Magnesium in PDB 4q8e: Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G

All present enzymatic activity of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G:
2.7.7.7;

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G, PDB code: 4q8e was solved by M.T.Gregory, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.94 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.766, 98.766, 82.197, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 22.5

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G also contains other interesting chemical elements:

Platinum

(Pt)

2 atoms

The binding sites of Magnesium atom in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G (pdb code 4q8e). 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 Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G, PDB code: 4q8e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:4.4 occ:1.00 OD1 A:ASP13 2.1 11.7 1.0 OD2 A:ASP115 2.2 8.9 1.0 O2B A:0KX501 2.2 6.9 1.0 O2G A:0KX501 2.2 8.6 1.0 O A:MET14 2.2 7.8 1.0 O1A A:0KX501 2.3 9.9 1.0 CG A:ASP13 3.1 11.6 1.0 CG A:ASP115 3.2 9.9 1.0 PB A:0KX501 3.2 7.5 1.0 PA A:0KX501 3.3 9.9 1.0 OD2 A:ASP13 3.4 18.9 1.0 MG A:MG503 3.4 10.2 0.6 C A:MET14 3.4 7.3 1.0 PG A:0KX501 3.5 8.3 1.0 N3A A:0KX501 3.6 10.7 1.0 OD1 A:ASP115 3.6 11.4 1.0 O3B A:0KX501 3.7 7.2 1.0 O A:HOH924 3.8 18.4 1.0 NZ A:LYS231 3.9 10.1 1.0 N A:MET14 3.9 7.3 1.0 C5' A:0KX501 4.0 9.4 1.0 CA A:MET14 4.1 7.0 1.0 O5' A:0KX501 4.1 9.1 1.0 O3G A:0KX501 4.2 8.6 1.0 O A:HOH930 4.2 20.0 1.0 C A:ASP13 4.3 7.3 1.0 CB A:ASP13 4.4 9.9 1.0 N A:ASP15 4.5 5.7 1.0 CB A:ASP115 4.5 7.1 1.0 CE A:LYS231 4.6 15.1 1.0 CB A:MET14 4.6 8.5 1.0 O1B A:0KX501 4.6 8.8 1.0 CA A:ASP15 4.6 7.1 1.0 N A:CYS16 4.6 6.1 1.0 O2A A:0KX501 4.6 13.5 1.0 O1G A:0KX501 4.6 10.0 1.0 O A:ASP13 4.7 8.6 1.0 C A:ASP15 4.7 8.2 1.0 N A:PHE17 4.8 5.4 1.0 CA A:ASP13 4.8 8.3 1.0 CB A:PHE17 4.8 6.9 1.0 O A:ASP115 4.9 8.4 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenanthriplatin Adducted G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:10.2 occ:0.60 OD2 A:ASP13 1.9 18.9 1.0 OE2 A:GLU116 1.9 26.4 1.0 O A:HOH930 2.1 20.0 1.0 OD1 A:ASP115 2.2 11.4 1.0 O1A A:0KX501 2.3 9.9 1.0 O3' P:DG8 2.5 17.5 1.0 CG A:ASP13 2.9 11.6 1.0 CD A:GLU116 3.0 23.1 1.0 CG A:ASP115 3.1 9.9 1.0 C3' P:DG8 3.2 17.3 1.0 OD1 A:ASP13 3.3 11.7 1.0 OD2 A:ASP115 3.4 8.9 1.0 MG A:MG502 3.4 4.4 1.0 PA A:0KX501 3.5 9.9 1.0 OE1 A:GLU116 3.7 23.7 1.0 OG A:SER113 3.9 12.9 1.0 CG A:GLU116 4.0 12.9 1.0 C4' P:DG8 4.0 14.1 1.0 O5' A:0KX501 4.0 9.1 1.0 O2A A:0KX501 4.1 13.5 1.0 CB A:GLU116 4.1 15.6 1.0 O A:HOH924 4.1 18.4 1.0 C5' A:0KX501 4.3 9.4 1.0 CB A:ASP13 4.3 9.9 1.0 C5' P:DG8 4.4 19.6 0.5 NZ A:LYS224 4.4 16.3 0.5 C2' P:DG8 4.4 20.3 1.0 C5' P:DG8 4.5 19.3 0.5 C A:ASP115 4.5 9.8 1.0 O A:ASP115 4.5 8.4 1.0 CB A:ASP115 4.5 7.1 1.0 N A:GLU116 4.7 9.0 1.0 O2G A:0KX501 4.8 8.6 1.0 CA A:ASP115 4.9 8.3 1.0 O2B A:0KX501 4.9 6.9 1.0 N3A A:0KX501 5.0 10.7 1.0 CA A:ASP13 5.0 8.3 1.0

M.T.Gregory, G.Y.Park, T.C.Johnstone, Y.S.Lee, W.Yang, S.J.Lippard. Structural and Mechanistic Studies of Polymerase Eta Bypass of Phenanthriplatin Dna Damage. Proc.Natl.Acad.Sci.Usa V. 111 9133 2014.
ISSN: ISSN 0027-8424
PubMed: 24927576
DOI: 10.1073/PNAS.1405739111