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Sodium in PDB 5zpr: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 9 at 288 K (2)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 9 at 288 K (2)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 9 at 288 K (2):
1.4.3.21;

Protein crystallography data

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 9 at 288 K (2), PDB code: 5zpr 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) 40.43 / 1.92
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.849, 64.320, 159.026, 90.00, 116.94, 90.00
R / Rfree (%) 14.8 / 18.2

Other elements in 5zpr:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 9 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 Phenylethylamine at pH 9 at 288 K (2) (pdb code 5zpr). 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 9 at 288 K (2), PDB code: 5zpr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5zpr

Go back to Sodium Binding Sites List in 5zpr
Sodium binding site 1 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 9 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 Phenylethylamine at pH 9 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:9.2
occ:1.00
 OD1 A:ASP440 2.4 14.0 1.0
OD1 A:ASP581 2.4 17.2 1.0
O A:MET441 2.5 14.8 1.0
O A:ILE582 2.5 10.8 1.0
O A:HOH1094 2.8 12.2 1.0
N A:ILE582 3.2 12.3 1.0
C A:ILE582 3.5 11.9 1.0
N A:MET441 3.5 12.1 1.0
C A:MET441 3.6 12.4 1.0
CG A:ASP581 3.6 18.6 1.0
CG A:ASP440 3.7 15.5 1.0
NH2 A:ARG49 3.8 15.9 1.0
C A:ASP581 3.8 16.3 1.0
CA A:ILE582 3.9 8.3 1.0
CD1 A:PHE446 4.0 26.9 1.0
C A:ASP440 4.0 13.2 1.0
CA A:MET441 4.0 9.1 1.0
CA A:ASP581 4.1 12.9 1.0
CE1 A:PHE446 4.3 30.5 1.0
CA A:ASP440 4.4 15.3 1.0
OD2 A:ASP440 4.4 14.6 1.0
CB A:ASP581 4.5 17.8 1.0
OD2 A:ASP581 4.5 23.8 1.0
CB A:MET441 4.6 13.0 1.0
O A:ASP581 4.6 14.5 1.0
O A:ASP440 4.6 12.6 1.0
N A:VAL583 4.6 8.7 1.0
CB A:ASP440 4.6 14.1 1.0
N A:ALA442 4.7 10.1 1.0
CB A:TYR546 4.8 18.7 1.0
CG2 A:VAL583 4.8 14.4 1.0
CG1 A:ILE582 4.9 14.9 1.0

Sodium binding site 2 out of 3 in 5zpr

Go back to Sodium Binding Sites List in 5zpr
Sodium binding site 2 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 9 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 Phenylethylamine at pH 9 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:16.1
occ:1.00
 O B:VAL79 2.5 22.1 1.0
O A:HOH1154 2.8 36.6 1.0
OG A:SER562 2.9 27.4 1.0
O A:ALA93 3.0 24.8 1.0
O A:ALA94 3.0 16.0 1.0
OE1 B:GLU22 3.1 16.4 0.5
O B:THR80 3.4 21.7 1.0
C B:VAL79 3.7 23.6 1.0
CD B:GLU22 3.8 22.1 0.5
C B:THR80 3.8 25.4 1.0
C A:ALA94 3.8 14.2 1.0
CA A:ALA94 3.9 13.6 1.0
NH2 A:ARG148 3.9 43.1 1.0
CB A:SER562 4.1 26.8 1.0
C A:ALA93 4.1 21.2 1.0
N B:GLY82 4.1 21.4 1.0
O A:HOH882 4.2 41.3 1.0
CG B:GLU22 4.3 13.1 0.5
CA B:THR80 4.3 18.8 1.0
CA B:GLY82 4.4 22.4 1.0
O A:HOH966 4.5 24.1 1.0
N B:ASN81 4.5 22.5 1.0
N A:ALA94 4.5 14.9 1.0
N B:THR80 4.5 18.2 1.0
C B:ASN81 4.6 25.4 1.0
OE2 B:GLU22 4.6 23.3 0.5
N A:SER562 4.7 10.6 1.0
OE1 B:GLU22 4.7 22.7 0.5
CA B:VAL79 4.7 21.2 1.0
CA B:ASN81 4.9 23.2 1.0

Sodium binding site 3 out of 3 in 5zpr

Go back to Sodium Binding Sites List in 5zpr
Sodium binding site 3 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 9 at 288 K (2)


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 9 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:8.6
occ:1.00
 OD1 B:ASP440 2.4 12.2 1.0
OD1 B:ASP581 2.4 17.9 1.0
O B:MET441 2.4 13.6 1.0
O B:ILE582 2.5 8.3 1.0
O B:HOH952 2.9 14.7 1.0
N B:ILE582 3.3 12.4 1.0
N B:MET441 3.5 9.7 1.0
C B:ILE582 3.5 10.7 1.0
C B:MET441 3.5 8.1 1.0
CG B:ASP440 3.7 16.5 1.0
CG B:ASP581 3.7 22.6 1.0
NH2 B:ARG49 3.8 15.4 1.0
C B:ASP581 3.8 11.1 1.0
C B:ASP440 3.9 11.9 1.0
CA B:MET441 4.0 11.0 1.0
CA B:ILE582 4.0 10.7 1.0
CD1 B:PHE446 4.0 27.1 1.0
CA B:ASP581 4.1 16.1 1.0
CE1 B:PHE446 4.4 31.5 1.0
CA B:ASP440 4.4 15.4 1.0
OD2 B:ASP440 4.4 15.9 1.0
CB B:ASP581 4.5 17.5 1.0
O B:ASP440 4.5 12.3 1.0
OD2 B:ASP581 4.5 23.3 1.0
CB B:MET441 4.6 9.8 1.0
O B:ASP581 4.6 12.8 1.0
N B:VAL583 4.6 8.2 1.0
CB B:ASP440 4.6 15.5 1.0
N B:ALA442 4.7 8.7 1.0
CB B:TYR546 4.8 11.1 1.0
CG2 B:VAL583 4.8 11.6 1.0
CG1 B:ILE582 4.9 15.1 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 01:40:04 2024

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