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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

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