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Sodium in PDB 2vnx: Crystal Structure of Soybean Ascorbate Peroxidase Mutant W41A After Exposure to A High Dose of X-Rays

Enzymatic activity of Crystal Structure of Soybean Ascorbate Peroxidase Mutant W41A After Exposure to A High Dose of X-Rays

All present enzymatic activity of Crystal Structure of Soybean Ascorbate Peroxidase Mutant W41A After Exposure to A High Dose of X-Rays:
1.11.11.1;

Protein crystallography data

The structure of Crystal Structure of Soybean Ascorbate Peroxidase Mutant W41A After Exposure to A High Dose of X-Rays, PDB code: 2vnx 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) 37.80 / 1.50
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.002, 82.002, 75.570, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.9

Other elements in 2vnx:

The structure of Crystal Structure of Soybean Ascorbate Peroxidase Mutant W41A After Exposure to A High Dose of X-Rays also contains other interesting chemical elements:

Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Soybean Ascorbate Peroxidase Mutant W41A After Exposure to A High Dose of X-Rays (pdb code 2vnx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Soybean Ascorbate Peroxidase Mutant W41A After Exposure to A High Dose of X-Rays, PDB code: 2vnx:

Sodium binding site 1 out of 1 in 2vnx

Go back to Sodium Binding Sites List in 2vnx
Sodium binding site 1 out of 1 in the Crystal Structure of Soybean Ascorbate Peroxidase Mutant W41A After Exposure to A High Dose of X-Rays


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 Soybean Ascorbate Peroxidase Mutant W41A After Exposure to A High Dose of X-Rays within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na252

b:20.6
occ:1.00
 O X:HOH2250 2.6 61.9 1.0
O X:THR164 2.7 11.0 1.0
O X:ILE185 2.8 10.1 1.0
OG X:SER189 2.9 14.8 0.5
O X:ASN182 2.9 13.5 1.0
OG1 X:THR180 2.9 15.8 1.0
OD1 X:ASP187 2.9 16.0 1.0
OG1 X:THR164 3.1 13.2 1.0
CB X:THR180 3.5 13.7 1.0
CG2 X:THR180 3.6 13.4 1.0
CG X:ASP187 3.8 16.2 1.0
C X:THR164 3.8 9.9 1.0
C X:ASN182 3.8 13.1 1.0
C X:ILE185 4.0 10.0 1.0
CB X:SER189 4.0 12.6 0.5
OD2 X:ASP187 4.1 22.1 1.0
CB X:THR164 4.2 10.2 1.0
CB X:ASN182 4.2 14.7 1.0
CB X:SER189 4.2 13.5 0.5
CA X:THR164 4.3 10.1 1.0
OG X:SER189 4.3 12.3 0.5
CA X:ASN182 4.4 13.9 1.0
N X:ASP187 4.5 11.4 1.0
N X:ASN182 4.6 13.8 1.0
CG2 X:THR164 4.6 9.9 1.0
CB X:ILE185 4.6 10.5 1.0
CA X:ILE185 4.7 10.0 1.0
N X:PRO183 4.8 12.7 1.0
N X:ILE185 4.8 9.4 1.0
O X:ASP187 4.9 11.5 1.0
CA X:PRO183 4.9 12.3 1.0
CB X:ASP187 4.9 12.9 1.0
N X:ILE165 4.9 9.5 1.0
N X:PHE186 5.0 9.5 1.0
N X:SER189 5.0 12.5 1.0

Reference:

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
Page generated: Sun Aug 17 11:48:39 2025

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