Magnesium in PDB 5dg8: Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion:
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion, PDB code: 5dg8 was solved by A.Patra, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.34 / 2.12
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.132, 99.132, 81.401, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 23.9

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion (pdb code 5dg8). 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 Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion, PDB code: 5dg8:
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 Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine 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 Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:15.2 occ:1.00 O A:MET14 2.2 20.9 1.0 OD1 A:ASP13 2.2 28.9 1.0 O3G A:DZ4501 2.2 23.1 1.0 OD2 A:ASP115 2.2 21.4 1.0 O2A A:DZ4501 2.3 26.6 1.0 O2B A:DZ4501 2.3 18.9 1.0 PB A:DZ4501 3.3 24.6 1.0 CG A:ASP13 3.3 25.7 1.0 CG A:ASP115 3.3 25.6 1.0 C A:MET14 3.4 17.1 1.0 PA A:DZ4501 3.4 28.8 1.0 PG A:DZ4501 3.4 25.9 1.0 N3A A:DZ4501 3.6 25.1 1.0 O3B A:DZ4501 3.6 28.7 1.0 OD1 A:ASP115 3.7 25.2 1.0 OD2 A:ASP13 3.7 37.1 1.0 O A:HOH644 3.8 37.2 1.0 MG A:MG503 3.8 42.1 1.0 N A:MET14 4.0 18.9 1.0 C5' A:DZ4501 4.0 29.6 1.0 O2G A:DZ4501 4.1 23.4 1.0 O5' A:DZ4501 4.1 27.9 1.0 CA A:MET14 4.2 21.9 1.0 NZ A:LYS231 4.2 27.4 1.0 C A:ASP13 4.3 18.7 1.0 N A:ASP15 4.4 17.1 1.0 O1G A:DZ4501 4.5 23.9 1.0 O1A A:DZ4501 4.5 23.9 1.0 CB A:ASP13 4.5 21.8 1.0 O1B A:DZ4501 4.5 22.8 1.0 N A:CYS16 4.6 19.7 1.0 CA A:ASP15 4.6 20.1 1.0 CB A:ASP115 4.6 20.0 1.0 CB A:MET14 4.6 21.9 1.0 C A:ASP15 4.7 21.0 1.0 N A:PHE17 4.7 16.8 1.0 O A:ASP13 4.7 21.0 1.0 CB A:PHE17 4.8 14.1 1.0 CA A:ASP13 4.8 17.6 1.0 O A:ASP115 4.9 20.9 1.0 OE2 A:GLU116 4.9 43.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine 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 Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:42.1 occ:1.00 O3' P:DT8 2.0 34.5 1.0 OE2 A:GLU116 2.2 43.0 1.0 OD1 A:ASP115 2.2 25.2 1.0 O2A A:DZ4501 2.5 26.6 1.0 C3' P:DT8 2.8 37.1 1.0 CD A:GLU116 2.8 37.6 1.0 CG A:GLU116 2.8 30.8 1.0 CG A:ASP115 3.2 25.6 1.0 PA A:DZ4501 3.4 28.8 1.0 OG A:SER113 3.5 24.9 1.0 OD2 A:ASP115 3.6 21.4 1.0 OD1 A:ASP13 3.6 28.9 1.0 C4' P:DT8 3.6 31.4 1.0 O5' A:DZ4501 3.6 27.9 1.0 O1A A:DZ4501 3.7 23.9 1.0 OD2 A:ASP13 3.7 37.1 1.0 MG A:MG502 3.8 15.2 1.0 CG A:ASP13 3.9 25.7 1.0 OE1 A:GLU116 3.9 33.8 1.0 C5' A:DZ4501 4.0 29.6 1.0 C2' P:DT8 4.1 38.1 1.0 CB A:GLU116 4.1 21.4 1.0 C5' P:DT8 4.4 37.5 1.0 O A:HOH644 4.4 37.2 1.0 C A:ASP115 4.5 23.2 1.0 CB A:SER113 4.6 25.2 1.0 CB A:ASP115 4.6 20.0 1.0 O A:ASP115 4.6 20.9 1.0 N A:GLU116 4.6 22.1 1.0 O4' P:DT8 4.8 33.7 1.0 N3A A:DZ4501 4.9 25.1 1.0 CA A:ASP115 4.9 19.7 1.0 C1' P:DT8 4.9 37.9 1.0 N A:ASP115 4.9 23.7 1.0 CA A:GLU116 4.9 26.4 1.0

A.Patra, Y.Su, Q.Zhang, K.M.Johnson, F.P.Guengerich, M.Egli. Structural and Kinetic Analysis of Miscoding Opposite the Dna Adduct 1,N6-Ethenodeoxyadenosine By Human Translesion Dna Polymerase Eta. J.Biol.Chem. V. 291 14134 2016.
ISSN: ESSN 1083-351X
PubMed: 27226627
DOI: 10.1074/JBC.M116.732487