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

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

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Opposite O4-Ethylthymidine, PDB code: 5dqg 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)	59.21 / 2.29
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.820, 98.820, 82.017, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 22.7

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Opposite O4-Ethylthymidine (pdb code 5dqg). 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 Dampnpp Opposite O4-Ethylthymidine, PDB code: 5dqg:
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 Dampnpp 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 Dampnpp Opposite O4-Ethylthymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:16.2 occ:1.00 OD2 A:ASP13 2.0 15.4 1.0 O3G A:DZ4501 2.0 15.2 1.0 OD2 A:ASP115 2.1 17.2 1.0 O2B A:DZ4501 2.1 15.8 1.0 O A:MET14 2.2 14.8 1.0 O2A A:DZ4501 2.2 18.4 1.0 CG A:ASP13 2.8 16.5 1.0 OD1 A:ASP13 3.2 19.6 1.0 CG A:ASP115 3.2 19.8 1.0 PB A:DZ4501 3.3 19.5 1.0 PG A:DZ4501 3.3 18.1 1.0 C A:MET14 3.3 15.0 1.0 MG A:MG503 3.3 19.4 1.0 PA A:DZ4501 3.5 18.8 1.0 OD1 A:ASP115 3.7 20.3 1.0 NZ A:LYS231 3.7 26.6 1.0 O3B A:DZ4501 3.7 16.6 1.0 N A:MET14 3.8 14.8 1.0 N3A A:DZ4501 3.8 19.1 1.0 O A:HOH698 4.0 22.8 1.0 C A:ASP13 4.0 15.4 1.0 O2G A:DZ4501 4.0 14.7 1.0 CA A:MET14 4.1 15.3 1.0 CB A:ASP13 4.1 15.7 1.0 C5' A:DZ4501 4.1 19.2 1.0 O A:HOH690 4.2 10.9 1.0 O5' A:DZ4501 4.3 19.5 1.0 N A:ASP15 4.4 15.1 1.0 CE A:LYS231 4.4 27.9 1.0 CB A:ASP115 4.4 19.7 1.0 O A:ASP13 4.4 15.5 1.0 CA A:ASP13 4.5 15.5 1.0 O1G A:DZ4501 4.5 16.4 1.0 CB A:MET14 4.6 16.4 1.0 O1B A:DZ4501 4.6 18.1 1.0 CA A:ASP15 4.6 15.0 1.0 N A:CYS16 4.7 16.1 1.0 O1A A:DZ4501 4.8 16.1 1.0 C A:ASP15 4.8 15.5 1.0 O A:ASP115 4.8 18.1 1.0 N A:PHE17 4.9 17.0 1.0 CB A:PHE17 4.9 17.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp 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 Dampnpp Opposite O4-Ethylthymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:19.4 occ:1.00 O A:HOH690 2.0 10.9 1.0 OD1 A:ASP13 2.0 19.6 1.0 OE1 A:GLU116 2.2 15.1 1.0 O2A A:DZ4501 2.2 18.4 1.0 OD1 A:ASP115 2.2 20.3 1.0 O3' P:DT8 2.3 20.5 1.0 CG A:ASP115 3.0 19.8 1.0 CG A:ASP13 3.1 16.5 1.0 OD2 A:ASP115 3.1 17.2 1.0 PA A:DZ4501 3.2 18.8 1.0 CD A:GLU116 3.2 16.3 1.0 C3' P:DT8 3.3 21.9 1.0 MG A:MG502 3.3 16.2 1.0 OD2 A:ASP13 3.5 15.4 1.0 O1A A:DZ4501 3.6 16.1 1.0 O5' A:DZ4501 3.7 19.5 1.0 OG A:SER113 3.9 16.8 1.0 OE2 A:GLU116 4.0 17.3 1.0 C5' A:DZ4501 4.0 19.2 1.0 O A:HOH698 4.1 22.8 1.0 O A:HOH681 4.2 34.5 1.0 CG A:GLU116 4.2 16.6 1.0 C4' P:DT8 4.2 23.2 1.0 CB A:GLU116 4.3 16.9 1.0 CB A:ASP13 4.4 15.7 1.0 O3G A:DZ4501 4.4 15.2 1.0 O2B A:DZ4501 4.5 15.8 1.0 CB A:ASP115 4.5 19.7 1.0 C2' P:DT8 4.5 22.2 1.0 N3A A:DZ4501 4.7 19.1 1.0 C A:ASP115 4.7 18.6 1.0 O A:ASP115 4.7 18.1 1.0 C5' P:DT8 4.9 24.6 1.0 CB A:SER113 5.0 18.7 1.0 N A:GLU116 5.0 18.1 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