9 21.4 1.0

Sodium binding site 2 out of 3 in 5zpl

Go back to Sodium Binding Sites List in 5zpl
Sodium binding site 2 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 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 Phenylethylamine at pH 7 at 288 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:20.7
occ:1.00
 O B:VAL79 2.5 26.2 1.0
O A:HOH1124 2.7 35.1 1.0
OG A:SER562 2.8 36.9 1.0
O A:ALA94 2.9 25.8 1.0
O A:ALA93 3.0 29.2 1.0
OE1 B:GLU22 3.1 26.3 0.5
O B:THR80 3.4 30.4 1.0
NH2 A:ARG148 3.5 64.5 1.0
C A:ALA94 3.8 25.0 1.0
C B:VAL79 3.8 28.0 1.0
CD B:GLU22 3.8 30.7 0.5
CB A:SER562 3.8 35.4 1.0
C B:THR80 3.9 28.6 1.0
CA A:ALA94 3.9 23.2 1.0
C A:ALA93 4.1 27.9 1.0
N B:GLY82 4.1 27.2 1.0
O A:HOH835 4.2 43.7 1.0
CG B:GLU22 4.3 23.3 0.5
CA B:THR80 4.3 27.4 1.0
O A:HOH1011 4.4 31.3 1.0
CA B:GLY82 4.5 30.1 1.0
N A:ALA94 4.5 23.9 1.0
N B:ASN81 4.5 28.1 1.0
N B:THR80 4.5 24.7 1.0
N A:SER562 4.5 22.1 1.0
OE1 B:GLU22 4.6 30.7 0.5
OE2 B:GLU22 4.6 31.0 0.5
C B:ASN81 4.6 28.1 1.0
CZ A:ARG148 4.8 63.3 1.0
CA B:VAL79 4.8 24.0 1.0
CA A:SER562 4.8 26.8 1.0
CA B:ASN81 4.9 29.3 1.0
N A:THR95 5.0 20.3 1.0

Sodium binding site 3 out of 3 in 5zpl

Go back to Sodium Binding Sites List in 5zpl
Sodium binding site 3 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 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 Phenylethylamine at pH 7 at 288 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:13.8
occ:1.00
 OD1 B:ASP440 2.4 19.0 1.0
OD1 B:ASP581 2.4 20.8 1.0
O B:MET441 2.4 17.6 1.0
O B:ILE582 2.5 17.4 1.0
O B:HOH984 2.8 18.7 1.0
N B:ILE582 3.3 18.8 1.0
N B:MET441 3.5 15.1 1.0
C B:MET441 3.5 16.3 1.0
C B:ILE582 3.5 17.5 1.0
CG B:ASP440 3.6 19.3 1.0
CG B:ASP581 3.6 22.9 1.0
NH2 B:ARG49 3.8 32.6 1.0
C B:ASP581 3.9 17.9 1.0
C B:ASP440 3.9 15.7 1.0
CD1 B:PHE446 3.9 28.9 1.0
CA B:ILE582 4.0 18.4 1.0
CA B:MET441 4.0 14.8 1.0
CA B:ASP581 4.1 19.2 1.0
CE1 B:PHE446 4.2 29.3 1.0
CA B:ASP440 4.3 13.6 1.0
OD2 B:ASP440 4.4 19.4 1.0
O B:ASP440 4.5 17.7 1.0
CB B:ASP581 4.5 18.1 1.0
OD2 B:ASP581 4.5 27.1 1.0
CB B:ASP440 4.6 13.8 1.0
N B:VAL583 4.7 17.3 1.0
N B:ALA442 4.7 15.8 1.0
O B:ASP581 4.7 20.0 1.0
CB B:MET441 4.7 18.8 1.0
CB B:TYR546 4.8 20.8 1.0
CG2 B:VAL583 4.8 19.6 1.0
CG1 B:ILE582 5.0 23.9 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 01:38:33 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy