Magnesium in PDB 5dg9: Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion

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

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion, PDB code: 5dg9 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)	42.32 / 2.15
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.929, 98.929, 81.712, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 22.2

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion (pdb code 5dg9). 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 Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion, PDB code: 5dg9:
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 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 Dgmpnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:35.7 occ:1.00 OD1 A:ASP13 2.2 33.7 1.0 O A:HOH601 2.2 33.8 1.0 OD1 A:ASP115 2.3 31.0 1.0 O1A A:XG4501 2.3 33.9 1.0 CG A:GLU116 2.4 28.0 1.0 O3' P:DT8 2.5 37.7 1.0 OE2 A:GLU116 2.5 43.1 1.0 CD A:GLU116 2.9 34.6 1.0 CG A:ASP115 3.0 32.3 1.0 OD2 A:ASP115 3.1 31.7 1.0 CG A:ASP13 3.2 30.8 1.0 C3' P:DT8 3.3 37.2 1.0 PA A:XG4501 3.5 39.3 1.0 MG A:MG503 3.5 37.0 1.0 OD2 A:ASP13 3.6 30.3 1.0 O2A A:XG4501 3.8 37.6 1.0 OG A:SER113 3.9 22.8 1.0 CB A:GLU116 3.9 23.3 1.0 O5' A:XG4501 3.9 39.9 1.0 C4' P:DT8 4.0 31.4 1.0 OE1 A:GLU116 4.1 35.6 1.0 C5' A:XG4501 4.1 33.6 1.0 C A:ASP115 4.2 27.0 1.0 O A:ASP115 4.2 22.0 1.0 O A:HOH638 4.2 34.4 1.0 N A:GLU116 4.3 22.8 1.0 CB A:ASP115 4.4 23.0 1.0 CB A:ASP13 4.4 25.5 1.0 O A:HOH604 4.5 40.1 1.0 CA A:GLU116 4.5 25.6 1.0 O1G A:XG4501 4.5 29.9 1.0 C2' P:DT8 4.6 35.0 1.0 C5' P:DT8 4.8 39.0 1.0 CA A:ASP115 4.8 22.6 1.0 O A:HOH679 4.8 34.8 1.0 O1B A:XG4501 4.9 27.6 1.0 N3A A:XG4501 4.9 35.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dgmpnpp 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 Dgmpnpp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:37.0 occ:1.00 O1G A:XG4501 1.9 29.9 1.0 O1B A:XG4501 2.1 27.6 1.0 OD2 A:ASP115 2.1 31.7 1.0 OD2 A:ASP13 2.2 30.3 1.0 O A:MET14 2.2 26.7 1.0 O1A A:XG4501 2.4 33.9 1.0 PB A:XG4501 3.0 42.3 1.0 PG A:XG4501 3.1 37.9 1.0 CG A:ASP13 3.2 30.8 1.0 CG A:ASP115 3.2 32.3 1.0 PA A:XG4501 3.3 39.3 1.0 O3B A:XG4501 3.4 32.7 1.0 C A:MET14 3.4 20.1 1.0 N3A A:XG4501 3.4 35.9 1.0 OD1 A:ASP13 3.5 33.7 1.0 MG A:MG502 3.5 35.7 1.0 OD1 A:ASP115 3.7 31.0 1.0 C5' A:XG4501 3.8 33.6 1.0 O A:HOH638 3.8 34.4 1.0 O3G A:XG4501 3.8 28.7 1.0 N A:MET14 4.0 19.2 1.0 O5' A:XG4501 4.0 39.9 1.0 CA A:MET14 4.2 20.8 1.0 O A:HOH691 4.2 26.8 1.0 N A:CYS16 4.2 24.2 1.0 O A:HOH601 4.2 33.8 1.0 O2G A:XG4501 4.3 37.3 1.0 O2B A:XG4501 4.3 32.0 1.0 N A:ASP15 4.3 19.1 1.0 CB A:ASP115 4.4 23.0 1.0 C A:ASP13 4.4 20.7 1.0 N A:PHE17 4.5 19.9 1.0 CB A:ASP13 4.5 25.5 1.0 CA A:ASP15 4.5 22.5 1.0 O2A A:XG4501 4.5 37.6 1.0 C A:ASP15 4.6 21.8 1.0 CB A:MET14 4.6 21.6 1.0 CB A:PHE17 4.7 17.3 1.0 O A:ASP13 4.8 17.5 1.0 O A:ASP115 4.8 22.0 1.0 CA A:CYS16 4.8 23.9 1.0 CA A:ASP13 4.9 18.5 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