Atomistry » Sodium » PDB 5zo8-5zu6 » 5zp1
Atomistry »
  Sodium »
    PDB 5zo8-5zu6 »
      5zp1 »

Sodium in PDB 5zp1: Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 9 at 288 K (1)

Enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 9 at 288 K (1)

All present enzymatic activity of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 9 at 288 K (1):
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 (1), PDB code: 5zp1 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) 40.49 / 1.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.665, 64.739, 158.920, 90.00, 117.16, 90.00
R / Rfree (%) 14.6 / 16.6

Other elements in 5zp1:

The structure of Copper Amine Oxidase From Arthrobacter Globiformis Anaerobically Reduced By Ethylamine at pH 9 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 Ethylamine at pH 9 at 288 K (1) (pdb code 5zp1). 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 (1), PDB code: 5zp1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5zp1

Go back to Sodium Binding Sites List in 5zp1
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 (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 Ethylamine at pH 9 at 288 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:12.2
occ:1.00
OD1 A:ASP581 2.4 20.2 1.0
OD1 A:ASP440 2.5 18.6 1.0
O A:MET441 2.5 16.7 1.0
O A:ILE582 2.5 15.7 1.0
O A:HOH1041 2.8 17.5 1.0
N A:ILE582 3.2 14.4 1.0
C A:ILE582 3.5 16.7 1.0
N A:MET441 3.5 15.3 1.0
C A:MET441 3.5 13.3 1.0
CG A:ASP581 3.6 25.8 1.0
CG A:ASP440 3.7 19.9 1.0
C A:ASP581 3.8 17.1 1.0
NH2 A:ARG49 3.8 36.1 1.0
C A:ASP440 3.9 14.8 1.0
CA A:ILE582 3.9 14.8 1.0
CD1 A:PHE446 4.0 31.0 1.0
CA A:MET441 4.0 14.8 1.0
CA A:ASP581 4.0 17.1 1.0
CE1 A:PHE446 4.4 28.4 1.0
CA A:ASP440 4.4 13.4 1.0
CB A:ASP581 4.4 20.5 1.0
OD2 A:ASP440 4.5 19.7 1.0
OD2 A:ASP581 4.5 28.0 1.0
O A:ASP440 4.5 15.2 1.0
O A:ASP581 4.6 17.9 1.0
CB A:MET441 4.6 16.8 1.0
N A:VAL583 4.6 12.7 1.0
CB A:ASP440 4.6 13.5 1.0
N A:ALA442 4.7 14.7 1.0
CB A:TYR546 4.8 21.5 1.0
CG2 A:VAL583 4.9 15.2 1.0
CG1 A:ILE582 4.9 16.1 1.0
O A:PHE446 5.0 29.5 1.0

Sodium binding site 2 out of 3 in 5zp1

Go back to Sodium Binding Sites List in 5zp1
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 (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 Ethylamine at pH 9 at 288 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:19.0
occ:1.00
O B:VAL79 2.5 24.4 1.0
O A:HOH1176 2.7 32.7 1.0
OG A:SER562 2.8 27.2 1.0
O A:ALA93 3.0 23.8 1.0
O A:ALA94 3.1 20.1 1.0
OE1 B:GLU22 3.1 23.0 0.5
O B:THR80 3.3 26.0 1.0
NH1 A:ARG148 3.5 50.9 1.0
C B:VAL79 3.8 23.3 1.0
C A:ALA94 3.8 17.9 1.0
C B:THR80 3.8 22.9 1.0
CD B:GLU22 3.8 25.7 0.5
CB A:SER562 3.9 21.6 1.0
CA A:ALA94 3.9 16.4 1.0
C A:ALA93 4.1 25.8 1.0
N B:GLY82 4.1 22.8 1.0
O A:HOH828 4.2 36.8 1.0
CG B:GLU22 4.3 19.4 0.5
CA B:THR80 4.3 23.2 1.0
CA B:GLY82 4.4 26.6 1.0
O A:HOH1002 4.4 28.7 1.0
N A:ALA94 4.5 19.6 1.0
N B:ASN81 4.5 24.7 1.0
N B:THR80 4.5 21.6 1.0
N A:SER562 4.6 19.0 1.0
OE2 B:GLU22 4.6 27.6 0.5
C B:ASN81 4.6 23.9 1.0
OE2 B:GLU22 4.7 28.6 0.5
CZ A:ARG148 4.8 51.9 1.0
CA B:VAL79 4.8 20.6 1.0
CA A:SER562 4.9 20.6 1.0
CA B:ASN81 4.9 28.9 1.0

Sodium binding site 3 out of 3 in 5zp1

Go back to Sodium Binding Sites List in 5zp1
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 (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 Ethylamine at pH 9 at 288 K (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:14.2
occ:1.00
OD1 B:ASP581 2.4 16.1 1.0
O B:MET441 2.5 14.6 1.0
O B:ILE582 2.5 12.6 1.0
OD1 B:ASP440 2.5 16.3 1.0
O B:HOH1071 2.6 16.4 1.0
N B:ILE582 3.2 13.5 1.0
C B:ILE582 3.4 15.3 1.0
N B:MET441 3.5 17.3 1.0
C B:MET441 3.5 13.2 1.0
CG B:ASP581 3.7 19.1 1.0
CG B:ASP440 3.7 18.4 1.0
C B:ASP581 3.8 15.4 1.0
NH2 B:ARG49 3.9 35.7 1.0
CA B:ILE582 3.9 13.9 1.0
C B:ASP440 4.0 15.2 1.0
CD1 B:PHE446 4.0 25.7 1.0
CA B:MET441 4.0 14.9 1.0
CA B:ASP581 4.1 17.9 1.0
CE1 B:PHE446 4.4 25.0 1.0
CA B:ASP440 4.4 12.0 1.0
CB B:ASP581 4.5 18.4 1.0
CB B:MET441 4.5 13.9 1.0
OD2 B:ASP440 4.5 17.9 1.0
OD2 B:ASP581 4.6 22.7 1.0
O B:ASP440 4.6 15.0 1.0
N B:VAL583 4.6 11.5 1.0
O B:ASP581 4.6 17.1 1.0
CB B:ASP440 4.7 13.0 1.0
N B:ALA442 4.7 13.7 1.0
CG1 B:ILE582 4.8 18.8 1.0
CB B:TYR546 4.8 17.2 1.0
CG2 B:VAL583 4.9 15.9 1.0
O B:PHE446 5.0 26.8 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 Dec 15 11:53:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy