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Sodium in PDB 5zpp: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 8 at 288 K (3)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 8 at 288 K (3)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 8 at 288 K (3):
1.4.3.21;

Protein crystallography data

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 8 at 288 K (3), PDB code: 5zpp 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) 40.51 / 1.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.019, 64.746, 158.925, 90.00, 117.00, 90.00
R / Rfree (%) 14.4 / 16.9

Other elements in 5zpp:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 8 at 288 K (3) 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 8 at 288 K (3) (pdb code 5zpp). 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 8 at 288 K (3), PDB code: 5zpp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5zpp

Go back to Sodium Binding Sites List in 5zpp
Sodium binding site 1 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 8 at 288 K (3)


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 8 at 288 K (3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:16.3
occ:1.00
 OD1 A:ASP581 2.5 16.3 1.0
O A:MET441 2.5 16.6 1.0
O A:ILE582 2.5 13.7 1.0
OD1 A:ASP440 2.5 14.8 1.0
O A:HOH1092 2.7 14.3 1.0
N A:ILE582 3.2 15.0 1.0
C A:ILE582 3.4 16.4 1.0
N A:MET441 3.4 15.5 1.0
C A:MET441 3.5 14.7 1.0
CG A:ASP581 3.7 25.4 1.0
C A:ASP581 3.7 17.1 1.0
CG A:ASP440 3.8 22.0 1.0
NH2 A:ARG49 3.9 23.1 1.0
CA A:ILE582 3.9 14.5 1.0
C A:ASP440 3.9 15.2 1.0
CA A:MET441 4.0 17.2 1.0
CD1 A:PHE446 4.0 30.6 1.0
CA A:ASP581 4.1 17.7 1.0
CA A:ASP440 4.4 11.8 1.0
CE1 A:PHE446 4.4 33.3 1.0
CB A:ASP581 4.5 21.3 1.0
CB A:MET441 4.6 13.5 1.0
O A:ASP581 4.6 17.6 1.0
N A:VAL583 4.6 11.9 1.0
OD2 A:ASP440 4.6 17.7 1.0
OD2 A:ASP581 4.6 23.2 1.0
O A:ASP440 4.6 14.1 1.0
CB A:ASP440 4.7 12.5 1.0
N A:ALA442 4.7 13.8 1.0
CB A:TYR546 4.8 20.9 1.0
CG2 A:VAL583 4.8 18.3 1.0
CG1 A:ILE582 4.8 17.1 1.0

Sodium binding site 2 out of 3 in 5zpp

Go back to Sodium Binding Sites List in 5zpp
Sodium binding site 2 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 8 at 288 K (3)


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 8 at 288 K (3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:23.8
occ:1.00
 O B:VAL79 2.6 21.5 1.0
OG A:SER562 2.7 25.6 1.0
O A:HOH1127 2.8 27.4 1.0
OE1 B:GLU22 2.9 20.9 0.6
O A:ALA94 3.1 20.1 1.0
O A:ALA93 3.2 23.2 1.0
O B:THR80 3.6 28.7 1.0
NH2 A:ARG148 3.6 49.2 1.0
CD B:GLU22 3.7 26.1 0.6
C B:VAL79 3.8 25.6 1.0
CB A:SER562 3.9 26.9 1.0
C A:ALA94 3.9 22.2 1.0
C B:THR80 4.0 29.4 1.0
N B:GLY82 4.0 22.2 1.0
CA A:ALA94 4.0 16.4 1.0
O A:HOH859 4.1 36.5 1.0
CG B:GLU22 4.2 19.2 0.6
C A:ALA93 4.3 23.0 1.0
CA B:GLY82 4.3 20.4 1.0
CA B:THR80 4.5 24.4 1.0
C B:ASN81 4.6 27.7 1.0
N B:ASN81 4.6 25.1 1.0
OE2 B:GLU22 4.6 25.0 0.6
N A:SER562 4.6 14.7 1.0
OE1 B:GLU22 4.6 25.4 0.4
N B:THR80 4.6 19.2 1.0
O A:HOH933 4.6 27.0 1.0
N A:ALA94 4.7 16.9 1.0
CA B:VAL79 4.8 24.2 1.0
CZ A:ARG148 4.8 45.9 1.0
CA A:SER562 4.9 22.0 1.0
CA B:ASN81 4.9 26.2 1.0

Sodium binding site 3 out of 3 in 5zpp

Go back to Sodium Binding Sites List in 5zpp
Sodium binding site 3 out of 3 in the Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Phenylethylamine at pH 8 at 288 K (3)


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 8 at 288 K (3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:15.9
occ:1.00
 O B:MET441 2.5 15.3 1.0
O B:ILE582 2.5 11.8 1.0
OD1 B:ASP581 2.5 17.1 1.0
OD1 B:ASP440 2.6 15.1 1.0
O B:HOH1078 2.7 13.1 1.0
N B:ILE582 3.2 16.1 1.0
N B:MET441 3.4 16.0 1.0
C B:ILE582 3.4 15.7 1.0
C B:MET441 3.5 13.8 1.0
CG B:ASP581 3.7 24.3 1.0
CG B:ASP440 3.8 24.6 1.0
C B:ASP581 3.8 15.8 1.0
NH2 B:ARG49 3.9 22.7 1.0
C B:ASP440 3.9 13.3 1.0
CA B:ILE582 3.9 15.8 1.0
CA B:MET441 4.0 17.7 1.0
CD1 B:PHE446 4.0 27.2 1.0
CA B:ASP581 4.1 18.7 1.0
CA B:ASP440 4.4 10.5 1.0
CE1 B:PHE446 4.4 27.6 1.0
CB B:ASP581 4.5 18.4 1.0
CB B:MET441 4.5 14.6 1.0
O B:ASP440 4.6 14.7 1.0
OD2 B:ASP581 4.6 22.7 1.0
N B:VAL583 4.6 11.8 1.0
OD2 B:ASP440 4.6 17.2 1.0
O B:ASP581 4.6 16.2 1.0
CB B:ASP440 4.7 14.7 1.0
N B:ALA442 4.7 10.5 1.0
CB B:TYR546 4.8 16.8 1.0
CG1 B:ILE582 4.9 16.0 1.0
CG2 B:VAL583 4.9 16.9 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 01:39:13 2024

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