Magnesium in PDB 5dlg: Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Methylhymidine

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Methylhymidine:
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Methylhymidine, PDB code: 5dlg was solved by A.Patra, D.K.Oflaherty, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.90 / 2.35
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.656, 98.656, 82.131, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Methylhymidine (pdb code 5dlg). 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 Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Methylhymidine, PDB code: 5dlg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Methylhymidine


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 Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Methylhymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:24.2 occ:1.00 OD1 A:ASP13 1.9 29.2 1.0 OD2 A:ASP115 2.1 29.3 1.0 O1G A:XG4504 2.2 26.3 1.0 O A:MET14 2.2 22.6 1.0 O1B A:XG4504 2.2 22.2 1.0 O1A A:XG4504 2.3 24.9 1.0 CG A:ASP115 2.9 28.0 1.0 CG A:ASP13 2.9 28.1 1.0 OD1 A:ASP115 3.0 41.4 1.0 C A:MET14 3.3 21.0 1.0 PB A:XG4504 3.4 24.2 1.0 OD2 A:ASP13 3.4 30.7 1.0 PG A:XG4504 3.4 23.4 1.0 MG A:MG503 3.5 33.0 1.0 PA A:XG4504 3.6 26.6 1.0 N A:MET14 3.7 28.2 1.0 O3B A:XG4504 3.8 25.8 1.0 O A:HOH638 3.8 28.3 1.0 NZ A:LYS231 3.8 23.4 1.0 O3G A:XG4504 3.9 22.6 1.0 CA A:MET14 4.0 26.2 1.0 N3A A:XG4504 4.0 28.4 1.0 C A:ASP13 4.1 23.1 1.0 O A:HOH641 4.1 27.8 1.0 C5' A:XG4504 4.1 24.7 1.0 CB A:ASP13 4.2 26.5 1.0 CB A:ASP115 4.3 27.6 1.0 O5' A:XG4504 4.3 27.0 1.0 N A:ASP15 4.4 21.7 1.0 CB A:MET14 4.5 25.0 1.0 N A:CYS16 4.6 21.4 1.0 CA A:ASP13 4.6 24.7 1.0 O A:ASP13 4.6 22.5 1.0 CA A:ASP15 4.6 21.6 1.0 O2G A:XG4504 4.6 27.6 1.0 O2B A:XG4504 4.7 24.1 1.0 N A:PHE17 4.7 24.0 1.0 CE A:LYS231 4.8 25.4 1.0 C A:ASP15 4.8 22.3 1.0 O2A A:XG4504 4.8 32.4 1.0 CB A:PHE17 4.9 20.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Methylhymidine


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 Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Methylhymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:33.0 occ:1.00 OE2 A:GLU116 1.9 28.7 1.0 O A:HOH641 2.1 27.8 1.0 OD2 A:ASP13 2.2 30.7 1.0 O3' P:DT8 2.5 38.0 1.0 O1A A:XG4504 2.5 24.9 1.0 CG A:ASP115 3.0 28.0 1.0 OD1 A:ASP115 3.1 41.4 1.0 CD A:GLU116 3.1 27.2 1.0 CG A:ASP13 3.2 28.1 1.0 OD2 A:ASP115 3.3 29.3 1.0 OG A:SER113 3.5 24.6 1.0 CB A:ASP115 3.5 27.6 1.0 PA A:XG4504 3.5 26.6 1.0 C3' P:DT8 3.5 42.5 1.0 MG A:MG502 3.5 24.2 1.0 OD1 A:ASP13 3.6 29.2 1.0 O5' A:XG4504 3.6 27.0 1.0 C5' A:XG4504 3.8 24.7 1.0 OE1 A:GLU116 3.9 28.8 1.0 CG A:GLU116 4.0 23.7 1.0 CB A:GLU116 4.0 23.8 1.0 O2A A:XG4504 4.0 32.4 1.0 N A:GLU116 4.2 26.1 1.0 O A:HOH638 4.2 28.3 1.0 C A:ASP115 4.3 27.8 1.0 CA A:ASP115 4.4 23.7 1.0 C4' P:DT8 4.4 37.8 1.0 CB A:ASP13 4.5 26.5 1.0 CB A:SER113 4.6 24.6 1.0 O1G A:XG4504 4.7 26.3 1.0 O1B A:XG4504 4.7 22.2 1.0 CA A:GLU116 4.8 24.6 1.0 C2' P:DT8 4.8 38.3 1.0 NZ A:LYS224 4.8 29.8 1.0 N A:ASP115 4.8 24.9 1.0 O A:ASP115 4.9 28.1 1.0

D.K.O'flaherty, A.Patra, Y.Su, F.P.Guengerich, M.Egli, C.J.Wilds. Lesion Orientation OFO4-Alkylthymidine Influences Replication By Human Dna Polymeraseeta. Chem Sci V. 7 4896 2016.
ISSN: ISSN 2041-6520
PubMed: 27574558
DOI: 10.1039/C6SC00666C