Magnesium in PDB 5f9l: Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion:
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion, PDB code: 5f9l 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)	32.44 / 2.59
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.111, 99.111, 81.856, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dampnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion (pdb code 5f9l). 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,N2-Ethenodeoxyguanosine Lesion, PDB code: 5f9l:
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,N2-Ethenodeoxyguanosine 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,N2-Ethenodeoxyguanosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.4 occ:1.00 O2B A:DZ4501 2.0 27.6 1.0 OD2 A:ASP13 2.2 31.7 1.0 O3G A:DZ4501 2.2 31.9 1.0 OD2 A:ASP115 2.3 31.7 1.0 O2A A:DZ4501 2.3 34.7 1.0 O A:MET14 2.3 25.3 1.0 PB A:DZ4501 3.0 36.1 1.0 CG A:ASP13 3.1 26.8 1.0 PA A:DZ4501 3.3 34.1 1.0 N3A A:DZ4501 3.3 44.2 1.0 CG A:ASP115 3.4 33.7 1.0 PG A:DZ4501 3.4 33.6 1.0 OD1 A:ASP13 3.4 30.9 1.0 MG A:MG503 3.5 36.4 1.0 O3B A:DZ4501 3.5 35.8 1.0 C A:MET14 3.5 25.8 1.0 O A:HOH668 3.8 38.0 1.0 C5' A:DZ4501 3.9 35.5 1.0 O5' A:DZ4501 4.0 40.8 1.0 OD1 A:ASP115 4.0 35.5 1.0 N A:MET14 4.1 25.0 1.0 O2G A:DZ4501 4.2 32.5 1.0 NZ A:LYS231 4.3 25.4 1.0 CA A:MET14 4.3 24.9 1.0 O1B A:DZ4501 4.4 33.4 1.0 CB A:ASP115 4.4 24.7 1.0 CB A:ASP13 4.5 25.8 1.0 O1G A:DZ4501 4.5 33.1 1.0 N A:CYS16 4.5 25.5 1.0 C A:ASP13 4.5 25.2 1.0 N A:ASP15 4.5 24.9 1.0 O1A A:DZ4501 4.6 39.1 1.0 CA A:ASP15 4.7 27.1 1.0 N A:PHE17 4.8 22.9 1.0 CE A:LYS231 4.8 31.6 1.0 CB A:MET14 4.8 27.6 1.0 C A:ASP15 4.9 23.3 1.0 CA A:ASP13 5.0 23.6 1.0 O A:ASP13 5.0 29.5 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,N2-Ethenodeoxyguanosine 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,N2-Ethenodeoxyguanosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:36.4 occ:1.00 OE2 A:GLU116 2.1 43.7 1.0 O2A A:DZ4501 2.1 34.7 1.0 OD1 A:ASP13 2.2 30.9 1.0 OD1 A:ASP115 2.7 35.5 1.0 O3' P:DT8 2.9 44.4 1.0 CD A:GLU116 3.0 31.2 1.0 OD2 A:ASP115 3.0 31.7 1.0 CG A:ASP13 3.2 26.8 1.0 CG A:ASP115 3.2 33.7 1.0 C3' P:DT8 3.3 45.4 1.0 PA A:DZ4501 3.4 34.1 1.0 MG A:MG502 3.5 30.4 1.0 O A:HOH668 3.5 38.0 1.0 OD2 A:ASP13 3.5 31.7 1.0 OE1 A:GLU116 3.5 28.7 1.0 O1A A:DZ4501 3.7 39.1 1.0 CG A:GLU116 4.0 33.1 1.0 C4' P:DT8 4.1 43.8 1.0 OG A:SER113 4.1 29.9 1.0 C5' A:DZ4501 4.2 35.5 1.0 O5' A:DZ4501 4.2 40.8 1.0 CB A:GLU116 4.3 27.4 1.0 C5' P:DT8 4.5 47.0 1.0 CB A:ASP13 4.5 25.8 1.0 C2' P:DT8 4.6 46.1 1.0 O3G A:DZ4501 4.6 31.9 1.0 N3A A:DZ4501 4.7 44.2 1.0 CB A:ASP115 4.7 24.7 1.0 O2B A:DZ4501 4.8 27.6 1.0

A.Patra, M.Egli. Bypass of the 1, N2-Ethenodeoxyguanosine Lesion By Human Dna Polymerase Eta To Be Published.