Magnesium in PDB 6w0m: Human 8-Oxoguanine Glycosylase Crosslinked with Oxog Lesion Containing Dna

All present enzymatic activity of Human 8-Oxoguanine Glycosylase Crosslinked with Oxog Lesion Containing Dna:
4.2.99.18;

The structure of Human 8-Oxoguanine Glycosylase Crosslinked with Oxog Lesion Containing Dna, PDB code: 6w0m 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)	45.84 / 2.37
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.678, 91.678, 212.106, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 26.6

The binding sites of Magnesium atom in the Human 8-Oxoguanine Glycosylase Crosslinked with Oxog Lesion Containing Dna (pdb code 6w0m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human 8-Oxoguanine Glycosylase Crosslinked with Oxog Lesion Containing Dna, PDB code: 6w0m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human 8-Oxoguanine Glycosylase Crosslinked with Oxog Lesion Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human 8-Oxoguanine Glycosylase Crosslinked with Oxog Lesion Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:60.2 occ:1.00 O A:SER86 2.6 51.3 1.0 O A:LEU22 2.8 51.8 1.0 OG1 A:THR76 3.2 34.7 1.0 O A:VAL77 3.2 35.4 1.0 N A:VAL77 3.2 43.5 1.0 NH1 A:ARG14 3.3 50.0 1.0 CD A:PRO88 3.5 47.9 1.0 C A:SER86 3.5 61.6 1.0 N A:PRO88 3.7 43.0 1.0 CG1 A:VAL77 3.7 37.8 1.0 C A:ARG87 3.7 40.7 1.0 CA A:ARG87 3.8 54.1 1.0 CG A:PRO88 3.9 44.6 1.0 C A:LEU22 3.9 56.3 1.0 CA A:THR76 4.0 39.2 1.0 N A:ARG87 4.0 68.0 1.0 C A:VAL77 4.0 52.9 1.0 CA A:VAL77 4.0 34.5 1.0 C A:THR76 4.1 40.6 1.0 CB A:THR76 4.1 39.8 1.0 CB A:LEU22 4.3 47.7 1.0 O A:ARG87 4.3 41.0 1.0 CA A:LEU22 4.4 51.2 1.0 CZ A:ARG14 4.4 35.6 1.0 CB A:VAL77 4.4 42.5 1.0 CA A:PRO88 4.5 44.8 1.0 CA A:SER86 4.6 69.4 1.0 N A:SER86 4.7 62.8 1.0 CB A:PRO88 4.8 41.7 1.0 NH1 A:ARG79 4.9 42.2 1.0 CD2 A:LEU22 4.9 37.1 1.0 NH2 A:ARG79 5.0 50.6 1.0 NH2 A:ARG14 5.0 48.0 1.0

Magnesium binding site 2 out of 2 in the Human 8-Oxoguanine Glycosylase Crosslinked with Oxog Lesion Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human 8-Oxoguanine Glycosylase Crosslinked with Oxog Lesion Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:44.6 occ:1.00 O A:CYS241 2.3 44.8 1.0 O A:LEU243 2.5 41.0 1.0 O A:VAL246 2.6 40.6 1.0 OP1 B:DC28 2.6 58.1 1.0 OP2 B:DC28 2.6 65.1 1.0 O A:HOH581 2.7 56.7 1.0 P B:DC28 3.0 46.1 1.0 C A:CYS241 3.4 46.4 1.0 C A:VAL246 3.4 44.7 1.0 C A:LEU243 3.6 32.1 1.0 N A:VAL246 4.0 36.4 1.0 C A:ILE242 4.0 43.3 1.0 N A:LEU243 4.0 42.0 1.0 O A:ILE242 4.1 41.6 1.0 CA A:VAL246 4.1 39.7 1.0 CA A:CYS241 4.2 32.6 1.0 O3' B:DT27 4.2 54.1 1.0 O5' B:DC28 4.3 51.1 1.0 N A:GLY247 4.3 45.0 1.0 N A:ILE242 4.4 40.6 1.0 CA A:LEU243 4.4 40.2 1.0 CB A:VAL246 4.4 30.2 1.0 CA A:PRO244 4.4 33.2 1.0 N A:PRO244 4.4 40.0 1.0 CA A:ILE242 4.5 43.5 1.0 N A:GLY245 4.5 43.8 1.0 CA A:GLY247 4.7 29.8 1.0 C A:PRO244 4.7 39.9 1.0 C5' B:DC28 4.8 69.0 1.0 O A:LEU240 4.8 40.1 1.0 C A:GLY245 4.9 41.1 1.0 C3' B:DT27 4.9 50.0 1.0 CB A:CYS241 4.9 41.1 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