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

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

The structure of Crystal Structure of Human Polymerase Eta with Incoming Dgmpnpp Nucleotide Opposite Urea Lesion, PDB code: 8ujx 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)	42.84 / 2.17
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.929, 98.929, 81.568, 90, 90, 120
R / Rfree (%)	17.1 / 22.9

The binding sites of Magnesium atom in the Crystal Structure of Human Polymerase Eta with Incoming Dgmpnpp Nucleotide Opposite Urea Lesion (pdb code 8ujx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Polymerase Eta with Incoming Dgmpnpp Nucleotide Opposite Urea Lesion, PDB code: 8ujx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Polymerase Eta with Incoming Dgmpnpp 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 Dgmpnpp Nucleotide Opposite Urea Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:25.4 occ:1.00 O2B A:XG4501 2.1 24.1 1.0 O2G A:XG4501 2.1 20.8 1.0 O A:MET14 2.1 23.2 1.0 O1A A:XG4501 2.1 24.6 1.0 OD2 A:ASP115 2.2 25.1 1.0 OD1 A:ASP13 2.2 27.5 1.0 PB A:XG4501 3.2 27.5 1.0 CG A:ASP13 3.2 27.6 1.0 CG A:ASP115 3.3 28.7 1.0 C A:MET14 3.3 20.6 1.0 PG A:XG4501 3.4 26.7 1.0 PA A:XG4501 3.4 27.6 1.0 MG A:MG503 3.6 33.8 1.0 OD2 A:ASP13 3.6 35.1 1.0 O3B A:XG4501 3.6 30.0 1.0 N3A A:XG4501 3.7 28.9 1.0 OD1 A:ASP115 3.7 25.5 1.0 O A:HOH662 3.8 27.1 1.0 N A:MET14 3.9 27.0 1.0 NZ A:LYS231 4.0 27.6 1.0 O1G A:XG4501 4.0 26.6 1.0 C5' A:XG4501 4.1 28.6 1.0 CA A:MET14 4.1 25.7 1.0 O A:HOH669 4.1 32.9 1.0 C A:ASP13 4.2 28.2 1.0 O5' A:XG4501 4.3 30.2 1.0 N A:ASP15 4.3 21.9 1.0 CB A:ASP13 4.4 28.9 1.0 O1B A:XG4501 4.5 27.9 1.0 CA A:ASP15 4.5 23.4 1.0 CB A:ASP115 4.5 19.5 1.0 N A:CYS16 4.5 23.1 1.0 CE A:LYS231 4.6 33.8 1.0 O3G A:XG4501 4.6 29.2 1.0 O2A A:XG4501 4.6 31.2 1.0 O A:ASP13 4.6 25.6 1.0 CB A:MET14 4.6 29.0 1.0 N A:PHE17 4.7 22.1 1.0 C A:ASP15 4.7 24.4 1.0 CB A:PHE17 4.7 19.5 1.0 CA A:ASP13 4.8 26.6 1.0 O A:ASP115 5.0 27.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Polymerase Eta with Incoming Dgmpnpp Nucleotide Opposite Urea Lesion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Polymerase Eta with Incoming Dgmpnpp Nucleotide Opposite Urea Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:33.8 occ:1.00 O A:HOH669 2.1 32.9 1.0 OE1 A:GLU116 2.2 37.5 1.0 OD2 A:ASP13 2.2 35.1 1.0 OD1 A:ASP115 2.2 25.5 1.0 O3' P:DT8 2.3 32.4 0.9 O1A A:XG4501 2.4 24.6 1.0 CG A:ASP115 3.1 28.7 1.0 C3' P:DT8 3.1 38.0 0.9 CG A:ASP13 3.2 27.6 1.0 CD A:GLU116 3.2 35.7 1.0 PA A:XG4501 3.3 27.6 1.0 OD2 A:ASP115 3.4 25.1 1.0 OD1 A:ASP13 3.4 27.5 1.0 MG A:MG502 3.6 25.4 1.0 O2A A:XG4501 3.6 31.2 1.0 O5' A:XG4501 3.8 30.2 1.0 OG A:SER113 3.8 27.0 1.0 OE2 A:GLU116 3.9 38.5 1.0 C5' A:XG4501 4.0 28.6 1.0 O A:HOH662 4.0 27.1 1.0 C4' P:DT8 4.1 31.7 0.9 CB A:GLU116 4.2 27.0 1.0 CG A:GLU116 4.2 32.0 1.0 NZ A:LYS224 4.3 41.3 1.0 C2' P:DT8 4.4 37.9 0.9 CB A:ASP13 4.5 28.9 1.0 CB A:ASP115 4.5 19.5 1.0 C A:ASP115 4.6 27.0 1.0 O2G A:XG4501 4.7 20.8 1.0 O A:ASP115 4.7 27.2 1.0 O2B A:XG4501 4.7 24.1 1.0 N A:GLU116 4.8 26.1 1.0 O A:HOH671 4.8 35.0 1.0 C5' P:DT8 4.8 40.9 0.9 N3A A:XG4501 4.8 28.9 1.0 CB A:SER113 4.9 26.8 1.0

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