Magnesium in PDB 3mr3: Human Dna Polymerase Eta - Dna Ternary Complex with the 3'T of A Cpd in the Active Site (TT1)

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex with the 3'T of A Cpd in the Active Site (TT1):
2.7.7.7;

The structure of Human Dna Polymerase Eta - Dna Ternary Complex with the 3'T of A Cpd in the Active Site (TT1), PDB code: 3mr3 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)	37.05 / 1.75
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.243, 98.243, 82.306, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 20.5

The binding sites of Magnesium atom in the Human Dna Polymerase Eta - Dna Ternary Complex with the 3'T of A Cpd in the Active Site (TT1) (pdb code 3mr3). 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 the 3'T of A Cpd in the Active Site (TT1), PDB code: 3mr3:
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 the 3'T of A Cpd in the Active Site (TT1)


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 the 3'T of A Cpd in the Active Site (TT1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg434 b:9.5 occ:1.00 OD1 A:ASP13 2.0 9.6 1.0 OD1 A:ASP115 2.1 6.7 1.0 O A:MET14 2.1 7.5 1.0 O1B A:DZ4433 2.2 9.9 1.0 O1G A:DZ4433 2.2 9.9 1.0 O1A A:DZ4433 2.3 11.1 1.0 CG A:ASP13 3.0 8.2 1.0 PB A:DZ4433 3.1 9.5 1.0 CG A:ASP115 3.2 8.4 1.0 PG A:DZ4433 3.2 12.4 1.0 C A:MET14 3.3 9.4 1.0 PA A:DZ4433 3.3 9.1 1.0 OD2 A:ASP13 3.4 12.4 1.0 N3A A:DZ4433 3.4 10.7 1.0 O3B A:DZ4433 3.5 8.1 1.0 MG A:MG435 3.6 9.6 1.0 OD2 A:ASP115 3.6 7.1 1.0 N A:MET14 3.8 8.5 1.0 NZ A:LYS231 3.9 10.6 1.0 O A:HOH489 3.9 16.6 1.0 O2G A:DZ4433 3.9 7.3 1.0 CA A:MET14 4.0 7.7 1.0 C5' A:DZ4433 4.0 8.5 1.0 O5' A:DZ4433 4.1 7.9 1.0 C A:ASP13 4.2 7.6 1.0 O2B A:DZ4433 4.2 8.4 1.0 N A:ASP15 4.3 8.7 1.0 CB A:ASP13 4.3 8.8 1.0 O3G A:DZ4433 4.3 10.4 1.0 CB A:ASP115 4.4 7.3 1.0 O A:HOH449 4.4 7.8 1.0 N A:CYS16 4.5 9.3 1.0 CA A:ASP15 4.5 9.8 1.0 CB A:MET14 4.5 9.6 1.0 O2A A:DZ4433 4.5 10.3 1.0 O A:ASP13 4.6 8.2 1.0 CE A:LYS231 4.6 15.4 1.0 C A:ASP15 4.6 10.0 1.0 N A:PHE17 4.7 8.7 1.0 CA A:ASP13 4.7 8.1 1.0 CB A:PHE17 4.8 9.2 1.0 O A:ASP115 4.9 8.1 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta - Dna Ternary Complex with the 3'T of A Cpd in the Active Site (TT1)


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 the 3'T of A Cpd in the Active Site (TT1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg435 b:9.6 occ:1.00 OD2 A:ASP13 2.0 12.4 1.0 OD2 A:ASP115 2.0 7.1 1.0 OE2 A:GLU116 2.1 11.8 1.0 O A:HOH449 2.1 7.8 1.0 O3' P:DT9 2.2 12.9 1.0 O1A A:DZ4433 2.4 11.1 1.0 CG A:ASP115 3.0 8.4 1.0 CG A:ASP13 3.1 8.2 1.0 CD A:GLU116 3.1 14.3 1.0 C3' P:DT9 3.2 11.7 1.0 PA A:DZ4433 3.2 9.1 1.0 OD1 A:ASP115 3.3 6.7 1.0 OD1 A:ASP13 3.5 9.6 1.0 MG A:MG434 3.6 9.5 1.0 O5' A:DZ4433 3.6 7.9 1.0 O2A A:DZ4433 3.7 10.3 1.0 OG A:SER113 3.8 12.9 1.0 OE1 A:GLU116 3.8 17.1 1.0 C4' P:DT9 4.0 12.0 1.0 CG A:GLU116 4.1 12.4 1.0 C5' A:DZ4433 4.1 8.5 1.0 O A:HOH489 4.2 16.6 1.0 CB A:GLU116 4.2 10.1 1.0 O P:HOH57 4.3 13.8 1.0 NZ A:LYS224 4.3 1.1 0.2 CB A:ASP13 4.4 8.8 1.0 C2' P:DT9 4.4 13.0 1.0 CB A:ASP115 4.4 7.3 1.0 C A:ASP115 4.6 9.0 1.0 O A:ASP115 4.6 8.1 1.0 N3A A:DZ4433 4.7 10.7 1.0 CB A:SER113 4.7 13.1 1.0 C5' P:DT9 4.7 14.4 1.0 N A:GLU116 4.8 7.8 1.0 O1G A:DZ4433 4.9 9.9 1.0 CA A:ASP115 4.9 9.0 1.0 O1B A:DZ4433 5.0 9.9 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