Magnesium in PDB 6wk6: Crystal Structure of Human Polymerase Eta Complexed with Xanthine Containing Dna

All present enzymatic activity of Crystal Structure of Human Polymerase Eta Complexed with Xanthine Containing Dna:
2.7.7.7;

The structure of Crystal Structure of Human Polymerase Eta Complexed with Xanthine Containing Dna, PDB code: 6wk6 was solved by H.Jung, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.46 / 2.35
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.93, 98.93, 81.552, 90, 90, 120
R / Rfree (%)	18.9 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of Human Polymerase Eta Complexed with Xanthine Containing Dna (pdb code 6wk6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Polymerase Eta Complexed with Xanthine Containing Dna, PDB code: 6wk6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Polymerase Eta Complexed with Xanthine Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Polymerase Eta Complexed with Xanthine Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:12.9 occ:1.00 OE2 A:GLU116 1.8 29.6 1.0 O A:HOH631 2.0 28.5 1.0 OD2 A:ASP13 2.1 29.0 1.0 O2A A:0KX501 2.1 28.7 1.0 OD1 A:ASP115 2.1 32.2 1.0 O3' P:DG8 2.2 37.5 1.0 CG A:ASP115 3.0 34.9 1.0 CD A:GLU116 3.0 33.5 1.0 C3' P:DG8 3.1 37.1 1.0 OD2 A:ASP115 3.1 33.8 1.0 CG A:ASP13 3.1 31.7 1.0 PA A:0KX501 3.3 32.6 1.0 OD1 A:ASP13 3.5 31.6 1.0 MG A:MG503 3.6 10.1 1.0 O1A A:0KX501 3.6 31.0 1.0 OE1 A:GLU116 3.8 33.0 1.0 OG A:SER113 3.8 29.3 1.0 O5' A:0KX501 3.9 33.0 1.0 O A:HOH652 3.9 31.1 1.0 CG A:GLU116 4.0 32.9 1.0 C4' P:DG8 4.0 35.0 1.0 C5' A:0KX501 4.1 30.2 1.0 CB A:GLU116 4.2 32.6 1.0 C2' P:DG8 4.3 39.5 1.0 CB A:ASP13 4.4 31.4 1.0 CB A:ASP115 4.4 28.2 1.0 N3A A:0KX501 4.7 34.5 1.0 C5' P:DG8 4.7 40.3 1.0 C A:ASP115 4.7 32.5 1.0 O1G A:0KX501 4.7 32.8 1.0 CB A:SER113 4.8 32.8 1.0 O A:ASP115 4.8 33.7 1.0 N A:GLU116 4.8 33.0 1.0 O1B A:0KX501 4.8 33.3 1.0 CA A:ASP115 5.0 28.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Polymerase Eta Complexed with Xanthine Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Polymerase Eta Complexed with Xanthine Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:10.1 occ:1.00 OD1 A:ASP13 2.0 31.6 1.0 O1B A:0KX501 2.0 33.3 1.0 OD2 A:ASP115 2.0 33.8 1.0 O A:MET14 2.1 30.3 1.0 O1G A:0KX501 2.1 32.8 1.0 O2A A:0KX501 2.3 28.7 1.0 CG A:ASP13 3.0 31.7 1.0 PB A:0KX501 3.1 36.2 1.0 CG A:ASP115 3.2 34.9 1.0 C A:MET14 3.3 31.4 1.0 PG A:0KX501 3.4 31.3 1.0 OD2 A:ASP13 3.4 29.0 1.0 N3A A:0KX501 3.4 34.5 1.0 PA A:0KX501 3.5 32.6 1.0 O3B A:0KX501 3.6 28.2 1.0 MG A:MG502 3.6 12.9 1.0 OD1 A:ASP115 3.8 32.2 1.0 N A:MET14 3.9 30.4 1.0 O A:HOH652 3.9 31.1 1.0 NZ A:LYS231 4.0 30.0 1.0 C5' A:0KX501 4.0 30.2 1.0 O3G A:0KX501 4.1 30.5 1.0 CA A:MET14 4.1 31.9 1.0 O5' A:0KX501 4.2 33.0 1.0 C A:ASP13 4.2 29.3 1.0 CB A:ASP13 4.3 31.4 1.0 O A:HOH631 4.3 28.5 1.0 CB A:ASP115 4.3 28.2 1.0 N A:ASP15 4.3 31.0 1.0 O2B A:0KX501 4.5 29.6 1.0 O2G A:0KX501 4.5 27.9 1.0 CA A:ASP15 4.6 31.4 1.0 CE A:LYS231 4.6 33.2 1.0 N A:CYS16 4.6 30.4 1.0 CB A:MET14 4.6 26.4 1.0 O A:ASP13 4.7 32.1 1.0 O1A A:0KX501 4.7 31.0 1.0 N A:PHE17 4.7 32.3 1.0 CA A:ASP13 4.7 27.7 1.0 C A:ASP15 4.8 33.3 1.0 CB A:PHE17 4.8 26.2 1.0 O A:ASP115 4.9 33.7 1.0

H.Jung, M.Hawkins, S.Lee. Structural Insights Into the Bypass of the Major Deaminated Purines By Translesion Synthesis Dna Polymerase. Biochem.J. 2020.
ISSN: ESSN 1470-8728
PubMed: 33258913
DOI: 10.1042/BCJ20200800