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

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

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Ethylthymidine, PDB code: 5dqh 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)	42.64 / 1.99
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.471, 98.471, 82.230, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 21

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Opposite O4-Ethylthymidine (pdb code 5dqh). 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-Ethylthymidine, PDB code: 5dqh:
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-Ethylthymidine


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-Ethylthymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:18.1 occ:1.00 OD1 A:ASP115 2.0 16.8 1.0 OE2 A:GLU116 2.1 18.0 1.0 O3' P:DT8 2.1 17.9 1.0 O1A A:XG4501 2.1 16.4 1.0 OD1 A:ASP13 2.2 22.5 1.0 O A:HOH694 2.2 16.5 1.0 CG A:ASP115 3.0 22.6 1.0 C3' P:DT8 3.1 28.5 1.0 CG A:ASP13 3.2 17.6 1.0 CD A:GLU116 3.2 26.5 1.0 PA A:XG4501 3.2 23.1 1.0 OD2 A:ASP115 3.3 17.7 1.0 OD2 A:ASP13 3.5 17.8 1.0 MG A:MG503 3.5 19.7 1.0 O5' A:XG4501 3.7 22.1 1.0 O2A A:XG4501 3.7 20.7 1.0 OG A:SER113 3.8 18.4 1.0 OE1 A:GLU116 3.9 21.4 1.0 C5' A:XG4501 3.9 18.9 1.0 C4' P:DT8 4.0 25.6 1.0 O A:HOH631 4.0 22.0 1.0 CB A:GLU116 4.1 15.8 1.0 CG A:GLU116 4.1 18.4 1.0 CB A:ASP115 4.4 13.1 1.0 NZ A:LYS224 4.4 25.0 1.0 C2' P:DT8 4.4 24.4 1.0 O A:HOH703 4.4 27.6 1.0 CB A:ASP13 4.5 17.2 1.0 C A:ASP115 4.5 19.4 1.0 C5' P:DT8 4.6 28.3 0.4 O1G A:XG4501 4.6 15.4 1.0 O A:ASP115 4.6 15.9 1.0 N3A A:XG4501 4.7 23.1 1.0 C5' P:DT8 4.7 30.7 0.6 O1B A:XG4501 4.7 15.2 1.0 N A:GLU116 4.8 16.5 1.0 CA A:ASP115 4.9 15.2 1.0 CB A:SER113 4.9 21.4 1.0

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


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-Ethylthymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:19.7 occ:1.00 O1B A:XG4501 2.0 15.2 1.0 O1G A:XG4501 2.1 15.4 1.0 OD2 A:ASP115 2.1 17.7 1.0 OD2 A:ASP13 2.1 17.8 1.0 O A:MET14 2.2 15.3 1.0 O1A A:XG4501 2.2 16.4 1.0 PB A:XG4501 3.1 20.1 1.0 CG A:ASP13 3.1 17.6 1.0 CG A:ASP115 3.1 22.6 1.0 PG A:XG4501 3.3 23.0 1.0 PA A:XG4501 3.3 23.1 1.0 C A:MET14 3.4 14.4 1.0 MG A:MG502 3.5 18.1 1.0 OD1 A:ASP13 3.5 22.5 1.0 N3A A:XG4501 3.5 23.1 1.0 O3B A:XG4501 3.5 21.9 1.0 OD1 A:ASP115 3.6 16.8 1.0 O A:HOH631 3.7 22.0 1.0 NZ A:LYS231 3.9 12.8 1.0 C5' A:XG4501 3.9 18.9 1.0 O2G A:XG4501 3.9 21.4 1.0 N A:MET14 4.0 13.8 1.0 CA A:MET14 4.2 13.1 1.0 O5' A:XG4501 4.2 22.1 1.0 O A:HOH694 4.3 16.5 1.0 C A:ASP13 4.3 14.4 1.0 CB A:ASP13 4.4 17.2 1.0 N A:ASP15 4.4 15.2 1.0 CB A:ASP115 4.4 13.1 1.0 O2B A:XG4501 4.4 16.0 1.0 O3G A:XG4501 4.5 21.0 1.0 N A:CYS16 4.5 14.4 1.0 O2A A:XG4501 4.5 20.7 1.0 CA A:ASP15 4.6 16.4 1.0 CE A:LYS231 4.6 24.1 1.0 CB A:MET14 4.6 17.3 1.0 N A:PHE17 4.7 10.6 1.0 C A:ASP15 4.7 18.6 1.0 O A:ASP13 4.7 11.3 1.0 CA A:ASP13 4.8 15.6 1.0 CB A:PHE17 4.8 10.1 1.0 O A:ASP115 4.9 15.9 1.0 O3' P:DT8 5.0 17.9 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