Magnesium in PDB 6mq8: Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine

All present enzymatic activity of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine:
2.7.7.7;

The structure of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine, PDB code: 6mq8 was solved by M.A.Hawkins, H.Jung, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.27 / 1.97
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.539, 98.539, 81.664, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 20.8

The structure of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine (pdb code 6mq8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine, PDB code: 6mq8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:15.9 occ:1.00 OD1 A:ASP13 2.0 19.4 1.0 OD2 A:ASP115 2.0 18.4 1.0 O1A A:0KX501 2.0 18.8 1.0 O2B A:0KX501 2.1 16.6 1.0 O2G A:0KX501 2.1 17.4 1.0 O A:MET14 2.2 15.3 1.0 CG A:ASP13 3.0 21.4 1.0 CG A:ASP115 3.1 20.2 1.0 PB A:0KX501 3.1 18.6 1.0 H7 A:0KX501 3.2 22.9 1.0 PA A:0KX501 3.3 20.6 1.0 OD2 A:ASP13 3.3 22.0 1.0 HZ2 A:LYS231 3.3 22.3 1.0 C A:MET14 3.4 16.5 1.0 PG A:0KX501 3.4 18.0 1.0 MG A:MG503 3.4 17.9 0.9 HZ3 A:LYS231 3.5 22.3 1.0 N3A A:0KX501 3.5 19.4 1.0 OD1 A:ASP115 3.6 19.1 1.0 O A:HOH643 3.7 21.2 1.0 O3B A:0KX501 3.7 16.8 1.0 NZ A:LYS231 3.9 18.6 1.0 C5' A:0KX501 3.9 19.1 1.0 N A:MET14 3.9 17.2 1.0 H A:MET14 4.0 20.6 1.0 HB2 A:PHE17 4.0 17.2 1.0 HB2 A:MET14 4.0 19.9 1.0 H A:PHE17 4.1 17.5 1.0 O1G A:0KX501 4.1 17.2 1.0 H6 A:0KX501 4.1 22.9 1.0 HA A:ASP15 4.1 19.9 1.0 HE3 A:LYS231 4.1 27.7 1.0 O5' A:0KX501 4.2 20.4 1.0 CA A:MET14 4.2 15.9 1.0 C A:ASP13 4.2 18.4 1.0 CB A:ASP13 4.3 19.7 1.0 O A:HOH715 4.3 17.9 1.0 H5 A:0KX501 4.3 23.2 1.0 HB2 A:ASP115 4.4 21.8 1.0 CB A:ASP115 4.4 18.1 1.0 H A:CYS16 4.4 20.5 1.0 N A:ASP15 4.4 16.4 1.0 O2A A:0KX501 4.4 18.8 1.0 O1B A:0KX501 4.5 16.2 1.0 HB3 A:ASP13 4.5 23.7 1.0 O3G A:0KX501 4.6 19.3 1.0 O A:ASP13 4.6 16.6 1.0 HZ1 A:LYS231 4.6 22.3 1.0 CE A:LYS231 4.6 23.1 1.0 CA A:ASP15 4.6 16.6 1.0 N A:CYS16 4.6 17.1 1.0 CB A:MET14 4.7 16.6 1.0 CA A:ASP13 4.7 18.7 1.0 HA A:ASP13 4.7 22.5 1.0 HB3 A:ASP115 4.7 21.8 1.0 O A:ASP115 4.8 18.4 1.0 C A:ASP15 4.8 17.4 1.0 N A:PHE17 4.8 14.6 1.0 CB A:PHE17 4.8 14.4 1.0 HB3 A:PHE17 4.9 17.2 1.0 HA A:CYS16 5.0 19.9 1.0 O3' P:DT8 5.0 19.1 1.0 HB2 A:ASP13 5.0 23.7 1.0

Magnesium binding site 2 out of 2 in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:17.9 occ:0.95 OD2 A:ASP13 2.0 22.0 1.0 OE2 A:GLU116 2.1 22.9 1.0 OD1 A:ASP115 2.1 19.1 1.0 O3' P:DT8 2.2 19.1 1.0 O A:HOH715 2.2 17.9 1.0 O1A A:0KX501 2.2 18.8 1.0 CG A:ASP13 3.0 21.4 1.0 CG A:ASP115 3.0 20.2 1.0 CD A:GLU116 3.1 23.6 1.0 HG A:SER113 3.1 24.9 1.0 PA A:0KX501 3.2 20.6 1.0 OD2 A:ASP115 3.3 18.4 1.0 C3' P:DT8 3.3 22.5 1.0 H3' P:DT8 3.4 27.0 1.0 HB3 A:GLU116 3.4 25.8 1.0 OD1 A:ASP13 3.4 19.4 1.0 MG A:MG502 3.4 15.9 1.0 O2A A:0KX501 3.5 18.8 1.0 H6 A:0KX501 3.7 22.9 1.0 O5' A:0KX501 3.7 20.4 1.0 OE1 A:GLU116 3.8 22.4 1.0 OG A:SER113 3.9 20.8 1.0 H4' P:DT8 4.0 26.3 1.0 HZ3 A:LYS224 4.0 29.7 1.0 HZ2 A:LYS224 4.0 29.7 1.0 C5' A:0KX501 4.0 19.1 1.0 CG A:GLU116 4.1 20.1 1.0 O A:HOH643 4.1 21.2 1.0 H7 A:0KX501 4.1 22.9 1.0 H5'' P:DT8 4.1 31.2 1.0 C4' P:DT8 4.1 21.9 1.0 CB A:GLU116 4.1 21.5 1.0 HG2 A:GLU116 4.3 24.1 1.0 NZ A:LYS224 4.3 24.7 1.0 HZ1 A:LYS224 4.4 29.7 1.0 CB A:ASP13 4.4 19.7 1.0 HB2 A:ASP13 4.4 23.7 1.0 CB A:ASP115 4.4 18.1 1.0 H2'' P:DT8 4.4 25.6 1.0 O A:HOH746 4.5 19.6 1.0 C2' P:DT8 4.5 21.3 1.0 C A:ASP115 4.6 20.4 1.0 O A:ASP115 4.6 18.4 1.0 C5' P:DT8 4.6 26.0 1.0 O2G A:0KX501 4.7 17.4 1.0 H A:ASP115 4.7 22.6 1.0 HB3 A:ASP115 4.7 21.8 1.0 N3A A:0KX501 4.7 19.4 1.0 HA A:ASP13 4.7 22.5 1.0 HB2 A:GLU116 4.8 25.8 1.0 N A:GLU116 4.8 18.4 1.0 O2B A:0KX501 4.8 16.6 1.0 HG3 A:GLU116 4.9 24.1 1.0 O A:HOH795 4.9 23.3 1.0 CB A:SER113 5.0 21.7 1.0 CA A:ASP115 5.0 18.2 1.0 HB3 A:SER113 5.0 26.0 1.0

M.A.Hawkins, J.Hunmin, S.Lee. Structural Analysis of Translesion Synthesis Across Hypoxanthine Lesion Using Human Dna Polymerase Eta To Be Published.