Magnesium in PDB 4j9l: Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A C at the Primer 3' End (Ca/G)

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

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A C at the Primer 3' End (Ca/G), PDB code: 4j9l 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)	28.41 / 1.85
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.430, 98.430, 81.960, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 20.8

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A C at the Primer 3' End (Ca/G) (pdb code 4j9l). 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 C at the Primer 3' End (Ca/G), PDB code: 4j9l:
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 C at the Primer 3' End (Ca/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 C at the Primer 3' End (Ca/G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:10.7 occ:1.00 OD1 A:ASP13 2.1 13.2 1.0 O1G A:XG4503 2.1 8.3 1.0 O1B A:XG4503 2.1 9.4 1.0 OD2 A:ASP115 2.2 9.0 1.0 O1A A:XG4503 2.2 7.2 1.0 O A:MET14 2.4 7.6 1.0 PB A:XG4503 3.1 12.4 1.0 CG A:ASP13 3.1 11.7 1.0 CG A:ASP115 3.2 13.0 1.0 PG A:XG4503 3.2 11.6 1.0 O3B A:XG4503 3.4 8.1 1.0 PA A:XG4503 3.4 12.2 1.0 N3A A:XG4503 3.5 13.1 1.0 MG A:MG502 3.5 15.2 1.0 C A:MET14 3.5 8.7 1.0 OD2 A:ASP13 3.5 15.0 1.0 OD1 A:ASP115 3.6 8.6 1.0 O2G A:XG4503 3.7 10.3 1.0 O A:HOH644 3.7 13.3 1.0 NZ A:LYS231 3.8 8.2 1.0 N A:MET14 3.9 7.2 1.0 C5' A:XG4503 4.0 8.0 1.0 O5' A:XG4503 4.2 10.1 1.0 CA A:MET14 4.2 8.1 1.0 C A:ASP13 4.2 6.5 1.0 O2B A:XG4503 4.3 10.5 1.0 CB A:ASP13 4.3 12.0 1.0 O3G A:XG4503 4.4 12.7 1.0 N A:CYS16 4.5 9.8 1.0 CB A:ASP115 4.5 7.6 1.0 O A:HOH605 4.5 7.9 1.0 O2A A:XG4503 4.5 15.2 1.0 N A:ASP15 4.5 7.3 1.0 CE A:LYS231 4.6 8.9 1.0 CA A:ASP15 4.6 8.8 1.0 O A:ASP13 4.6 5.6 1.0 CB A:MET14 4.7 5.7 1.0 C A:ASP15 4.7 11.0 1.0 N A:PHE17 4.7 7.4 1.0 CA A:ASP13 4.8 10.3 1.0 CB A:PHE17 4.9 3.6 1.0 O A:ASP115 4.9 10.5 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Misincorporation G Opposite T After A C at the Primer 3' End (Ca/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 C at the Primer 3' End (Ca/G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:15.2 occ:1.00 OD1 A:ASP115 2.1 8.6 1.0 OD2 A:ASP13 2.2 15.0 1.0 OE2 A:GLU116 2.2 9.8 1.0 O1A A:XG4503 2.3 7.2 1.0 O A:HOH605 2.4 7.9 1.0 O A:HOH607 2.5 12.7 1.0 CG A:ASP115 3.1 13.0 1.0 CG A:ASP13 3.2 11.7 1.0 PA A:XG4503 3.2 12.2 1.0 CD A:GLU116 3.3 19.5 1.0 OD1 A:ASP13 3.5 13.2 1.0 OD2 A:ASP115 3.5 9.0 1.0 MG A:MG501 3.5 10.7 1.0 O2A A:XG4503 3.5 15.2 1.0 O5' A:XG4503 3.6 10.1 1.0 OG A:SER113 3.8 12.1 1.0 C5' A:XG4503 3.9 8.0 1.0 O A:HOH644 3.9 13.3 1.0 OE1 A:GLU116 4.0 20.2 1.0 O A:HOH695 4.2 29.5 1.0 CG A:GLU116 4.2 8.1 1.0 CB A:GLU116 4.3 11.2 1.0 CB A:ASP115 4.4 7.6 1.0 NZ A:LYS224 4.4 15.4 1.0 O A:HOH779 4.5 22.2 1.0 CB A:ASP13 4.5 12.0 1.0 C A:ASP115 4.6 12.6 1.0 N3A A:XG4503 4.6 13.1 1.0 O A:ASP115 4.6 10.5 1.0 O1G A:XG4503 4.6 8.3 1.0 N A:GLU116 4.8 10.2 1.0 O1B A:XG4503 4.8 9.4 1.0 CB A:SER113 4.9 11.3 1.0 CA A:ASP115 4.9 9.9 1.0 O A:HOH676 4.9 15.3 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