Magnesium in PDB 4j9k: Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A T at the Primer 3' End (Ta/G)

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A T at the Primer 3' End (Ta/G):
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A T at the Primer 3' End (Ta/G), PDB code: 4j9k was solved by Y.Zhao, M.Gregory, C.Biertumpfel, 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)	26.87 / 2.03
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.584, 98.584, 81.675, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 18.7

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A T at the Primer 3' End (Ta/G) (pdb code 4j9k). 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-Dna Ternary Complex: Misincorporation G Opposite T After A T at the Primer 3' End (Ta/G), PDB code: 4j9k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A T at the Primer 3' End (Ta/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-Dna Ternary Complex: Misincorporation G Opposite T After A T at the Primer 3' End (Ta/G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:15.5 occ:1.00 O1A A:XG4503 2.0 11.2 1.0 O1B A:XG4503 2.0 13.5 1.0 O1G A:XG4503 2.1 17.9 1.0 OD1 A:ASP13 2.1 15.4 1.0 OD1 A:ASP115 2.2 12.2 1.0 O A:MET14 2.4 12.3 1.0 CG A:ASP13 3.0 13.1 1.0 PB A:XG4503 3.1 15.0 1.0 OD2 A:ASP13 3.2 19.8 1.0 CG A:ASP115 3.2 14.3 1.0 PG A:XG4503 3.2 17.1 1.0 PA A:XG4503 3.3 14.3 1.0 O3B A:XG4503 3.4 14.5 1.0 N3A A:XG4503 3.4 19.2 1.0 MG A:MG502 3.4 20.1 1.0 C A:MET14 3.5 16.1 1.0 OD2 A:ASP115 3.6 14.1 1.0 O A:HOH643 3.7 19.3 1.0 NZ A:LYS231 3.9 13.6 1.0 C5' A:XG4503 3.9 17.9 1.0 O2G A:XG4503 4.0 14.3 1.0 O5' A:XG4503 4.0 15.1 1.0 N A:MET14 4.1 14.2 1.0 CA A:MET14 4.3 16.4 1.0 O A:HOH744 4.3 15.2 1.0 CB A:ASP13 4.4 17.8 1.0 C A:ASP13 4.4 18.0 1.0 O3G A:XG4503 4.4 18.5 1.0 O2A A:XG4503 4.4 21.0 1.0 O2B A:XG4503 4.5 13.6 1.0 CB A:ASP115 4.5 13.1 1.0 N A:ASP15 4.6 14.4 1.0 N A:CYS16 4.6 15.2 1.0 CE A:LYS231 4.7 16.9 1.0 CA A:ASP15 4.7 14.1 1.0 N A:PHE17 4.7 15.6 1.0 CB A:MET14 4.7 15.3 1.0 O A:ASP13 4.8 14.1 1.0 C A:ASP15 4.8 16.0 1.0 CB A:PHE17 4.8 14.1 1.0 CA A:ASP13 4.9 16.4 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A T at the Primer 3' End (Ta/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-Dna Ternary Complex: Misincorporation G Opposite T After A T at the Primer 3' End (Ta/G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.1 occ:1.00 OD2 A:ASP13 2.0 19.8 1.0 OE2 A:GLU116 2.2 19.4 1.0 O A:HOH744 2.2 15.2 1.0 O1A A:XG4503 2.2 11.2 1.0 OD2 A:ASP115 2.3 14.1 1.0 O A:HOH828 2.5 20.8 0.7 O3' P:DT9 2.7 22.1 0.3 CG A:ASP13 3.1 13.1 1.0 CG A:ASP115 3.2 14.3 1.0 PA A:XG4503 3.3 14.3 1.0 CD A:GLU116 3.3 24.4 1.0 C3' P:DT9 3.4 24.4 0.3 MG A:MG501 3.4 15.5 1.0 OD1 A:ASP115 3.5 12.2 1.0 O2A A:XG4503 3.5 21.0 1.0 O5' A:XG4503 3.6 15.1 1.0 OD1 A:ASP13 3.6 15.4 1.0 OG A:SER113 3.8 19.9 1.0 C5' A:XG4503 4.0 17.9 1.0 O A:HOH643 4.0 19.3 1.0 OE1 A:GLU116 4.0 27.1 1.0 O A:HOH829 4.1 23.6 0.7 CG A:GLU116 4.2 20.2 1.0 C4' P:DT9 4.2 22.8 0.3 CB A:GLU116 4.3 16.1 1.0 CB A:ASP13 4.4 17.8 1.0 NZ A:LYS224 4.4 26.9 1.0 CB A:ASP115 4.6 13.1 1.0 O A:HOH699 4.6 16.3 0.7 O1G A:XG4503 4.6 17.9 1.0 N3A A:XG4503 4.7 19.2 1.0 C2' P:DT9 4.7 20.9 0.3 C A:ASP115 4.7 23.1 1.0 O1B A:XG4503 4.8 13.5 1.0 O A:ASP115 4.8 14.6 1.0 CB A:SER113 4.8 18.1 1.0 C5' P:DT9 4.9 25.2 0.3 N A:GLU116 4.9 17.3 1.0

Y.Zhao, M.T.Gregory, C.Biertumpfel, Y.J.Hua, F.Hanaoka, W.Yang. Mechanism of Somatic Hypermutation at the Wa Motif By Human Dna Polymerase Eta. Proc.Natl.Acad.Sci.Usa V. 110 8146 2013.
ISSN: ISSN 0027-8424
PubMed: 23630267
DOI: 10.1073/PNAS.1303126110