Magnesium in PDB 3mr2: Human Dna Polymerase Eta in Complex with Normal Dna and Incoming Nucleotide (Nrm)

All present enzymatic activity of Human Dna Polymerase Eta in Complex with Normal Dna and Incoming Nucleotide (Nrm):
2.7.7.7;

The structure of Human Dna Polymerase Eta in Complex with Normal Dna and Incoming Nucleotide (Nrm), PDB code: 3mr2 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)	42.28 / 1.83
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.458, 98.458, 82.498, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 19.7

The binding sites of Magnesium atom in the Human Dna Polymerase Eta in Complex with Normal Dna and Incoming Nucleotide (Nrm) (pdb code 3mr2). 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 in Complex with Normal Dna and Incoming Nucleotide (Nrm), PDB code: 3mr2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta in Complex with Normal Dna and Incoming Nucleotide (Nrm)


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 in Complex with Normal Dna and Incoming Nucleotide (Nrm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg434 b:12.2 occ:1.00 OD1 A:ASP115 2.1 11.2 1.0 O A:MET14 2.1 12.1 1.0 OD1 A:ASP13 2.1 12.8 1.0 O1B A:DZ4433 2.1 10.2 1.0 O1G A:DZ4433 2.2 12.5 1.0 O1A A:DZ4433 2.3 11.0 1.0 CG A:ASP13 3.1 9.1 1.0 PB A:DZ4433 3.1 13.8 1.0 CG A:ASP115 3.1 11.9 1.0 C A:MET14 3.2 12.3 1.0 PG A:DZ4433 3.3 13.5 1.0 PA A:DZ4433 3.3 13.0 1.0 N3A A:DZ4433 3.4 11.8 1.0 OD2 A:ASP13 3.4 11.6 1.0 O3B A:DZ4433 3.6 12.3 1.0 MG A:MG435 3.6 13.9 1.0 OD2 A:ASP115 3.6 10.5 1.0 NZ A:LYS231 3.8 13.9 1.0 N A:MET14 3.8 11.4 1.0 O A:HOH491 3.9 19.2 1.0 O2G A:DZ4433 4.0 11.9 1.0 CA A:MET14 4.0 12.0 1.0 C5' A:DZ4433 4.0 11.3 1.0 O5' A:DZ4433 4.1 10.9 1.0 O2B A:DZ4433 4.2 11.8 1.0 C A:ASP13 4.2 11.6 1.0 N A:ASP15 4.3 11.8 1.0 CB A:ASP13 4.3 10.5 1.0 CB A:ASP115 4.4 12.1 1.0 O A:HOH463 4.4 9.4 1.0 O3G A:DZ4433 4.4 13.1 1.0 CA A:ASP15 4.5 14.0 1.0 N A:CYS16 4.5 13.8 1.0 O2A A:DZ4433 4.5 12.1 1.0 CB A:MET14 4.5 14.3 1.0 C A:ASP15 4.6 14.6 1.0 CE A:LYS231 4.6 13.7 1.0 O A:ASP13 4.7 11.6 1.0 N A:PHE17 4.7 10.6 1.0 CB A:PHE17 4.7 10.9 1.0 CA A:ASP13 4.8 9.8 1.0 O A:ASP115 4.9 12.4 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta in Complex with Normal Dna and Incoming Nucleotide (Nrm)


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 in Complex with Normal Dna and Incoming Nucleotide (Nrm) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg435 b:13.9 occ:1.00 OD2 A:ASP115 2.0 10.5 1.0 OD2 A:ASP13 2.0 11.6 1.0 OE2 A:GLU116 2.1 15.4 1.0 O A:HOH463 2.2 9.4 1.0 O3' P:DT9 2.2 14.6 1.0 O1A A:DZ4433 2.3 11.0 1.0 CG A:ASP115 3.0 11.9 1.0 CD A:GLU116 3.1 18.6 1.0 CG A:ASP13 3.1 9.1 1.0 C3' P:DT9 3.2 14.6 1.0 PA A:DZ4433 3.2 13.0 1.0 OD1 A:ASP115 3.4 11.2 1.0 OD1 A:ASP13 3.5 12.8 1.0 MG A:MG434 3.6 12.2 1.0 O5' A:DZ4433 3.6 10.9 1.0 O2A A:DZ4433 3.6 12.1 1.0 OG A:SER113 3.8 14.7 1.0 OE1 A:GLU116 3.8 20.8 1.0 C4' P:DT9 4.0 16.4 1.0 CG A:GLU116 4.1 16.8 1.0 C5' A:DZ4433 4.1 11.3 1.0 O A:HOH491 4.2 19.2 1.0 CB A:GLU116 4.2 14.3 1.0 O P:HOH75 4.3 16.8 1.0 O1 A:GOL438 4.3 30.7 1.0 CB A:ASP115 4.4 12.1 1.0 CB A:ASP13 4.4 10.5 1.0 C2' P:DT9 4.4 14.7 1.0 C1 A:GOL438 4.4 34.1 1.0 C A:ASP115 4.6 13.9 1.0 N3A A:DZ4433 4.6 11.8 1.0 O A:ASP115 4.6 12.4 1.0 O1G A:DZ4433 4.8 12.5 1.0 C5' P:DT9 4.8 15.8 1.0 CB A:SER113 4.8 13.9 1.0 N A:GLU116 4.9 13.8 1.0 O1B A:DZ4433 4.9 10.2 1.0 CA A:ASP115 4.9 12.8 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