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Sodium in PDB 5ykj: Structural Basis of the Thiol Resolving Mechanism in Yeast Mitochondrial 1-Cys Peroxiredoxin Via Glutathione/Thioredoxin Systems

Enzymatic activity of Structural Basis of the Thiol Resolving Mechanism in Yeast Mitochondrial 1-Cys Peroxiredoxin Via Glutathione/Thioredoxin Systems

All present enzymatic activity of Structural Basis of the Thiol Resolving Mechanism in Yeast Mitochondrial 1-Cys Peroxiredoxin Via Glutathione/Thioredoxin Systems:
1.11.1.15;

Protein crystallography data

The structure of Structural Basis of the Thiol Resolving Mechanism in Yeast Mitochondrial 1-Cys Peroxiredoxin Via Glutathione/Thioredoxin Systems, PDB code: 5ykj was solved by C.C.Li, J.Yang, M.J.Yang, L.Liu, C.T.Peng, T.Li, L.H.He, Y.J.Song, Y.B.Zhu, N.L.Zhao, C.Zhao, R.Bao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.16 / 1.53
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.030, 84.030, 62.784, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Basis of the Thiol Resolving Mechanism in Yeast Mitochondrial 1-Cys Peroxiredoxin Via Glutathione/Thioredoxin Systems (pdb code 5ykj). 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 Structural Basis of the Thiol Resolving Mechanism in Yeast Mitochondrial 1-Cys Peroxiredoxin Via Glutathione/Thioredoxin Systems, PDB code: 5ykj:

Sodium binding site 1 out of 1 in 5ykj

Go back to Sodium Binding Sites List in 5ykj
Sodium binding site 1 out of 1 in the Structural Basis of the Thiol Resolving Mechanism in Yeast Mitochondrial 1-Cys Peroxiredoxin Via Glutathione/Thioredoxin Systems


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis of the Thiol Resolving Mechanism in Yeast Mitochondrial 1-Cys Peroxiredoxin Via Glutathione/Thioredoxin Systems within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:41.3
occ:1.00
 H A:PHE248 2.5 17.7 1.0
HA A:GLN247 3.0 34.4 1.0
O A:PHE248 3.2 13.9 1.0
N A:PHE248 3.3 14.7 1.0
CA A:GLN247 3.9 28.6 1.0
CD2 A:PHE248 4.0 17.6 1.0
C A:GLN247 4.1 24.4 1.0
C A:PHE248 4.1 14.6 1.0
CG A:PHE248 4.1 16.2 1.0
CE2 A:PHE248 4.1 27.8 1.0
HG2 A:GLN247 4.2 41.5 1.0
CA A:PHE248 4.2 13.1 1.0
HB3 A:GLN247 4.2 36.6 1.0
HD2 A:PHE248 4.3 21.1 1.0
CD1 A:PHE248 4.3 17.7 1.0
HG2 A:LYS242 4.3 34.5 1.0
CZ A:PHE248 4.4 27.5 1.0
CE1 A:PHE248 4.4 22.4 1.0
HE2 A:PHE248 4.5 33.4 1.0
O A:GLY246 4.5 52.1 1.0
CB A:GLN247 4.5 30.5 1.0
CB A:PHE248 4.8 14.1 1.0
HD1 A:PHE248 4.8 21.3 1.0
HZ A:PHE248 4.8 33.0 1.0
O A:HOH514 4.8 22.8 1.0
HD3 A:LYS242 4.9 48.3 1.0
CG A:GLN247 4.9 34.6 1.0
HE1 A:PHE248 4.9 26.9 1.0
N A:GLN247 5.0 20.5 1.0
HD2 A:LYS242 5.0 48.3 1.0
O A:HOH471 5.0 23.8 1.0

Reference:

C.C.Li, J.Yang, M.J.Yang, L.Liu, C.T.Peng, T.Li, L.H.He, Y.J.Song, Y.B.Zhu, N.L.Zhao, C.Zhao, R.Bao. Structural Basis of the Thiol Resolving Mechanism in Yeast Mitochondrial 1-Cys Peroxiredoxin Via Glutathione/Thioredoxin Systems To Be Published.
Page generated: Tue Oct 8 01:23:54 2024

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