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Sodium in PDB 5zpt: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 10 at 288 K (2)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 10 at 288 K (2)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 10 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 10 at 288 K (2), PDB code: 5zpt 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) 47.63 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.269, 64.850, 159.119, 90.00, 117.10, 90.00
R / Rfree (%) 16.2 / 19.4

Other elements in 5zpt:

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

Sodium binding site 1 out of 3 in 5zpt

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

b:6.4
occ:1.00
 OD1 A:ASP581 2.4 15.8 1.0
OD2 A:ASP440 2.5 13.0 1.0
O A:MET441 2.5 15.3 1.0
O A:ILE582 2.5 7.8 1.0
O A:HOH1141 2.8 8.2 1.0
N A:ILE582 3.2 11.6 1.0
C A:ILE582 3.5 10.2 1.0
N A:MET441 3.5 6.0 1.0
C A:MET441 3.6 8.8 1.0
CG A:ASP581 3.6 16.3 1.0
CG A:ASP440 3.7 17.2 1.0
NH2 A:ARG49 3.7 15.0 1.0
C A:ASP581 3.8 9.5 1.0
C A:ASP440 4.0 6.1 1.0
CA A:ILE582 4.0 7.9 1.0
CD1 A:PHE446 4.0 26.8 1.0
CA A:MET441 4.0 9.2 1.0
CA A:ASP581 4.1 11.4 1.0
CE1 A:PHE446 4.3 27.7 1.0
CA A:ASP440 4.4 7.2 1.0
CB A:ASP581 4.4 17.7 1.0
OD2 A:ASP581 4.5 19.8 1.0
OD1 A:ASP440 4.5 16.2 1.0
O A:ASP440 4.6 10.9 1.0
CB A:MET441 4.6 8.6 1.0
N A:VAL583 4.6 8.3 1.0
O A:ASP581 4.6 12.3 1.0
CB A:ASP440 4.7 7.8 1.0
N A:ALA442 4.7 8.0 1.0
CB A:TYR546 4.8 14.4 1.0
CG2 A:VAL583 4.8 11.9 1.0
CG1 A:ILE582 4.9 10.7 1.0
CZ A:ARG49 5.0 21.7 1.0

Sodium binding site 2 out of 3 in 5zpt

Go back to Sodium Binding Sites List in 5zpt
Sodium binding site 2 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 10 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 10 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:15.3
occ:1.00
 O B:VAL79 2.6 20.9 1.0
O A:HOH1178 2.7 28.0 1.0
OG A:SER562 2.9 26.9 1.0
O A:ALA93 2.9 27.2 1.0
O A:ALA94 2.9 16.9 1.0
OE1 B:GLU22 3.0 30.1 1.0
O B:THR80 3.5 24.1 1.0
NH1 A:ARG148 3.6 42.0 1.0
CD B:GLU22 3.7 31.5 1.0
C A:ALA94 3.7 16.6 1.0
C B:VAL79 3.8 21.4 1.0
CA A:ALA94 3.9 12.9 1.0
C B:THR80 3.9 27.0 1.0
C A:ALA93 4.0 21.9 1.0
CB A:SER562 4.0 24.4 1.0
N B:GLY82 4.2 19.7 1.0
CG B:GLU22 4.2 22.5 1.0
O A:HOH841 4.2 42.5 1.0
CA B:THR80 4.4 25.2 1.0
N A:ALA94 4.4 17.9 1.0
O A:HOH1003 4.5 27.1 1.0
CA B:GLY82 4.5 19.8 1.0
OE2 B:GLU22 4.5 20.6 1.0
N B:THR80 4.6 15.7 1.0
N B:ASN81 4.6 23.2 1.0
N A:SER562 4.6 12.6 1.0
C B:ASN81 4.7 27.2 1.0
CZ A:ARG148 4.8 49.0 1.0
CA B:VAL79 4.9 19.4 1.0
N A:THR95 4.9 12.9 1.0

Sodium binding site 3 out of 3 in 5zpt

Go back to Sodium Binding Sites List in 5zpt
Sodium binding site 3 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 10 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 10 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:7.4
occ:1.00
 OD1 B:ASP581 2.4 13.7 1.0
O B:MET441 2.4 11.8 1.0
OD1 B:ASP440 2.5 13.0 1.0
O B:ILE582 2.6 8.2 1.0
O B:HOH929 2.7 11.3 1.0
N B:ILE582 3.2 8.3 1.0
N B:MET441 3.5 9.8 1.0
C B:MET441 3.5 11.2 1.0
C B:ILE582 3.5 12.0 1.0
CG B:ASP581 3.6 18.8 1.0
CG B:ASP440 3.7 17.4 1.0
NH2 B:ARG49 3.8 15.5 1.0
C B:ASP581 3.8 10.2 1.0
CD1 B:PHE446 3.9 21.8 1.0
C B:ASP440 3.9 8.5 1.0
CA B:ILE582 4.0 12.7 1.0
CA B:MET441 4.0 11.2 1.0
CA B:ASP581 4.1 11.8 1.0
CE1 B:PHE446 4.3 26.5 1.0
CA B:ASP440 4.4 9.8 1.0
CB B:ASP581 4.4 17.2 1.0
OD2 B:ASP581 4.5 20.5 1.0
O B:ASP440 4.5 10.7 1.0
OD2 B:ASP440 4.5 11.1 1.0
CB B:MET441 4.6 9.5 1.0
O B:ASP581 4.6 11.4 1.0
N B:ALA442 4.7 8.6 1.0
CB B:ASP440 4.7 11.3 1.0
N B:VAL583 4.7 9.7 1.0
CB B:TYR546 4.8 11.2 1.0
CG1 B:ILE582 5.0 9.9 1.0
CG2 B:VAL583 5.0 6.3 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 01:40:40 2024

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