Sodium in PDB 4yph: Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced, PDB code: 4yph 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)	41.37 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.636, 83.757, 142.735, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 25.9

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced 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 with the Disulfide Cross-Linker Reduced (pdb code 4yph). 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 with the Disulfide Cross-Linker Reduced, PDB code: 4yph:

Sodium binding site 1 out of 1 in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced


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 with the Disulfide Cross-Linker Reduced within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:64.6 occ:1.00 O A:SER118 2.3 63.5 1.0 O A:VAL123 2.5 39.0 1.0 O A:HOH540 2.7 64.0 1.0 O A:LEU120 2.8 38.3 1.0 OP1 C:DC21 3.1 67.3 1.0 OP2 C:DC21 3.4 53.9 1.0 C A:SER118 3.4 44.5 1.0 C A:VAL123 3.7 44.8 1.0 P C:DC21 3.7 50.6 1.0 C A:LEU120 3.8 47.0 1.0 C A:ARG119 3.9 49.4 1.0 O C:HOH111 4.0 61.4 1.0 O A:ARG119 4.1 50.9 1.0 CA A:ARG119 4.1 55.7 1.0 N A:VAL123 4.2 37.8 1.0 N A:ARG119 4.2 57.0 1.0 N A:LEU120 4.2 42.7 1.0 CA A:VAL123 4.3 36.2 1.0 CA A:SER118 4.5 43.9 1.0 CB A:VAL123 4.5 38.1 1.0 CA A:LYS121 4.6 57.1 1.0 N A:LYS121 4.6 53.5 1.0 CA A:LEU120 4.6 45.6 1.0 N A:GLY124 4.7 47.6 1.0 N A:GLY122 4.7 42.0 1.0 O5' C:DC21 4.9 45.7 1.0 O3' C:DT20 4.9 45.4 1.0 C A:LYS121 4.9 48.4 1.0 CA A:GLY124 4.9 36.0 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