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Sodium in PDB 5zp3: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 10 at 288 K (1)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 10 at 288 K (1)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 10 at 288 K (1):
1.4.3.21;

Protein crystallography data

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 10 at 288 K (1), PDB code: 5zp3 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) 33.27 / 1.78
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.811, 64.969, 159.054, 90.00, 117.20, 90.00
R / Rfree (%) 14.7 / 17.2

Other elements in 5zp3:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 10 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 Ethylamine at pH 10 at 288 K (1) (pdb code 5zp3). 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 10 at 288 K (1), PDB code: 5zp3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5zp3

Go back to Sodium Binding Sites List in 5zp3
Sodium binding site 1 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 10 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 Ethylamine at pH 10 at 288 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:13.8
occ:1.00
O A:MET441 2.4 18.6 1.0
OD1 A:ASP581 2.4 21.1 1.0
OD1 A:ASP440 2.4 21.9 1.0
O A:ILE582 2.5 19.8 1.0
O A:HOH1023 2.8 19.9 1.0
N A:ILE582 3.2 14.9 1.0
N A:MET441 3.4 16.4 1.0
C A:ILE582 3.5 15.6 1.0
C A:MET441 3.5 16.2 1.0
CG A:ASP581 3.7 24.9 1.0
CG A:ASP440 3.7 20.9 1.0
NH2 A:ARG49 3.7 39.0 1.0
C A:ASP581 3.8 16.0 1.0
C A:ASP440 3.9 15.2 1.0
CA A:ILE582 3.9 15.6 1.0
CD1 A:PHE446 4.0 31.1 1.0
CA A:MET441 4.0 17.6 1.0
CA A:ASP581 4.1 20.4 1.0
CE1 A:PHE446 4.3 31.8 1.0
CA A:ASP440 4.3 14.3 1.0
OD2 A:ASP440 4.5 23.3 1.0
CB A:ASP581 4.5 23.0 1.0
O A:ASP440 4.5 16.4 1.0
OD2 A:ASP581 4.5 28.9 1.0
CB A:MET441 4.6 16.2 1.0
CB A:ASP440 4.6 16.8 1.0
N A:VAL583 4.6 15.0 1.0
O A:ASP581 4.7 20.5 1.0
N A:ALA442 4.7 17.6 1.0
CB A:TYR546 4.8 23.1 1.0
CG2 A:VAL583 4.9 16.8 1.0
CG1 A:ILE582 4.9 20.1 1.0
CZ A:ARG49 5.0 38.7 1.0
O A:PHE446 5.0 31.7 1.0

Sodium binding site 2 out of 3 in 5zp3

Go back to Sodium Binding Sites List in 5zp3
Sodium binding site 2 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 10 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 Ethylamine at pH 10 at 288 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:19.3
occ:1.00
O B:VAL79 2.6 24.9 1.0
O A:HOH1175 2.7 29.6 1.0
OG A:SER562 2.8 30.1 1.0
O A:ALA93 3.1 26.6 1.0
O A:ALA94 3.1 21.2 1.0
OE1 B:GLU22 3.2 38.5 1.0
O B:THR80 3.4 28.1 1.0
NH1 A:ARG148 3.7 45.1 1.0
C B:VAL79 3.8 23.4 1.0
CD B:GLU22 3.8 42.0 1.0
C A:ALA94 3.8 21.4 1.0
CB A:SER562 3.9 27.1 1.0
C B:THR80 3.9 29.5 1.0
CA A:ALA94 4.0 20.9 1.0
O A:HOH834 4.1 36.3 1.0
N B:GLY82 4.1 26.5 1.0
C A:ALA93 4.1 28.0 1.0
CG B:GLU22 4.3 36.7 1.0
CA B:GLY82 4.4 26.2 1.0
CA B:THR80 4.4 28.0 1.0
O A:HOH937 4.5 28.6 1.0
N A:ALA94 4.6 23.0 1.0
N A:SER562 4.6 18.9 1.0
N B:ASN81 4.6 26.3 1.0
N B:THR80 4.6 23.0 1.0
OE2 B:GLU22 4.6 33.2 1.0
C B:ASN81 4.7 31.9 1.0
CA B:VAL79 4.8 22.4 1.0
CZ A:ARG148 4.9 46.7 1.0
CA A:SER562 4.9 23.1 1.0
NE2 A:HIS561 4.9 25.7 1.0
CA B:ASN81 5.0 33.9 1.0

Sodium binding site 3 out of 3 in 5zp3

Go back to Sodium Binding Sites List in 5zp3
Sodium binding site 3 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 10 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 Ethylamine at pH 10 at 288 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:14.9
occ:1.00
OD1 B:ASP581 2.4 22.2 1.0
O B:MET441 2.4 18.4 1.0
OD1 B:ASP440 2.4 19.8 1.0
O B:ILE582 2.6 18.1 1.0
O B:HOH1051 2.7 19.8 1.0
N B:ILE582 3.3 16.3 1.0
N B:MET441 3.4 16.6 1.0
C B:MET441 3.5 15.2 1.0
C B:ILE582 3.5 19.0 1.0
CG B:ASP581 3.6 23.0 1.0
CG B:ASP440 3.7 19.1 1.0
NH2 B:ARG49 3.8 38.1 1.0
C B:ASP581 3.9 18.5 1.0
CD1 B:PHE446 3.9 27.5 1.0
C B:ASP440 3.9 17.6 1.0
CA B:MET441 4.0 18.3 1.0
CA B:ILE582 4.0 16.9 1.0
CA B:ASP581 4.1 21.8 1.0
CE1 B:PHE446 4.2 33.5 1.0
CA B:ASP440 4.4 15.4 1.0
OD2 B:ASP440 4.5 21.8 1.0
CB B:ASP581 4.5 25.1 1.0
OD2 B:ASP581 4.5 27.6 1.0
O B:ASP440 4.5 15.2 1.0
CB B:MET441 4.6 17.8 1.0
N B:ALA442 4.6 15.4 1.0
CB B:ASP440 4.7 17.6 1.0
N B:VAL583 4.7 14.7 1.0
O B:ASP581 4.7 19.2 1.0
CB B:TYR546 4.8 20.9 1.0
CG2 B:VAL583 4.9 18.4 1.0
CG1 B:ILE582 4.9 24.3 1.0
O B:PHE446 5.0 32.2 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 Dec 15 11:53:47 2020

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