Magnesium in PDB 6plc: Structure of Human Dna Polymerase Eta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

All present enzymatic activity of Structure of Human Dna Polymerase Eta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp:
2.7.7.7;

The structure of Structure of Human Dna Polymerase Eta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 6plc was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.447, 98.447, 81.856, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 27.3

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Eta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp (pdb code 6plc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Dna Polymerase Eta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 6plc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Eta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Dna Polymerase Eta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:5.6 occ:1.00 O1B A:XG4501 1.9 26.8 1.0 O1A A:XG4501 1.9 25.4 1.0 OD2 A:ASP13 1.9 21.2 1.0 O A:MET14 2.1 21.9 1.0 OD2 A:ASP115 2.1 25.3 1.0 O1G A:XG4501 2.1 24.7 1.0 CG A:ASP13 2.9 23.0 1.0 PB A:XG4501 3.0 29.1 1.0 CG A:ASP115 3.1 26.2 1.0 PA A:XG4501 3.1 27.1 1.0 PG A:XG4501 3.3 25.8 1.0 OD1 A:ASP13 3.3 22.4 1.0 C A:MET14 3.3 24.0 1.0 N3A A:XG4501 3.4 27.6 1.0 OD1 A:ASP115 3.5 26.8 1.0 MG A:MG503 3.5 6.5 1.0 O3B A:XG4501 3.6 28.5 1.0 NZ A:LYS231 3.8 37.5 1.0 N A:MET14 4.0 25.7 1.0 O2G A:XG4501 4.0 25.7 1.0 C5' A:XG4501 4.0 27.2 1.0 O5' A:XG4501 4.1 30.2 1.0 CA A:MET14 4.2 25.0 1.0 O A:HOH611 4.2 20.0 1.0 CB A:ASP13 4.2 23.9 1.0 C A:ASP13 4.3 26.6 1.0 N A:ASP15 4.4 23.7 1.0 CB A:ASP115 4.4 25.6 1.0 N A:CYS16 4.4 29.5 1.0 O2A A:XG4501 4.4 24.4 1.0 O2B A:XG4501 4.5 26.7 1.0 CE A:LYS231 4.5 37.0 1.0 CA A:ASP15 4.6 26.3 1.0 O3G A:XG4501 4.7 28.7 1.0 CA A:ASP13 4.7 26.1 1.0 CB A:MET14 4.8 26.9 1.0 C A:ASP15 4.8 28.3 1.0 N A:PHE17 4.8 27.0 1.0 O A:ASP13 4.8 27.0 1.0 O3' P:DT8 4.9 33.6 1.0 CB A:PHE17 4.9 24.2 1.0

Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Eta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Dna Polymerase Eta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:6.5 occ:1.00 OD1 A:ASP115 1.8 26.8 1.0 OE1 A:GLU116 1.9 26.8 1.0 OD1 A:ASP13 1.9 22.4 1.0 O A:HOH611 1.9 20.0 1.0 O3' P:DT8 2.1 33.6 1.0 O1A A:XG4501 2.2 25.4 1.0 CG A:ASP115 2.9 26.2 1.0 CD A:GLU116 3.0 27.0 1.0 CG A:ASP13 3.0 23.0 1.0 PA A:XG4501 3.2 27.1 1.0 C3' P:DT8 3.2 36.8 1.0 OD2 A:ASP115 3.3 25.3 1.0 O2A A:XG4501 3.5 24.4 1.0 MG A:MG502 3.5 5.6 1.0 OD2 A:ASP13 3.5 21.2 1.0 OE2 A:GLU116 3.7 29.9 1.0 O5' A:XG4501 3.8 30.2 1.0 OG A:SER113 3.8 25.6 1.0 C5' A:XG4501 3.9 27.2 1.0 CG A:GLU116 4.1 27.4 1.0 C4' P:DT8 4.1 36.5 1.0 NZ A:LYS224 4.2 28.8 1.0 CB A:ASP115 4.2 25.6 1.0 CB A:GLU116 4.3 27.5 1.0 CB A:ASP13 4.3 23.9 1.0 C2' P:DT8 4.4 33.4 1.0 O1G A:XG4501 4.6 24.7 1.0 O1B A:XG4501 4.6 26.8 1.0 C A:ASP115 4.6 30.1 1.0 N3A A:XG4501 4.7 27.6 1.0 N A:GLU116 4.7 31.1 1.0 C5' P:DT8 4.7 42.8 1.0 O5' P:DT8 4.7 51.6 1.0 CB A:SER113 4.9 25.8 1.0 CA A:ASP115 4.9 29.6 1.0 O A:ASP115 4.9 34.2 1.0

M.C.Koag, H.Jung, S.Lee. Mutagenesis Mechanism of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-Oxoadenine. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 32282906
DOI: 10.1093/NAR/GKAA193