Sodium in PDB 3ply: Structure of Oxidized P96G Mutant of Amicyanin

The structure of Structure of Oxidized P96G Mutant of Amicyanin, PDB code: 3ply was solved by N.Sukumar, V.L.Davidson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.279, 97.279, 109.875, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 29.1

The structure of Structure of Oxidized P96G Mutant of Amicyanin also contains other interesting chemical elements:

Potassium	(K)	1 atom
Copper	(Cu)	4 atoms

The binding sites of Sodium atom in the Structure of Oxidized P96G Mutant of Amicyanin (pdb code 3ply). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Oxidized P96G Mutant of Amicyanin, PDB code: 3ply:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Oxidized P96G Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Oxidized P96G Mutant of Amicyanin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:58.9 occ:1.00 O A:SER79 2.8 54.4 1.0 O A:SER7 2.8 50.5 1.0 N A:SER79 3.0 47.9 1.0 N A:SER7 3.0 63.5 1.0 C A:SER79 3.5 66.2 1.0 CA A:SER79 3.5 57.1 1.0 CD1 A:TYR78 3.5 62.6 1.0 C A:SER7 3.5 55.7 1.0 CA A:SER7 3.5 66.5 1.0 CB A:SER7 3.7 68.9 1.0 CB A:SER79 3.7 60.0 1.0 CE1 A:TYR78 3.7 48.9 1.0 CD A:PRO6 3.8 68.6 1.0 N A:PRO6 3.9 62.1 1.0 CG2 A:ILE5 3.9 57.7 1.0 CB A:PRO6 4.0 73.4 1.0 C A:PRO6 4.0 71.4 1.0 C A:TYR78 4.1 62.6 1.0 CE1 A:PHE11 4.2 51.8 1.0 CG A:TYR78 4.2 47.5 1.0 CA A:PRO6 4.3 63.7 1.0 CG A:PRO6 4.3 77.4 1.0 CA A:TYR78 4.3 59.6 1.0 OG A:SER79 4.5 66.6 1.0 CZ A:TYR78 4.5 51.9 1.0 C A:ILE5 4.5 63.8 1.0 OG A:SER7 4.6 67.4 1.0 N A:LEU80 4.8 47.1 1.0 CD1 A:PHE11 4.8 58.1 1.0 N A:GLU8 4.8 44.5 1.0 CA A:ILE5 4.8 54.9 1.0 O A:SER9 4.8 58.9 1.0 CB A:TYR78 4.9 51.0 1.0 CD2 A:TYR78 4.9 45.0 1.0

Sodium binding site 2 out of 2 in the Structure of Oxidized P96G Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Oxidized P96G Mutant of Amicyanin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:68.0 occ:1.00 O A:VAL58 2.9 48.3 1.0 O A:ALA65 2.9 56.7 1.0 N A:LEU62 3.1 54.2 1.0 O A:PHE57 3.3 50.6 1.0 N A:LEU67 3.4 49.0 1.0 N A:VAL61 3.7 68.6 1.0 CB A:LEU62 3.7 46.0 1.0 CA A:ALA66 3.7 55.9 1.0 C A:VAL58 3.7 56.9 1.0 N A:GLY63 3.8 66.3 1.0 CB A:PHE57 3.8 48.1 1.0 CA A:LEU62 3.8 52.0 1.0 C A:ALA66 3.8 59.8 1.0 C A:PHE57 3.8 47.5 1.0 C A:ALA65 3.9 55.5 1.0 CB A:VAL61 3.9 56.1 1.0 C A:VAL61 4.0 49.2 1.0 CA A:VAL61 4.0 59.1 1.0 O A:GLY63 4.1 61.8 1.0 C A:LEU62 4.2 72.3 1.0 CB A:LEU67 4.2 44.1 1.0 N A:GLY60 4.2 62.3 1.0 N A:ALA66 4.3 55.2 1.0 CG A:LEU62 4.3 50.6 1.0 CA A:ALA59 4.3 48.7 1.0 N A:ALA59 4.4 49.8 1.0 CA A:LEU67 4.4 46.2 1.0 N A:VAL58 4.4 47.6 1.0 CA A:PHE57 4.5 44.7 1.0 C A:ALA59 4.5 53.5 1.0 CA A:VAL58 4.6 57.1 1.0 C A:GLY60 4.7 72.1 1.0 CA A:GLY63 4.7 53.5 1.0 O A:ALA66 4.8 57.0 1.0 C A:GLY63 4.8 68.2 1.0 CG2 A:VAL61 4.9 46.8 1.0 CB A:ALA66 4.9 46.8 1.0 CD1 A:LEU62 4.9 58.2 1.0 CG1 A:VAL61 5.0 46.0 1.0

M.Choi, N.Sukumar, F.S.Mathews, A.Liu, V.L.Davidson. Proline 96 of the Copper Ligand Loop of Amicyanin Regulates Electron Transfer From Methylamine Dehydrogenase By Positioning Other Residues at the Protein-Protein Interface. Biochemistry V. 50 1265 2011.
ISSN: ISSN 0006-2960
PubMed: 21268585
DOI: 10.1021/BI101794Y