Magnesium in PDB 3si8: Human Dna Polymerase Eta - Dna Ternary Complex with the 5'T of A Cpd in the Active Site (TT2)

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex with the 5'T of A Cpd in the Active Site (TT2):
2.7.7.7;

The structure of Human Dna Polymerase Eta - Dna Ternary Complex with the 5'T of A Cpd in the Active Site (TT2), PDB code: 3si8 was solved by C.Biertumpfel, Y.Zhao, Y.Kondo, S.Ramon-Maiques, M.Gregory, J.Y.Lee, C.Masutani, A.R.Lehmann, F.Hanaoka, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.28 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.236, 80.259, 139.759, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 25.8

The structure of Human Dna Polymerase Eta - Dna Ternary Complex with the 5'T of A Cpd in the Active Site (TT2) also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Magnesium atom in the Human Dna Polymerase Eta - Dna Ternary Complex with the 5'T of A Cpd in the Active Site (TT2) (pdb code 3si8). 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 5'T of A Cpd in the Active Site (TT2), PDB code: 3si8:
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 5'T of A Cpd in the Active Site (TT2)


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 5'T of A Cpd in the Active Site (TT2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg450 b:40.3 occ:1.00 OD1 A:ASP13 2.1 59.4 1.0 OD1 A:ASP115 2.2 54.1 1.0 O A:MET14 2.2 47.9 1.0 O1G A:DZ4433 2.3 48.2 1.0 O1A A:DZ4433 2.4 51.2 1.0 O1B A:DZ4433 2.4 54.6 1.0 CG A:ASP13 3.0 55.6 1.0 OD2 A:ASP13 3.2 57.2 1.0 PB A:DZ4433 3.2 54.1 1.0 PG A:DZ4433 3.3 54.3 1.0 PA A:DZ4433 3.3 51.2 1.0 CG A:ASP115 3.4 50.2 1.0 N3A A:DZ4433 3.4 49.0 1.0 C A:MET14 3.5 50.0 1.0 O3B A:DZ4433 3.6 53.8 1.0 MG A:MG451 3.6 40.1 1.0 O2G A:DZ4433 3.9 50.3 1.0 OD2 A:ASP115 3.9 51.7 1.0 O A:HOH475 4.0 57.0 1.0 C5' A:DZ4433 4.1 45.5 1.0 N A:MET14 4.1 50.9 1.0 O5' A:DZ4433 4.2 45.5 1.0 CA A:MET14 4.3 50.4 1.0 CB A:ASP13 4.3 53.1 1.0 O2B A:DZ4433 4.3 57.6 1.0 O A:HOH495 4.4 46.2 1.0 O3G A:DZ4433 4.4 50.6 1.0 NZ A:LYS231 4.4 63.8 1.0 C A:ASP13 4.4 52.2 1.0 N A:CYS16 4.4 53.0 1.0 N A:ASP15 4.4 49.2 1.0 O2A A:DZ4433 4.5 41.7 1.0 CB A:ASP115 4.6 49.7 1.0 CA A:ASP15 4.6 53.0 1.0 N A:PHE17 4.7 55.5 1.0 C A:ASP15 4.7 52.9 1.0 CB A:MET14 4.7 50.9 1.0 CB A:PHE17 4.8 49.3 1.0 O A:ASP13 4.9 53.2 1.0 CA A:ASP13 4.9 52.8 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta - Dna Ternary Complex with the 5'T of A Cpd in the Active Site (TT2)


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 5'T of A Cpd in the Active Site (TT2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg451 b:40.1 occ:1.00 OE2 A:GLU116 1.9 58.2 1.0 OD2 A:ASP13 2.1 57.2 1.0 O A:HOH495 2.2 46.2 1.0 O3' P:DA9 2.2 54.6 1.0 OD2 A:ASP115 2.3 51.7 1.0 O1A A:DZ4433 2.4 51.2 1.0 CD A:GLU116 3.1 57.2 1.0 CG A:ASP115 3.2 50.2 1.0 C3' P:DA9 3.2 53.6 1.0 CG A:ASP13 3.3 55.6 1.0 OD1 A:ASP115 3.3 54.1 1.0 PA A:DZ4433 3.4 51.2 1.0 MG A:MG450 3.6 40.3 1.0 O5' A:DZ4433 3.8 45.5 1.0 OD1 A:ASP13 3.8 59.4 1.0 O2A A:DZ4433 3.8 41.7 1.0 OG A:SER113 3.9 51.0 1.0 OE1 A:GLU116 4.0 60.6 1.0 C4' P:DA9 4.0 57.1 1.0 CG A:GLU116 4.0 55.5 1.0 C5' A:DZ4433 4.2 45.5 1.0 CB A:GLU116 4.2 50.8 1.0 O A:HOH475 4.3 57.0 1.0 O1 A:GOL437 4.3 77.2 1.0 CB A:ASP13 4.5 53.1 1.0 C5' P:DA9 4.5 58.1 1.0 C2' P:DA9 4.5 54.5 1.0 C1 A:GOL437 4.5 77.1 1.0 CB A:ASP115 4.6 49.7 1.0 C A:ASP115 4.7 48.6 1.0 O A:ASP115 4.8 46.6 1.0 N3A A:DZ4433 4.8 49.0 1.0 N A:GLU116 4.8 50.2 1.0 O5' P:DA9 4.9 62.4 1.0 CB A:SER113 4.9 48.9 1.0 C2 A:GOL437 4.9 78.2 1.0 O1G A:DZ4433 4.9 48.2 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