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Magnesium in PDB 6m7u: Human Dna Polymerase Eta in A Non-Productive Ternary Complex with MG2+ and Dtmpnpp Oppositing Cda

Enzymatic activity of Human Dna Polymerase Eta in A Non-Productive Ternary Complex with MG2+ and Dtmpnpp Oppositing Cda

All present enzymatic activity of Human Dna Polymerase Eta in A Non-Productive Ternary Complex with MG2+ and Dtmpnpp Oppositing Cda:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta in A Non-Productive Ternary Complex with MG2+ and Dtmpnpp Oppositing Cda, PDB code: 6m7u was solved by P.Weng, Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.46 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.310, 80.470, 142.070, 90.00, 90.00, 90.00
R / Rfree (%) 25.5 / 28.4

Other elements in 6m7u:

The structure of Human Dna Polymerase Eta in A Non-Productive Ternary Complex with MG2+ and Dtmpnpp Oppositing Cda also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Eta in A Non-Productive Ternary Complex with MG2+ and Dtmpnpp Oppositing Cda (pdb code 6m7u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Dna Polymerase Eta in A Non-Productive Ternary Complex with MG2+ and Dtmpnpp Oppositing Cda, PDB code: 6m7u:

Magnesium binding site 1 out of 1 in 6m7u

Go back to Magnesium Binding Sites List in 6m7u
Magnesium binding site 1 out of 1 in the Human Dna Polymerase Eta in A Non-Productive Ternary Complex with MG2+ and Dtmpnpp Oppositing Cda


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 A Non-Productive Ternary Complex with MG2+ and Dtmpnpp Oppositing Cda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:0.9
occ:1.00
 OD1 A:ASP13 2.0 0.5 1.0
O2B A:1FZ502 2.1 0.6 1.0
O1G A:1FZ502 2.3 0.1 1.0
O A:MET14 2.3 0.1 1.0
OD1 A:ASP115 2.5 93.8 1.0
O1A A:1FZ502 2.6 0.2 1.0
CG A:ASP13 2.8 90.8 1.0
OD2 A:ASP13 3.0 89.0 1.0
PB A:1FZ502 3.2 0.3 1.0
C A:MET14 3.5 95.7 1.0
PG A:1FZ502 3.5 0.2 1.0
O3B A:1FZ502 3.6 0.0 1.0
CG A:ASP115 3.6 93.2 1.0
N3A A:1FZ502 3.7 0.9 1.0
PA A:1FZ502 3.7 1.0 1.0
N A:MET14 4.0 94.8 1.0
NZ A:LYS231 4.1 87.4 1.0
OD2 A:ASP115 4.1 94.7 1.0
CB A:ASP13 4.2 82.0 1.0
C A:ASP13 4.3 87.1 1.0
CA A:MET14 4.3 91.5 1.0
O3G A:1FZ502 4.5 0.3 1.0
O1B A:1FZ502 4.5 0.3 1.0
N A:ASP15 4.5 94.7 1.0
O2G A:1FZ502 4.6 0.3 1.0
C5' A:1FZ502 4.6 0.9 1.0
CA A:ASP15 4.6 99.9 1.0
OE2 A:GLU116 4.6 85.6 1.0
N A:CYS16 4.6 0.9 1.0
O5' A:1FZ502 4.6 0.8 1.0
CA A:ASP13 4.7 77.1 1.0
O2A A:1FZ502 4.8 0.5 1.0
CE A:LYS231 4.8 90.9 1.0
O A:ASP13 4.8 84.4 1.0
CB A:MET14 4.8 90.9 1.0
CB A:ASP115 4.9 89.2 1.0
C A:ASP15 4.9 0.6 1.0
O A:ASP115 4.9 87.2 1.0

Reference:

P.J.Weng, Y.Gao, M.T.Gregory, P.Wang, Y.Wang, W.Yang. Bypassing A 8,5'-Cyclo-2'-Deoxyadenosine Lesion By Human Dna Polymerase Eta at Atomic Resolution. Proc. Natl. Acad. Sci. V. 115 10660 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30275308
DOI: 10.1073/PNAS.1812856115
Page generated: Tue Oct 1 11:35:13 2024

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