Magnesium in PDB 4j9o: Human Dna Polymerase Eta-Dna Ternary Complex: Primer Extension After A T:G Mispair

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Primer Extension After A T:G Mispair:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Primer Extension After A T:G Mispair, PDB code: 4j9o 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)	27.09 / 2.60
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.490, 99.490, 81.580, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 23.4

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Primer Extension After A T:G Mispair (pdb code 4j9o). 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: Primer Extension After A T:G Mispair, PDB code: 4j9o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Primer Extension After A T:G Mispair


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: Primer Extension After A T:G Mispair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:28.4 occ:1.00 OD2 A:ASP115 2.1 29.4 1.0 O A:MET14 2.1 29.0 1.0 O1B A:DZ4503 2.1 30.9 1.0 OD1 A:ASP13 2.1 30.0 1.0 O1A A:DZ4503 2.3 30.2 1.0 O1G A:DZ4503 2.4 27.3 1.0 CG A:ASP13 2.9 30.1 1.0 PB A:DZ4503 3.1 34.7 1.0 OD2 A:ASP13 3.2 31.2 1.0 CG A:ASP115 3.2 30.8 1.0 O3B A:DZ4503 3.3 30.3 1.0 C A:MET14 3.3 28.4 1.0 MG A:MG502 3.4 29.5 1.0 PG A:DZ4503 3.4 28.9 1.0 PA A:DZ4503 3.5 31.3 1.0 N3A A:DZ4503 3.6 34.0 1.0 N A:MET14 3.9 29.0 1.0 OD1 A:ASP115 3.9 32.7 1.0 O2G A:DZ4503 3.9 30.4 1.0 O5' A:DZ4503 4.0 32.2 1.0 C5' A:DZ4503 4.0 29.5 1.0 CA A:MET14 4.1 27.8 1.0 C A:ASP13 4.2 28.7 1.0 NZ A:LYS231 4.2 25.8 1.0 CB A:ASP13 4.3 28.9 1.0 N A:ASP15 4.3 26.2 1.0 CB A:ASP115 4.4 28.1 1.0 N A:CYS16 4.4 28.6 1.0 O2B A:DZ4503 4.4 31.7 1.0 O A:ASP13 4.5 29.2 1.0 CA A:ASP15 4.6 26.6 1.0 CB A:MET14 4.6 26.5 1.0 N A:PHE17 4.7 26.8 1.0 CA A:ASP13 4.7 27.6 1.0 O3G A:DZ4503 4.7 35.0 1.0 C A:ASP15 4.7 27.4 1.0 O2A A:DZ4503 4.8 33.0 1.0 O A:ASP115 4.9 31.4 1.0 CB A:PHE17 4.9 23.4 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Primer Extension After A T:G Mispair


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: Primer Extension After A T:G Mispair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:29.5 occ:1.00 O1A A:DZ4503 2.1 30.2 1.0 OD2 A:ASP13 2.1 31.2 1.0 OE1 A:GLU116 2.3 34.2 1.0 OD1 A:ASP115 2.4 32.7 1.0 O3' P:DG9 2.6 38.3 1.0 OD2 A:ASP115 3.0 29.4 1.0 CG A:ASP115 3.1 30.8 1.0 PA A:DZ4503 3.1 31.3 1.0 O5' A:DZ4503 3.2 32.2 1.0 CG A:ASP13 3.2 30.1 1.0 MG A:MG501 3.4 28.4 1.0 O2A A:DZ4503 3.5 33.0 1.0 CD A:GLU116 3.5 32.7 1.0 C3' P:DG9 3.6 49.1 1.0 OD1 A:ASP13 3.6 30.0 1.0 C5' A:DZ4503 4.1 29.5 1.0 OG A:SER113 4.2 31.0 1.0 OE2 A:GLU116 4.3 34.5 1.0 CG A:GLU116 4.4 30.1 1.0 CB A:GLU116 4.4 29.8 1.0 N3A A:DZ4503 4.5 34.0 1.0 CB A:ASP13 4.5 28.9 1.0 CB A:ASP115 4.5 28.1 1.0 O1G A:DZ4503 4.6 27.3 1.0 C4' P:DG9 4.7 45.4 1.0 O1B A:DZ4503 4.7 30.9 1.0 C2' P:DG9 4.7 46.7 1.0 C A:ASP115 4.8 30.5 1.0 O A:ASP115 4.8 31.4 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