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Sodium in PDB 2wo0: Edta Treated E. Coli Copper Amine Oxidase

Enzymatic activity of Edta Treated E. Coli Copper Amine Oxidase

All present enzymatic activity of Edta Treated E. Coli Copper Amine Oxidase:
1.4.3.6;

Protein crystallography data

The structure of Edta Treated E. Coli Copper Amine Oxidase, PDB code: 2wo0 was solved by M.A.Smith, P.Pirrat, A.R.Pearson, P.F.Knowles, S.E.V.Phillips, M.J.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.52 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.676, 166.619, 79.834, 90.00, 90.00, 90.00
R / Rfree (%) 18.201 / 24.794

Other elements in 2wo0:

The structure of Edta Treated E. Coli Copper Amine Oxidase also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Edta Treated E. Coli Copper Amine Oxidase (pdb code 2wo0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Edta Treated E. Coli Copper Amine Oxidase, PDB code: 2wo0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2wo0

Go back to Sodium Binding Sites List in 2wo0
Sodium binding site 1 out of 4 in the Edta Treated E. Coli Copper Amine Oxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Edta Treated E. Coli Copper Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1726

b:26.7
occ:1.00
OD1 A:ASP533 2.2 21.6 1.0
OD1 A:ASP535 2.2 23.1 1.0
OD1 A:ASP678 2.4 30.0 1.0
O A:LEU534 2.4 21.5 1.0
O A:ALA679 2.5 26.8 1.0
O A:HOH2227 2.6 21.7 1.0
C A:LEU534 3.2 21.2 1.0
NZ A:LYS133 3.2 22.5 1.0
CG A:ASP533 3.4 20.1 1.0
CG A:ASP535 3.5 22.0 1.0
C A:ALA679 3.6 26.6 1.0
CG A:ASP678 3.6 29.7 1.0
N A:LEU534 3.6 20.2 1.0
N A:ALA679 3.7 27.6 1.0
C A:ASP533 3.9 20.3 1.0
N A:ASP535 3.9 21.2 1.0
CA A:LEU534 4.0 20.8 1.0
CA A:ASP535 4.1 21.2 1.0
OD2 A:ASP533 4.2 25.4 1.0
CA A:ASP533 4.2 19.8 1.0
OD2 A:ASP678 4.3 32.6 1.0
CA A:ALA679 4.3 26.9 1.0
OD2 A:ASP535 4.4 22.4 1.0
C A:ASP678 4.4 28.2 1.0
CB A:ASP535 4.4 20.6 1.0
CB A:ASP533 4.4 19.7 1.0
O A:ASP533 4.4 21.6 1.0
CE A:LYS133 4.6 23.5 1.0
CA A:ASP678 4.6 28.8 1.0
N A:VAL680 4.7 25.5 1.0
CB A:ASP678 4.7 28.7 1.0
O A:GLU539 4.8 24.5 1.0
CB A:GLU539 4.8 25.3 1.0
CG2 A:VAL680 4.8 24.4 1.0
CA A:VAL680 5.0 24.8 1.0

Sodium binding site 2 out of 4 in 2wo0

Go back to Sodium Binding Sites List in 2wo0
Sodium binding site 2 out of 4 in the Edta Treated E. Coli Copper Amine Oxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Edta Treated E. Coli Copper Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1727

b:35.7
occ:1.00
OE2 A:GLU573 2.4 30.9 1.0
O A:TYR667 2.4 30.8 1.0
OE1 A:GLU672 2.8 37.4 1.0
CD A:GLU573 3.1 32.7 1.0
OE1 A:GLU573 3.2 33.0 1.0
C A:TYR667 3.6 31.0 1.0
CD A:GLU672 3.9 37.9 1.0
OE1 A:GLU647 4.0 26.3 1.0
N A:ARG642 4.0 26.3 1.0
CB A:THR641 4.3 25.0 1.0
CA A:TYR667 4.3 31.2 1.0
CG A:GLU672 4.4 34.1 1.0
O A:ARG642 4.5 27.1 1.0
OE2 A:GLU647 4.5 26.5 1.0
N A:SER668 4.5 31.7 1.0
CB A:ARG642 4.6 26.7 1.0
CG A:GLU573 4.6 32.3 1.0
CG2 A:THR641 4.6 23.1 1.0
CA A:SER668 4.6 32.5 1.0
CB A:TYR667 4.7 31.6 1.0
CD A:GLU647 4.7 25.7 1.0
CA A:THR641 4.8 24.9 1.0
CA A:ARG642 4.8 26.9 1.0
C A:THR641 4.9 25.6 1.0
OE2 A:GLU672 5.0 39.1 1.0

