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Sodium in PDB 5zp2: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 9 at 288 K (2)

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

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine 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 Ethylamine at pH 9 at 288 K (2), PDB code: 5zp2 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) 34.64 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.765, 64.920, 158.953, 90.00, 117.16, 90.00
R / Rfree (%) 15.1 / 17.5

Other elements in 5zp2:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine 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 Ethylamine at pH 9 at 288 K (2) (pdb code 5zp2). 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 9 at 288 K (2), PDB code: 5zp2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5zp2

Go back to Sodium Binding Sites List in 5zp2
Sodium binding site 1 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine 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 Ethylamine at pH 9 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:13.7
occ:1.00
 OD1 A:ASP581 2.4 20.3 1.0
OD1 A:ASP440 2.4 18.9 1.0
O A:MET441 2.4 16.7 1.0
O A:ILE582 2.5 18.6 1.0
O A:HOH1009 2.8 18.4 1.0
N A:ILE582 3.2 16.4 1.0
N A:MET441 3.5 16.7 1.0
C A:ILE582 3.5 18.3 1.0
C A:MET441 3.5 14.2 1.0
CG A:ASP581 3.6 26.3 1.0
CG A:ASP440 3.7 20.4 1.0
NH2 A:ARG49 3.8 39.7 1.0
C A:ASP581 3.8 19.6 1.0
C A:ASP440 3.9 16.0 1.0
CA A:ILE582 3.9 15.9 1.0
CD1 A:PHE446 4.0 28.8 1.0
CA A:MET441 4.0 15.6 1.0
CA A:ASP581 4.1 16.6 1.0
CE1 A:PHE446 4.3 25.9 1.0
CA A:ASP440 4.4 12.8 1.0
CB A:ASP581 4.4 24.5 1.0
OD2 A:ASP440 4.5 20.6 1.0
OD2 A:ASP581 4.5 27.1 1.0
O A:ASP440 4.5 15.6 1.0
CB A:MET441 4.6 15.6 1.0
O A:ASP581 4.6 19.7 1.0
CB A:ASP440 4.6 13.4 1.0
N A:VAL583 4.6 14.5 1.0
N A:ALA442 4.7 14.9 1.0
CG2 A:VAL583 4.8 18.9 1.0
CB A:TYR546 4.8 22.9 1.0
CG1 A:ILE582 4.9 19.6 1.0
O A:PHE446 5.0 30.3 1.0

Sodium binding site 2 out of 3 in 5zp2

Go back to Sodium Binding Sites List in 5zp2
Sodium binding site 2 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine 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 Ethylamine at pH 9 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:20.6
occ:1.00
 O B:VAL79 2.6 23.1 1.0
O A:HOH1115 2.7 33.4 1.0
OG A:SER562 2.8 28.0 1.0
O A:ALA93 3.0 23.9 1.0
O A:ALA94 3.0 19.3 1.0
OE1 B:GLU22 3.2 26.7 0.5
O B:THR80 3.4 27.3 1.0
NH1 A:ARG148 3.5 53.0 1.0
C A:ALA94 3.8 18.8 1.0
C B:VAL79 3.8 23.8 1.0
C B:THR80 3.9 26.4 1.0
CA A:ALA94 3.9 16.6 1.0
CD B:GLU22 3.9 25.8 0.5
CB A:SER562 3.9 27.7 1.0
C A:ALA93 4.1 24.0 1.0
N B:GLY82 4.2 25.2 1.0
O A:HOH860 4.3 44.2 1.0
CG B:GLU22 4.3 20.1 0.5
O A:HOH972 4.3 28.1 1.0
CA B:THR80 4.4 27.2 1.0
CA B:GLY82 4.4 23.4 1.0
N A:ALA94 4.5 19.9 1.0
N A:SER562 4.5 17.1 1.0
OE2 B:GLU22 4.5 27.7 0.5
N B:ASN81 4.6 24.7 1.0
N B:THR80 4.6 23.6 1.0
C B:ASN81 4.7 31.3 1.0
OE2 B:GLU22 4.7 30.3 0.5
CZ A:ARG148 4.8 53.9 1.0
CA B:VAL79 4.8 26.5 1.0
CA A:SER562 4.9 23.3 1.0
CA B:ASN81 4.9 28.0 1.0

Sodium binding site 3 out of 3 in 5zp2

Go back to Sodium Binding Sites List in 5zp2
Sodium binding site 3 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine 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 Ethylamine at pH 9 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:15.5
occ:1.00
 O B:MET441 2.5 15.2 1.0
OD1 B:ASP581 2.5 17.4 1.0
O B:ILE582 2.5 15.1 1.0
OD1 B:ASP440 2.6 17.6 1.0
O B:HOH1072 2.6 17.0 1.0
N B:ILE582 3.1 14.5 1.0
C B:ILE582 3.4 15.5 1.0
N B:MET441 3.5 15.6 1.0
C B:MET441 3.5 16.8 1.0
CG B:ASP581 3.7 22.5 1.0
C B:ASP581 3.7 19.1 1.0
CG B:ASP440 3.8 22.0 1.0
CA B:ILE582 3.9 15.7 1.0
NH2 B:ARG49 3.9 38.5 1.0
CD1 B:PHE446 3.9 28.8 1.0
C B:ASP440 4.0 17.3 1.0
CA B:MET441 4.0 17.5 1.0
CA B:ASP581 4.0 20.3 1.0
CE1 B:PHE446 4.3 31.1 1.0
CA B:ASP440 4.4 12.1 1.0
CB B:ASP581 4.5 20.2 1.0
CB B:MET441 4.6 16.2 1.0
O B:ASP581 4.6 20.5 1.0
OD2 B:ASP581 4.6 24.3 1.0
N B:VAL583 4.6 12.7 1.0
OD2 B:ASP440 4.6 18.5 1.0
O B:ASP440 4.6 14.2 1.0
N B:ALA442 4.7 13.5 1.0
CB B:ASP440 4.7 14.8 1.0
CB B:TYR546 4.8 18.5 1.0
CG1 B:ILE582 4.8 22.5 1.0
CG2 B:VAL583 4.8 17.5 1.0
O B:PHE446 4.9 29.7 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 01:34:51 2024

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