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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 3si8:

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

Magnesium Binding Sites:

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 3si8

Go back to Magnesium Binding Sites List in 3si8
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 3si8

Go back to Magnesium Binding Sites List in 3si8
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

Reference:

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
Page generated: Thu Aug 15 11:01:36 2024

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