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

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

The structure of Edta Treated E. Coli Copper Amine Oxidase, PDB code: 2wof 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)	19.96 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	135.079, 166.880, 79.802, 90.00, 90.00, 90.00
R / Rfree (%)	16.686 / 22.041

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

Copper

(Cu)

2 atoms

The binding sites of Sodium atom in the Edta Treated E. Coli Copper Amine Oxidase (pdb code 2wof). 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: 2wof:
Jump to Sodium binding site number: 1; 2; 3; 4;

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:Na1727 b:30.9 occ:1.00 OE2 A:GLU573 2.3 33.9 1.0 O A:TYR667 2.3 30.1 1.0 O A:HOH2554 2.5 39.6 1.0 OE1 A:GLU672 2.7 42.5 1.0 OE1 A:GLU573 2.9 33.0 1.0 CD A:GLU573 3.0 34.9 1.0 O A:HOH2574 3.1 43.2 1.0 C A:TYR667 3.5 32.9 1.0 CD A:GLU672 3.8 43.8 1.0 OE1 A:GLU647 4.2 29.3 1.0 CG A:GLU672 4.2 40.6 1.0 N A:ARG642 4.3 30.0 1.0 CA A:TYR667 4.4 32.7 1.0 N A:SER668 4.5 34.7 1.0 CG A:GLU573 4.5 34.5 1.0 CB A:THR641 4.5 30.9 1.0 CA A:SER668 4.5 36.1 1.0 OE2 A:GLU647 4.6 33.9 1.0 CB A:ARG642 4.6 31.6 1.0 CB A:TYR667 4.8 32.6 1.0 O A:ARG642 4.8 29.0 1.0 CG2 A:THR641 4.8 31.5 1.0 CD A:GLU647 4.8 32.6 1.0 OE2 A:GLU672 4.9 47.8 1.0 CA A:ARG642 5.0 31.0 1.0

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:Na1728 b:26.8 occ:1.00 O A:ALA679 2.3 28.1 1.0 OD1 A:ASP533 2.4 25.6 1.0 OD1 A:ASP678 2.4 29.8 1.0 OD1 A:ASP535 2.4 29.1 1.0 O A:LEU534 2.4 25.9 1.0 O A:HOH2477 2.7 22.4 1.0 C A:LEU534 3.3 26.4 1.0 C A:ALA679 3.4 28.2 1.0 N A:ALA679 3.5 29.9 1.0 NZ A:LYS133 3.5 21.6 1.0 CG A:ASP533 3.6 25.3 1.0 CG A:ASP678 3.6 31.9 1.0 CG A:ASP535 3.7 28.2 1.0 N A:LEU534 3.9 26.9 1.0 C A:ASP533 4.0 25.9 1.0 CA A:ALA679 4.0 29.5 1.0 N A:ASP535 4.1 27.1 1.0 C A:ASP678 4.1 30.4 1.0 CA A:ASP535 4.2 26.8 1.0 CA A:LEU534 4.2 26.4 1.0 CA A:ASP533 4.3 25.5 1.0 CA A:ASP678 4.4 30.6 1.0 OD2 A:ASP533 4.4 26.4 1.0 OD2 A:ASP678 4.4 32.9 1.0 N A:VAL680 4.5 27.9 1.0 O A:ASP533 4.5 24.7 1.0 CB A:ASP533 4.6 26.1 1.0 CB A:ASP535 4.6 26.3 1.0 OD2 A:ASP535 4.6 25.8 1.0 CB A:ASP678 4.6 31.2 1.0 O A:GLU539 4.7 31.4 1.0 CE A:LYS133 4.8 28.2 1.0 CG2 A:VAL680 4.8 28.3 1.0 CA A:VAL680 4.9 28.4 1.0 CB A:GLU539 4.9 32.8 1.0 CB A:ALA679 4.9 29.6 1.0 O A:ASP678 5.0 29.6 1.0

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:Na1728 b:36.7 occ:1.00 OE2 B:GLU573 2.2 32.7 1.0 O B:TYR667 2.4 36.6 1.0 OE2 B:GLU672 2.6 50.6 1.0 O B:HOH2417 2.7 43.2 1.0 OE1 B:GLU573 2.7 34.2 1.0 O B:HOH2378 2.8 47.5 1.0 CD B:GLU573 2.8 38.1 1.0 CD B:GLU672 3.5 49.9 1.0 C B:TYR667 3.6 37.6 1.0 CG B:GLU672 3.7 46.1 1.0 CG B:GLU573 4.3 39.2 1.0 CA B:SER668 4.4 38.2 1.0 CB B:GLU672 4.4 42.7 1.0 N B:ARG642 4.4 35.8 1.0 OE1 B:GLU647 4.5 39.9 1.0 N B:SER668 4.5 37.5 1.0 CA B:TYR667 4.5 37.3 1.0 CB B:THR641 4.6 34.7 1.0 CB B:ARG642 4.6 37.3 1.0 OE1 B:GLU672 4.7 51.2 1.0 OE2 B:GLU647 4.8 43.0 1.0 CG2 B:THR641 4.9 37.9 1.0 CB B:TYR667 4.9 36.8 1.0 O B:ARG642 5.0 36.2 1.0

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:Na1729 b:30.2 occ:1.00 OD1 B:ASP533 2.2 27.9 1.0 O B:ALA679 2.3 31.2 1.0 O B:LEU534 2.4 27.0 1.0 OD1 B:ASP535 2.4 31.6 1.0 OD1 B:ASP678 2.5 31.3 1.0 O B:HOH2353 2.5 29.2 1.0 C B:LEU534 3.3 28.4 1.0 C B:ALA679 3.4 31.4 1.0 N B:ALA679 3.5 32.6 1.0 CG B:ASP533 3.5 28.0 1.0 NZ B:LYS133 3.6 30.7 1.0 CG B:ASP535 3.6 29.6 1.0 N B:LEU534 3.7 28.5 1.0 CG B:ASP678 3.7 32.9 1.0 C B:ASP533 3.9 28.2 1.0 CA B:ALA679 4.0 31.7 1.0 N B:ASP535 4.0 28.5 1.0 CA B:LEU534 4.1 27.9 1.0 C B:ASP678 4.2 33.1 1.0 CA B:ASP535 4.3 28.9 1.0 CA B:ASP533 4.3 27.6 1.0 OD2 B:ASP533 4.3 25.8 1.0 O B:ASP533 4.4 28.8 1.0 OD2 B:ASP678 4.4 33.3 1.0 OD2 B:ASP535 4.5 29.8 1.0 N B:VAL680 4.5 31.4 1.0 CA B:ASP678 4.5 32.2 1.0 CB B:ASP533 4.5 27.9 1.0 CB B:ASP535 4.6 29.4 1.0 CB B:ASP678 4.7 32.5 1.0 CB B:ALA679 4.8 31.9 1.0 O B:GLU539 4.8 35.7 1.0 CA B:VAL680 4.8 31.5 1.0 CE B:LYS133 4.9 32.3 1.0 CG2 B:VAL680 4.9 32.1 1.0

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