Magnesium in PDB 6w13: Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion Dna

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

The structure of Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion Dna, PDB code: 6w13 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)	45.35 / 2.38
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.707, 90.707, 210.803, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 27.1

The binding sites of Magnesium atom in the Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion Dna (pdb code 6w13). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion Dna, PDB code: 6w13:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion 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 Interrogating Fully Intrahelical Oxog Lesion Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:49.6 occ:1.00 OE1 A:GLN135 2.7 44.6 1.0 O A:GLN43 2.9 36.6 1.0 O A:HOH555 3.0 39.4 1.0 CD A:GLN135 3.5 43.2 1.0 OG A:SER143 3.6 42.6 1.0 CB A:SER143 3.7 45.5 1.0 NE2 A:GLN135 3.7 35.8 1.0 CA A:CYS140 3.7 37.0 1.0 CE1 A:PHE144 3.8 60.8 1.0 CA A:SER44 3.9 38.2 1.0 C A:GLN43 4.0 37.7 1.0 O A:GLU139 4.2 37.6 1.0 CD1 A:PHE144 4.2 61.4 1.0 CB A:CYS140 4.3 42.3 1.0 CD1 A:PHE45 4.3 52.1 1.0 SG A:CYS140 4.3 57.0 1.0 N A:CYS140 4.3 38.4 1.0 N A:SER44 4.4 36.6 1.0 CG A:GLU139 4.4 46.0 1.0 C A:GLU139 4.5 39.1 1.0 CE1 A:PHE45 4.6 41.1 1.0 O A:CYS140 4.6 41.7 1.0 N A:PHE45 4.6 35.0 1.0 C A:CYS140 4.7 30.2 1.0 C A:SER44 4.7 38.8 1.0 CB A:SER44 4.8 46.5 1.0 CG A:GLN135 4.8 34.4 1.0 O A:HOH542 5.0 52.2 1.0

Magnesium binding site 2 out of 4 in the Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion 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 Interrogating Fully Intrahelical Oxog Lesion Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:51.0 occ:1.00 OP2 B:DC26 2.3 62.2 1.0 O A:CYS241 2.4 47.6 1.0 O A:HOH536 2.5 48.0 1.0 O A:LEU243 2.6 42.7 1.0 O A:VAL246 2.6 52.4 1.0 P B:DC26 3.3 62.9 1.0 C A:VAL246 3.4 39.0 1.0 C A:CYS241 3.4 45.1 1.0 OP1 B:DC26 3.5 68.9 1.0 C A:LEU243 3.5 42.2 1.0 N A:VAL246 3.8 38.8 1.0 CA A:VAL246 4.1 42.7 1.0 C A:ILE242 4.1 51.9 1.0 N A:LEU243 4.1 47.2 1.0 CA A:CYS241 4.2 45.2 1.0 O5' B:DC26 4.3 69.5 1.0 N A:GLY247 4.3 34.9 1.0 N A:PRO244 4.3 44.5 1.0 CA A:PRO244 4.4 40.4 1.0 O A:ILE242 4.4 57.3 1.0 N A:ILE242 4.4 45.9 1.0 CA A:LEU243 4.4 43.0 1.0 CB A:VAL246 4.5 37.8 1.0 CA A:ILE242 4.5 58.7 1.0 N A:GLY245 4.5 41.0 1.0 O3' B:DT25 4.6 70.9 1.0 C A:PRO244 4.7 45.1 1.0 CA A:GLY247 4.7 43.5 1.0 C A:GLY245 4.9 53.0 1.0 O A:LEU240 4.9 47.5 1.0 C3' B:DT25 5.0 68.1 1.0 CB A:CYS241 5.0 46.3 1.0

Magnesium binding site 3 out of 4 in the Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:56.6 occ:1.00 O A:TRP307 2.5 41.6 1.0 N A:TYR310 3.3 39.7 1.0 NE1 A:TRP113 3.3 43.6 1.0 C A:GLY308 3.3 42.6 1.0 CA A:GLY308 3.5 35.4 1.0 C A:TRP307 3.5 36.4 1.0 CD2 A:HIS112 3.5 54.5 1.0 N A:PRO309 3.6 44.2 1.0 CB A:TYR310 3.7 33.9 1.0 O A:GLY308 3.7 35.3 1.0 NE2 A:HIS112 3.8 52.1 1.0 CA A:TYR310 3.8 36.2 1.0 N A:GLY308 3.9 40.6 1.0 CD A:PRO309 3.9 39.2 1.0 CD1 A:TRP113 3.9 38.7 1.0 C A:TYR310 4.0 34.4 1.0 C A:PRO309 4.3 43.7 1.0 CE2 A:TRP113 4.4 41.1 1.0 O A:TYR310 4.4 39.0 1.0 N A:ALA311 4.4 32.7 1.0 CA A:PRO309 4.4 39.5 1.0 CD1 A:TYR310 4.6 37.9 1.0 CG A:TYR310 4.6 31.5 1.0 CA A:TRP307 4.7 38.8 1.0 CG A:HIS112 4.8 51.0 1.0 CZ2 A:TRP113 4.9 37.4 1.0 CB A:TRP307 4.9 43.6 1.0 CB A:PRO309 4.9 39.8 1.0 CG A:PRO309 5.0 48.8 1.0

Magnesium binding site 4 out of 4 in the Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human 8-Oxoguanine Glycosylase Interrogating Fully Intrahelical Oxog Lesion Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:55.1 occ:1.00 OG A:SER209 2.3 40.9 1.0 O A:LEU187 2.9 34.4 1.0 O A:GLY189 2.9 40.0 1.0 C A:ALA188 3.1 47.3 1.0 O A:ALA188 3.2 44.7 1.0 CB A:SER209 3.3 38.5 1.0 NE A:ARG213 3.4 34.7 1.0 CA A:ALA188 3.4 45.1 1.0 CZ A:ARG213 3.5 33.8 1.0 N A:GLY189 3.5 39.4 1.0 NH2 A:ARG213 3.5 37.2 1.0 CA A:SER209 3.6 35.6 1.0 CB A:VAL192 3.7 58.1 1.0 C A:LEU187 3.8 37.8 1.0 C A:GLY189 3.9 44.8 1.0 O A:SER209 4.0 32.0 1.0 CG2 A:VAL192 4.0 53.1 1.0 N A:ALA188 4.0 37.0 1.0 CD A:ARG213 4.1 35.5 1.0 C A:SER209 4.1 40.7 1.0 NH1 A:ARG213 4.2 35.7 1.0 CA A:GLY189 4.3 48.7 1.0 CG1 A:VAL192 4.3 54.9 1.0 CG A:ARG213 4.4 38.3 1.0 N A:VAL192 4.7 49.9 1.0 CA A:VAL192 4.7 49.5 1.0 CB A:ALA188 4.8 40.3 1.0 N A:SER209 4.8 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