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Sodium in PDB 5zpm: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 K (2)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 at 288 K (2)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 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 7 at 288 K (2), PDB code: 5zpm 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) 36.68 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.866, 64.320, 158.903, 90.00, 116.92, 90.00
R / Rfree (%) 14.9 / 17.1

Other elements in 5zpm:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 7 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 7 at 288 K (2) (pdb code 5zpm). 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 (2), PDB code: 5zpm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5zpm

Go back to Sodium Binding Sites List in 5zpm
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 (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 7 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:12.8
occ:1.00
 OD1 A:ASP581 2.4 19.5 1.0
OD1 A:ASP440 2.4 17.5 1.0
O A:MET441 2.5 18.9 1.0
O A:ILE582 2.6 15.6 1.0
O A:HOH1039 2.8 15.6 1.0
N A:ILE582 3.2 15.0 1.0
N A:MET441 3.5 14.9 1.0
C A:ILE582 3.5 14.9 1.0
C A:MET441 3.6 15.8 1.0
CG A:ASP581 3.6 22.0 1.0
CG A:ASP440 3.7 18.4 1.0
NH2 A:ARG49 3.8 33.9 1.0
C A:ASP581 3.8 18.5 1.0
CD1 A:PHE446 3.9 32.6 1.0
C A:ASP440 3.9 15.8 1.0
CA A:ILE582 4.0 15.4 1.0
CA A:ASP581 4.1 17.4 1.0
CA A:MET441 4.1 13.8 1.0
CE1 A:PHE446 4.2 32.5 1.0
CA A:ASP440 4.4 12.2 1.0
CB A:ASP581 4.4 19.7 1.0
OD2 A:ASP581 4.5 26.7 1.0
OD2 A:ASP440 4.5 18.9 1.0
O A:ASP440 4.6 16.4 1.0
CB A:MET441 4.6 16.4 1.0
O A:ASP581 4.6 19.1 1.0
CB A:ASP440 4.6 14.2 1.0
N A:VAL583 4.7 12.3 1.0
N A:ALA442 4.7 16.0 1.0
CB A:TYR546 4.8 20.7 1.0
CG2 A:VAL583 4.9 15.7 1.0
CG1 A:ILE582 4.9 20.3 1.0

Sodium binding site 2 out of 3 in 5zpm

Go back to Sodium Binding Sites List in 5zpm
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 (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 7 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:19.5
occ:1.00
 O B:VAL79 2.5 25.8 1.0
O A:HOH1156 2.7 32.1 1.0
OG A:SER562 2.7 35.1 1.0
O A:ALA94 3.0 22.8 1.0
O A:ALA93 3.0 28.7 1.0
OE1 B:GLU22 3.1 24.2 0.5
O B:THR80 3.4 30.0 1.0
NH2 A:ARG148 3.5 56.8 1.0
C B:VAL79 3.8 25.3 1.0
C B:THR80 3.8 28.1 1.0
CD B:GLU22 3.8 29.4 0.5
C A:ALA94 3.8 21.1 1.0
CB A:SER562 3.9 31.3 1.0
CA A:ALA94 3.9 21.9 1.0
C A:ALA93 4.1 28.9 1.0
N B:GLY82 4.2 26.7 1.0
CA B:THR80 4.3 26.8 1.0
O A:HOH818 4.3 41.4 1.0
CG B:GLU22 4.3 23.4 0.5
O A:HOH942 4.5 31.0 1.0
CA B:GLY82 4.5 30.6 1.0
N B:ASN81 4.5 27.3 1.0
N B:THR80 4.5 24.0 1.0
N A:ALA94 4.5 24.2 1.0
N A:SER562 4.5 21.4 1.0
OE1 B:GLU22 4.6 30.0 0.5
OE2 B:GLU22 4.6 29.4 0.5
C B:ASN81 4.6 29.5 1.0
CZ A:ARG148 4.8 52.0 1.0
CA B:VAL79 4.8 23.8 1.0
CA A:SER562 4.9 27.4 1.0
CA B:ASN81 4.9 28.9 1.0

Sodium binding site 3 out of 3 in 5zpm

Go back to Sodium Binding Sites List in 5zpm
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 (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 7 at 288 K (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:11.9
occ:1.00
 OD1 B:ASP581 2.4 19.6 1.0
OD1 B:ASP440 2.4 17.4 1.0
O B:MET441 2.4 16.5 1.0
O B:ILE582 2.6 14.3 1.0
O B:HOH1008 2.8 16.3 1.0
N B:ILE582 3.3 13.5 1.0
N B:MET441 3.5 13.1 1.0
C B:MET441 3.5 15.3 1.0
C B:ILE582 3.5 14.9 1.0
CG B:ASP581 3.6 21.4 1.0
CG B:ASP440 3.6 17.8 1.0
NH2 B:ARG49 3.8 31.4 1.0
C B:ASP581 3.8 16.4 1.0
CD1 B:PHE446 3.9 26.8 1.0
C B:ASP440 3.9 12.5 1.0
CA B:MET441 4.0 13.7 1.0
CA B:ILE582 4.0 14.1 1.0
CA B:ASP581 4.1 18.2 1.0
CE1 B:PHE446 4.2 27.7 1.0
CA B:ASP440 4.3 12.1 1.0
OD2 B:ASP440 4.4 17.5 1.0
CB B:ASP581 4.5 18.9 1.0
OD2 B:ASP581 4.5 23.7 1.0
O B:ASP440 4.5 15.4 1.0
CB B:MET441 4.6 15.4 1.0
CB B:ASP440 4.6 13.9 1.0
N B:VAL583 4.7 12.2 1.0
O B:ASP581 4.7 17.9 1.0
N B:ALA442 4.7 13.2 1.0
CB B:TYR546 4.8 18.9 1.0
CG2 B:VAL583 4.9 16.6 1.0
CG1 B:ILE582 5.0 20.2 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 Oct 8 01:38:40 2024

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