Magnesium in PDB 3mr5: Human Dna Polymerase Eta - Dna Ternary Complex with A Cpd 1BP Upstream of the Active Site (TT3)

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex with A Cpd 1BP Upstream of the Active Site (TT3):
2.7.7.7;

The structure of Human Dna Polymerase Eta - Dna Ternary Complex with A Cpd 1BP Upstream of the Active Site (TT3), PDB code: 3mr5 was solved by C.Biertumpfel, Y.Zhao, S.Ramon-Maiques, M.T.Gregory, J.Y.Lee, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.96 / 1.80
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.125, 99.125, 81.703, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 20.7

The binding sites of Magnesium atom in the Human Dna Polymerase Eta - Dna Ternary Complex with A Cpd 1BP Upstream of the Active Site (TT3) (pdb code 3mr5). 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 with A Cpd 1BP Upstream of the Active Site (TT3), PDB code: 3mr5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta - Dna Ternary Complex with A Cpd 1BP Upstream of the Active Site (TT3)


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 with A Cpd 1BP Upstream of the Active Site (TT3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg434 b:14.0 occ:1.00 OD1 A:ASP13 2.0 11.1 1.0 OD1 A:ASP115 2.1 9.7 1.0 O A:MET14 2.1 10.9 1.0 O1B A:XG4433 2.2 11.5 1.0 O1A A:XG4433 2.2 10.4 1.0 O1G A:XG4433 2.3 11.0 1.0 CG A:ASP13 3.0 10.2 1.0 PB A:XG4433 3.0 11.8 1.0 CG A:ASP115 3.2 11.7 1.0 PA A:XG4433 3.2 13.2 1.0 C A:MET14 3.3 11.0 1.0 N3A A:XG4433 3.3 13.1 1.0 PG A:XG4433 3.3 12.4 1.0 OD2 A:ASP13 3.3 10.9 1.0 O3B A:XG4433 3.5 12.7 1.0 MG A:MG435 3.5 13.8 1.0 OD2 A:ASP115 3.7 10.8 1.0 NZ A:LYS231 3.8 11.6 1.0 N A:MET14 3.9 9.6 1.0 O A:HOH480 3.9 15.6 1.0 C5' A:XG4433 3.9 11.1 1.0 O2G A:XG4433 4.0 10.5 1.0 O5' A:XG4433 4.0 12.1 1.0 CA A:MET14 4.1 9.2 1.0 O2B A:XG4433 4.2 12.5 1.0 C A:ASP13 4.2 9.4 1.0 CB A:ASP13 4.3 11.8 1.0 N A:ASP15 4.3 10.5 1.0 O A:HOH448 4.3 12.6 1.0 O3G A:XG4433 4.4 12.2 1.0 O2A A:XG4433 4.4 12.2 1.0 CB A:ASP115 4.4 11.8 1.0 CA A:ASP15 4.5 13.2 1.0 CB A:MET14 4.6 10.3 1.0 CE A:LYS231 4.6 16.1 1.0 N A:CYS16 4.6 13.1 1.0 O A:ASP13 4.7 9.8 1.0 C A:ASP15 4.7 12.8 1.0 N A:PHE17 4.7 11.1 1.0 CA A:ASP13 4.7 10.5 1.0 CB A:PHE17 4.8 10.3 1.0 O A:ASP115 4.9 13.5 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta - Dna Ternary Complex with A Cpd 1BP Upstream of the Active Site (TT3)


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 with A Cpd 1BP Upstream of the Active Site (TT3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg435 b:13.8 occ:1.00 OD2 A:ASP13 2.0 10.9 1.0 OD2 A:ASP115 2.1 10.8 1.0 OE2 A:GLU116 2.1 15.0 1.0 O A:HOH448 2.1 12.6 1.0 O1A A:XG4433 2.3 10.4 1.0 O3' P:DA9 2.3 14.6 1.0 CG A:ASP115 3.0 11.7 1.0 CG A:ASP13 3.0 10.2 1.0 CD A:GLU116 3.1 16.5 1.0 C3' P:DA9 3.2 17.8 1.0 OD1 A:ASP115 3.2 9.7 1.0 PA A:XG4433 3.2 13.2 1.0 OD1 A:ASP13 3.5 11.1 1.0 MG A:MG434 3.5 14.0 1.0 O2A A:XG4433 3.6 12.2 1.0 O5' A:XG4433 3.6 12.1 1.0 OE1 A:GLU116 3.8 17.4 1.0 OG A:SER113 3.8 16.0 1.0 O1 A:GOL438 4.0 37.8 1.0 C4' P:DA9 4.0 18.6 1.0 CG A:GLU116 4.0 16.6 1.0 C5' A:XG4433 4.1 11.1 1.0 O A:HOH480 4.1 15.6 1.0 CB A:GLU116 4.1 14.7 1.0 CB A:ASP13 4.3 11.8 1.0 O P:HOH18 4.3 14.5 1.0 CB A:ASP115 4.4 11.8 1.0 O2 A:GOL438 4.4 44.4 1.0 C2' P:DA9 4.5 15.0 1.0 C A:ASP115 4.6 14.6 1.0 O A:ASP115 4.6 13.5 1.0 N3A A:XG4433 4.6 13.1 1.0 C1 A:GOL438 4.7 43.9 1.0 C5' P:DA9 4.7 23.2 1.0 CB A:SER113 4.8 13.5 1.0 N A:GLU116 4.8 13.4 1.0 O1G A:XG4433 4.9 11.0 1.0 O1B A:XG4433 4.9 11.5 1.0 CA A:ASP115 5.0 13.3 1.0

C.Biertumpfel, Y.Zhao, Y.Kondo, S.Ramon-Maiques, M.Gregory, J.Y.Lee, C.Masutani, A.R.Lehmann, F.Hanaoka, W.Yang. Structure and Mechanism of Human Dna Polymerase Eta. Nature V. 465 1044 2010.
ISSN: ISSN 0028-0836
PubMed: 20577208
DOI: 10.1038/NATURE09196