Sodium in PDB 4yoq: Crystal Structure of Muty Bound to Its Anti-Substrate

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate, PDB code: 4yoq was solved by L.Wang, S.Lee, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.41 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.697, 84.594, 142.457, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 25

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Muty Bound to Its Anti-Substrate (pdb code 4yoq). 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 Muty Bound to Its Anti-Substrate, PDB code: 4yoq:

Sodium binding site 1 out of 1 in the Crystal Structure of Muty Bound to Its Anti-Substrate


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 Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:44.6 occ:1.00 O C:HOH205 2.3 46.2 1.0 O A:SER118 2.3 47.3 1.0 O A:VAL123 2.4 39.8 1.0 O A:LEU120 2.6 41.9 1.0 OP1 C:DC21 2.9 45.4 1.0 C A:SER118 3.5 41.3 1.0 C A:VAL123 3.5 41.0 1.0 OP2 C:DC21 3.6 39.7 1.0 C A:LEU120 3.7 35.7 1.0 P C:DC21 3.7 44.5 1.0 N A:VAL123 3.9 30.6 1.0 C A:ARG119 4.0 46.0 1.0 CA A:VAL123 4.1 35.3 1.0 O A:ARG119 4.2 47.3 1.0 N A:LEU120 4.2 43.9 1.0 CB A:VAL123 4.2 34.0 1.0 CA A:ARG119 4.3 44.0 1.0 N A:ARG119 4.3 43.3 1.0 CA A:SER118 4.4 45.1 1.0 N A:LYS121 4.5 47.7 1.0 CA A:LYS121 4.6 40.0 1.0 CA A:LEU120 4.6 43.1 1.0 N A:GLY122 4.6 37.7 1.0 N A:GLY124 4.6 36.5 1.0 O3' C:DT20 4.7 43.3 1.0 C A:LYS121 4.8 35.1 1.0 C A:GLY122 4.9 29.1 1.0 CA A:GLY124 4.9 33.2 1.0 O5' C:DC21 4.9 40.5 1.0

L.Wang, S.-J.Lee, G.Verdine. Structural Basis For Avoidance of Promutagenic Dna Repair By Muty Adenine Dna Glycosylase. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M115.657866