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Magnesium in PDB 8uk4: Crystal Structure of Human Polymerase Eta with Incoming Dtmpnpp Nucleotide Opposite Urea Lesion

Enzymatic activity of Crystal Structure of Human Polymerase Eta with Incoming Dtmpnpp Nucleotide Opposite Urea Lesion

All present enzymatic activity of Crystal Structure of Human Polymerase Eta with Incoming Dtmpnpp Nucleotide Opposite Urea Lesion:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Polymerase Eta with Incoming Dtmpnpp Nucleotide Opposite Urea Lesion, PDB code: 8uk4 was solved by R.Tomar, M.Egli, M.P.Stone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.78 / 3.02
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.795, 98.795, 80.29, 90, 90, 120
R / Rfree (%) 17.4 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Polymerase Eta with Incoming Dtmpnpp Nucleotide Opposite Urea Lesion (pdb code 8uk4). 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 Crystal Structure of Human Polymerase Eta with Incoming Dtmpnpp Nucleotide Opposite Urea Lesion, PDB code: 8uk4:

Magnesium binding site 1 out of 1 in 8uk4

Go back to Magnesium Binding Sites List in 8uk4
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Polymerase Eta with Incoming Dtmpnpp Nucleotide Opposite Urea Lesion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Polymerase Eta with Incoming Dtmpnpp Nucleotide Opposite Urea Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:72.9
occ:1.00
 OD2 A:ASP115 1.8 75.2 1.0
O1B A:1FZ501 2.1 83.8 1.0
O1G A:1FZ501 2.3 73.5 1.0
O2A A:1FZ501 2.5 70.1 1.0
O A:MET14 2.5 82.1 1.0
OD2 A:ASP13 2.8 79.2 1.0
CG A:ASP115 2.9 84.1 1.0
OD1 A:ASP13 3.2 85.2 1.0
PB A:1FZ501 3.2 79.4 1.0
CG A:ASP13 3.2 79.2 1.0
OD1 A:ASP115 3.4 78.2 1.0
PA A:1FZ501 3.5 84.5 1.0
PG A:1FZ501 3.6 77.3 1.0
N3A A:1FZ501 3.6 86.1 1.0
C A:MET14 3.7 80.3 1.0
O3B A:1FZ501 3.8 77.5 1.0
N A:MET14 4.1 70.0 1.0
C5' A:1FZ501 4.1 78.5 1.0
CB A:ASP115 4.2 72.4 1.0
O5' A:1FZ501 4.4 84.3 1.0
CA A:MET14 4.4 73.8 1.0
O2G A:1FZ501 4.5 76.5 1.0
C A:ASP13 4.5 68.3 1.0
O2B A:1FZ501 4.5 75.5 1.0
CB A:ASP13 4.6 71.4 1.0
O3G A:1FZ501 4.6 84.3 1.0
O3' P:DT8 4.7 75.7 1.0
N A:ASP15 4.7 67.3 1.0
N A:CYS16 4.7 77.8 0.4
O1A A:1FZ501 4.7 88.4 1.0
N A:PHE17 4.8 72.7 1.0
N A:CYS16 4.8 77.8 0.6
O A:ASP115 4.8 59.1 1.0
CB A:PHE17 4.9 77.2 1.0
CA A:ASP13 4.9 64.3 1.0
CA A:ASP15 4.9 74.9 1.0
OE2 A:GLU116 4.9 82.7 1.0
CB A:MET14 4.9 66.6 1.0
NZ A:LYS231 5.0 81.9 1.0

Reference:

R.Tomar, S.Li, M.Egli, M.P.Stone. Replication Bypass of the N -(2-Deoxy-D-Erythro-Pentofuranosyl)-Urea Dna Lesion By Human Dna Polymerase Eta. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 38413007
DOI: 10.1021/ACS.BIOCHEM.3C00569
Page generated: Fri Aug 15 16:58:19 2025

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