Sodium in PDB 2vnz: Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A.

All present enzymatic activity of Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A.:
1.11.11.1;

The structure of Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A., PDB code: 2vnz was solved by C.L.Metcalfe, S.K.Badyal, E.L.Raven, P.C.E.Moody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.18 / 1.30
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.780, 81.780, 75.244, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 19.9

The structure of Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A. also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A. (pdb code 2vnz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A., PDB code: 2vnz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A. within 5.0Å range: probe atom residue distance (Å) B Occ X:Na9252 b:9.7 occ:1.00 O X:THR164 2.2 9.2 1.0 O X:HOH2181 2.3 17.6 1.0 O X:ILE185 2.4 7.1 1.0 O X:ASN182 2.4 8.8 1.0 OG1 X:THR180 2.7 9.6 1.0 OG1 X:THR164 3.1 14.5 1.0 C X:THR164 3.3 8.8 1.0 C X:ASN182 3.4 9.5 1.0 C X:ILE185 3.5 7.1 1.0 CB X:THR180 3.6 9.6 1.0 CG2 X:THR180 3.9 9.6 1.0 OD1 X:ASP187 4.0 13.9 1.0 N X:ILE185 4.0 6.9 1.0 CA X:THR164 4.1 9.4 1.0 CB X:THR164 4.1 10.2 1.0 CA X:ILE185 4.2 7.5 1.0 CA X:PRO183 4.2 9.1 1.0 N X:PRO183 4.2 9.2 1.0 CA X:ASN182 4.2 10.6 1.0 CB X:ASN182 4.3 11.4 1.0 CB X:ILE185 4.3 7.8 1.0 N X:ILE165 4.4 7.8 1.0 N X:ASN182 4.5 10.5 1.0 C X:PRO183 4.6 8.5 1.0 CA X:ILE165 4.6 7.6 1.0 N X:PHE186 4.6 6.6 1.0 CG2 X:THR164 4.6 9.3 1.0 CG2 X:ILE165 4.6 7.9 1.0 O X:HOH2174 4.7 29.1 1.0 O X:HOH2158 4.7 9.0 1.0 N X:ASP187 4.8 8.8 1.0 CG X:ASP187 4.8 12.7 1.0 N X:LEU184 4.8 8.0 1.0 O X:HOH2180 4.9 36.1 1.0 CA X:PHE186 4.9 7.3 1.0 CG2 X:ILE185 4.9 8.8 1.0 CB X:SER189 5.0 11.8 1.0 CA X:THR180 5.0 9.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dithinonite Reduced Soybean Ascorbate Peroxidase Mutant W41A. within 5.0Å range: probe atom residue distance (Å) B Occ X:Na9253 b:13.7 occ:1.00 O X:HOH2063 1.6 19.8 1.0 OG X:SER43 1.7 12.7 1.0 O X:HOH2048 1.8 15.7 1.0 CB X:SER43 2.7 10.3 1.0 O X:HOH2047 3.7 13.5 1.0 CB X:TYR97 3.7 6.2 1.0 CD2 X:TYR97 3.8 8.8 1.0 NE2 X:GLN98 3.8 6.6 1.0 CA X:SER43 4.0 10.2 1.0 N X:GLY58 4.0 10.4 1.0 CA X:PRO56 4.0 9.5 1.0 CG2 X:ILE60 4.1 14.5 1.0 C X:PRO56 4.2 9.8 1.0 CG X:TYR97 4.3 7.0 1.0 O X:ALA94 4.4 7.1 1.0 CA X:GLY58 4.4 11.5 1.0 CA X:ALA94 4.4 7.1 1.0 N X:PHE57 4.4 9.4 1.0 CB X:PRO56 4.4 9.7 1.0 C X:SER43 4.5 10.1 1.0 O X:PRO56 4.7 10.7 1.0 CD X:GLN98 4.9 5.6 1.0 CE2 X:TYR97 4.9 9.8 1.0 C X:ALA94 4.9 6.8 1.0 CG X:GLN98 4.9 5.9 1.0 O X:SER43 4.9 10.9 1.0 O X:TYR93 5.0 7.3 1.0 CB X:ILE60 5.0 13.9 1.0 N X:ALA44 5.0 9.3 1.0

S.K.Badyal, C.L.Metcalfe, J.Basran, I.Efimov, P.C.E.Moody, E.L.Raven. Iron Oxidation State Modulates Active Site Structure in A Heme Peroxidase. Biochemistry V. 47 4403 2008.
ISSN: ISSN 0006-2960
PubMed: 18351739
DOI: 10.1021/BI702337N