Sodium in PDB 6w0r: Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Undamaged Dna

All present enzymatic activity of Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Undamaged Dna:
4.2.99.18;

The structure of Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Undamaged Dna, PDB code: 6w0r was solved by U.Shigdel, G.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.50 / 2.35
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	88.928, 88.928, 210.539, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 24.9

The binding sites of Sodium atom in the Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Undamaged Dna (pdb code 6w0r). 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 Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Undamaged Dna, PDB code: 6w0r:

Sodium binding site 1 out of 1 in the Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Undamaged Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Undamaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:43.1 occ:1.00 O A:LEU243 2.6 32.2 1.0 O A:CYS241 2.7 28.2 1.0 OP2 B:DC26 2.9 43.0 1.0 O A:VAL246 2.9 30.8 1.0 OP1 B:DC26 3.5 46.6 1.0 C A:LEU243 3.5 31.3 1.0 P B:DC26 3.7 44.1 1.0 C A:CYS241 3.7 29.9 1.0 C A:VAL246 3.8 32.0 1.0 N A:LEU243 4.0 28.9 1.0 N A:VAL246 4.1 31.9 1.0 C A:ILE242 4.1 30.0 1.0 N A:PRO244 4.3 33.2 1.0 O A:ILE242 4.3 29.4 1.0 CA A:PRO244 4.3 33.1 1.0 CA A:LEU243 4.4 26.2 1.0 CA A:CYS241 4.4 29.7 1.0 CA A:VAL246 4.4 34.7 1.0 N A:GLY245 4.4 32.9 1.0 N A:ILE242 4.6 27.7 1.0 CA A:ILE242 4.6 28.9 1.0 CB A:VAL246 4.7 30.3 1.0 C A:PRO244 4.7 32.9 1.0 O3' B:DT25 4.8 45.7 1.0 N A:GLY247 4.8 30.8 1.0 O5' B:DC26 4.8 54.9 1.0

U.K.Shigdel, V.Ovchinnikov, S.J.Lee, J.A.Shih, M.Karplus, K.Nam, G.L.Verdine. The Trajectory of Intrahelical Lesion Recognition and Extrusion By the Human 8-Oxoguanine Dna Glycosylase. Nat Commun V. 11 4437 2020.
ISSN: ESSN 2041-1723
PubMed: 32895378
DOI: 10.1038/S41467-020-18290-2