Magnesium in PDB 4dl2: Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Cg Template (GG0A)

All present enzymatic activity of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Cg Template (GG0A):
2.7.7.7;

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Cg Template (GG0A), PDB code: 4dl2 was solved by Y.Zhao, C.Biertumpfel, M.Gregory, Y.Hua, F.Hanaoka, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.15
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	97.860, 97.860, 80.530, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 22.2

The binding sites of Magnesium atom in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Cg Template (GG0A) (pdb code 4dl2). 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 Cg Template (GG0A), PDB code: 4dl2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Cg Template (GG0A)


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 Cg Template (GG0A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:14.6 occ:1.00 OD1 A:ASP13 2.0 16.0 1.0 O A:MET14 2.1 11.1 1.0 O1A P:0KX10 2.2 16.8 1.0 O2B P:0KX10 2.2 14.8 1.0 OD1 A:ASP115 2.3 12.8 1.0 O2G P:0KX10 2.3 14.4 1.0 CG A:ASP13 3.0 15.4 1.0 PB P:0KX10 3.2 17.7 1.0 PG P:0KX10 3.3 17.4 1.0 CG A:ASP115 3.3 17.4 1.0 C A:MET14 3.3 15.1 1.0 OD2 A:ASP13 3.4 17.0 1.0 PA P:0KX10 3.5 16.1 1.0 O3B P:0KX10 3.5 14.2 1.0 MG A:MG503 3.5 18.1 1.0 O A:HOH648 3.7 15.8 1.0 OD2 A:ASP115 3.8 13.2 1.0 N3A P:0KX10 3.8 19.7 1.0 O3G P:0KX10 3.8 13.0 1.0 NZ A:LYS231 3.8 14.6 1.0 N A:MET14 3.9 13.2 1.0 C5' P:0KX10 4.0 14.5 1.0 CA A:MET14 4.1 15.4 1.0 O5' P:0KX10 4.2 17.9 1.0 N A:CYS16 4.3 12.3 1.0 C A:ASP13 4.3 16.5 1.0 N A:ASP15 4.3 12.8 1.0 CB A:ASP13 4.3 16.8 1.0 CE A:LYS231 4.4 16.1 1.0 CA A:ASP15 4.4 13.4 1.0 O1B P:0KX10 4.5 14.6 1.0 O A:HOH787 4.5 15.6 1.0 N A:PHE17 4.5 12.3 1.0 C A:ASP15 4.6 13.9 1.0 O1G P:0KX10 4.6 17.2 1.0 CB A:ASP115 4.6 10.8 1.0 O2A P:0KX10 4.6 19.3 1.0 CB A:MET14 4.6 16.6 1.0 CB A:PHE17 4.7 11.9 1.0 O A:ASP13 4.7 15.7 1.0 CA A:ASP13 4.8 15.2 1.0 O A:ASP115 5.0 17.3 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Cg Template (GG0A)


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 Cg Template (GG0A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:18.1 occ:1.00 OD2 A:ASP13 2.1 17.0 1.0 O1A P:0KX10 2.3 16.8 1.0 O A:HOH787 2.4 15.6 1.0 OD2 A:ASP115 2.4 13.2 1.0 O3' P:DG9 2.4 18.2 0.5 OE2 A:GLU116 2.4 18.9 1.0 O3' P:DG9 2.5 18.2 0.5 C3' P:DG9 3.1 20.3 0.5 C3' P:DG9 3.1 20.3 0.5 CG A:ASP13 3.1 15.4 1.0 CG A:ASP115 3.3 17.4 1.0 PA P:0KX10 3.3 16.1 1.0 CD A:GLU116 3.4 20.9 1.0 OD1 A:ASP115 3.4 12.8 1.0 O2A P:0KX10 3.5 19.3 1.0 OD1 A:ASP13 3.5 16.0 1.0 MG A:MG502 3.5 14.6 1.0 O5' P:0KX10 3.7 17.9 1.0 O A:HOH648 3.8 15.8 1.0 OG A:SER113 3.9 16.0 1.0 C5' P:0KX10 4.0 14.5 1.0 C4' P:DG9 4.0 21.9 0.5 OE1 A:GLU116 4.1 22.1 1.0 C4' P:DG9 4.1 21.7 0.5 NZ A:LYS224 4.2 18.1 1.0 CB A:GLU116 4.2 12.8 1.0 CG A:GLU116 4.2 16.8 1.0 C2' P:DG9 4.3 21.9 0.5 C2' P:DG9 4.3 21.9 0.5 CB A:ASP13 4.5 16.8 1.0 O2G P:0KX10 4.6 14.4 1.0 CB A:ASP115 4.6 10.8 1.0 C5' P:DG9 4.7 23.4 0.5 O2B P:0KX10 4.7 14.8 1.0 C5' P:DG9 4.7 22.5 0.5 C A:ASP115 4.8 18.9 1.0 N3A P:0KX10 4.8 19.7 1.0 O A:HOH657 4.8 22.3 1.0 O A:ASP115 4.9 17.3 1.0 N A:GLU116 4.9 15.2 1.0 O5' P:DG9 5.0 25.8 0.5 CB A:SER113 5.0 17.2 1.0

Y.Zhao, C.Biertumpfel, M.T.Gregory, Y.J.Hua, F.Hanaoka, W.Yang. Structural Basis For Chemoresistance to Cisplatin Mediated By Dna Polymerase Eta Proc.Natl.Acad.Sci.Usa V. 109 7269 2012.
ISSN: ISSN 0027-8424
PubMed: 22529383
DOI: 10.1073/PNAS.1202681109