Sodium binding site 3 out of 4 in 2wo0

Go back to Sodium Binding Sites List in 2wo0
Sodium binding site 3 out of 4 in the Edta Treated E. Coli Copper Amine Oxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Edta Treated E. Coli Copper Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1727

b:25.8
occ:1.00
OD1 B:ASP533 2.1 19.0 1.0
OD1 B:ASP535 2.2 19.0 1.0
O B:ALA679 2.4 25.9 1.0
O B:LEU534 2.4 20.8 1.0
OD1 B:ASP678 2.5 32.0 1.0
O B:HOH2152 3.0 33.6 1.0
C B:LEU534 3.2 20.1 1.0
CG B:ASP533 3.3 20.9 1.0
NZ B:LYS133 3.3 24.7 1.0
CG B:ASP535 3.5 20.7 1.0
C B:ALA679 3.5 26.0 1.0
C B:ASP533 3.6 20.1 1.0
N B:LEU534 3.6 19.4 1.0
CG B:ASP678 3.7 30.4 1.0
N B:ALA679 3.8 27.8 1.0
N B:ASP535 3.9 20.3 1.0
O B:ASP533 3.9 20.5 1.0
CA B:LEU534 4.0 19.6 1.0
CA B:ASP533 4.1 20.1 1.0
OD2 B:ASP533 4.1 22.3 1.0
CA B:ASP535 4.2 20.4 1.0
CA B:ALA679 4.3 26.2 1.0
OD2 B:ASP678 4.3 29.8 1.0
CB B:ASP533 4.3 19.9 1.0
OD2 B:ASP535 4.3 23.6 1.0
CB B:ASP535 4.4 19.9 1.0
C B:ASP678 4.5 28.7 1.0
CE B:LYS133 4.5 26.7 1.0
N B:VAL680 4.6 26.1 1.0
CA B:ASP678 4.7 29.2 1.0
CB B:ASP678 4.8 29.3 1.0
CA B:VAL680 4.9 25.5 1.0
CG2 B:VAL680 4.9 25.4 1.0
O B:GLU539 5.0 27.7 1.0
CB B:GLU539 5.0 28.3 1.0

Sodium binding site 4 out of 4 in 2wo0

Go back to Sodium Binding Sites List in 2wo0
Sodium binding site 4 out of 4 in the Edta Treated E. Coli Copper Amine Oxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Edta Treated E. Coli Copper Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1728

b:40.1
occ:1.00
O B:TYR667 2.2 33.8 1.0
OE2 B:GLU672 2.3 46.2 1.0
OE2 B:GLU573 2.5 35.7 1.0
OE1 B:GLU573 2.9 40.2 1.0
CD B:GLU573 3.0 37.3 1.0
C B:TYR667 3.4 33.5 1.0
CD B:GLU672 3.5 45.7 1.0
OE1 B:GLU647 4.2 35.1 1.0
CA B:TYR667 4.2 32.7 1.0
OE2 B:GLU647 4.2 38.5 1.0
CG B:GLU672 4.3 43.1 1.0
N B:SER668 4.3 34.4 1.0
CA B:SER668 4.3 36.1 1.0
OE1 B:GLU672 4.4 47.9 1.0
CG B:GLU573 4.5 35.1 1.0
CB B:THR641 4.5 28.6 1.0
N B:ARG642 4.5 30.6 1.0
CD B:GLU647 4.6 36.8 1.0
CB B:TYR667 4.7 32.1 1.0
CB B:GLU672 4.8 40.2 1.0
CB B:ARG642 4.8 30.7 1.0
CG2 B:THR641 4.9 28.9 1.0

Reference:

M.A.Smith, P.Pirrat, A.R.Pearson, C.R.Kurtis, T.G.Gaule, P.F.Knowles, S.E.Phillips, M.J.Mcpherson. Exploring the Roles of the Metal Ions in Escherichia Coli Copper Amine Oxidase. Biochemistry V. 49 1268 2010.
ISSN: ISSN 0006-2960
PubMed: 20052994
DOI: 10.1021/BI901738K
Page generated: Tue Dec 15 05:57:57 2020

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