Magnesium in PDB 5f9n: Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion

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

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion, PDB code: 5f9n 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)	42.90 / 2.23
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.080, 99.080, 81.890, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 21

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion (pdb code 5f9n). 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 Dcmpnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion, PDB code: 5f9n:
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 Dcmpnpp 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 Dcmpnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:25.6 occ:1.00 OD2 A:ASP13 2.0 33.8 1.0 O1B A:0KX501 2.2 20.8 1.0 OD2 A:ASP115 2.2 29.7 1.0 O3G A:0KX501 2.2 24.2 1.0 O2A A:0KX501 2.2 31.7 1.0 O A:MET14 2.3 22.3 1.0 CG A:ASP13 2.8 27.8 1.0 OD1 A:ASP13 3.0 37.0 1.0 PB A:0KX501 3.2 31.4 1.0 CG A:ASP115 3.3 31.8 1.0 MG A:MG503 3.3 27.3 0.6 PA A:0KX501 3.4 34.9 1.0 PG A:0KX501 3.4 33.5 1.0 C A:MET14 3.5 20.6 1.0 N3A A:0KX501 3.6 31.4 1.0 O3B A:0KX501 3.7 29.6 1.0 O A:HOH619 3.7 36.4 1.0 OD1 A:ASP115 3.8 32.3 1.0 N A:MET14 3.9 21.5 1.0 NZ A:LYS231 4.0 21.5 1.0 C5' A:0KX501 4.0 31.7 1.0 O A:HOH601 4.1 25.7 1.0 O1G A:0KX501 4.1 22.1 1.0 O5' A:0KX501 4.2 37.4 1.0 C A:ASP13 4.2 24.3 1.0 CA A:MET14 4.2 23.4 1.0 CB A:ASP13 4.2 28.8 1.0 N A:ASP15 4.5 19.4 1.0 CB A:ASP115 4.5 21.7 1.0 O2B A:0KX501 4.6 26.1 1.0 O1A A:0KX501 4.6 27.2 1.0 N A:CYS16 4.6 20.1 1.0 CA A:ASP13 4.6 21.1 1.0 O A:ASP13 4.6 22.7 1.0 O2G A:0KX501 4.6 30.5 1.0 CA A:ASP15 4.7 22.6 1.0 CB A:MET14 4.7 21.6 1.0 C A:ASP15 4.8 18.9 1.0 N A:PHE17 4.8 18.9 1.0 O A:ASP115 4.9 27.9 1.0 CE A:LYS231 4.9 37.4 1.0 CB A:PHE17 4.9 15.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp 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 Dcmpnpp Across A Dna Template Containing 1,N2-Ethenodeoxyguanosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:27.3 occ:0.57 OE1 A:GLU116 2.0 47.6 1.0 OD1 A:ASP13 2.2 37.0 1.0 O2A A:0KX501 2.2 31.7 1.0 O A:HOH601 2.3 25.7 1.0 OD1 A:ASP115 2.3 32.3 1.0 O3' P:DT8 2.3 42.3 1.0 CD A:GLU116 2.7 36.2 1.0 CG A:GLU116 2.7 36.3 1.0 CG A:ASP115 3.1 31.8 1.0 C3' P:DT8 3.1 32.3 1.0 OD2 A:ASP115 3.2 29.7 1.0 CG A:ASP13 3.3 27.8 1.0 MG A:MG502 3.3 25.6 1.0 PA A:0KX501 3.4 34.9 1.0 OD2 A:ASP13 3.8 33.8 1.0 OG A:SER113 3.8 26.5 1.0 O5' A:0KX501 3.8 37.4 1.0 O1A A:0KX501 3.8 27.2 1.0 OE2 A:GLU116 3.9 36.2 1.0 C4' P:DT8 4.0 37.6 1.0 C5' A:0KX501 4.1 31.7 1.0 CB A:GLU116 4.2 25.4 1.0 O A:HOH619 4.2 36.4 1.0 C2' P:DT8 4.4 37.3 1.0 C A:ASP115 4.4 28.0 1.0 CB A:ASP115 4.5 21.7 1.0 CB A:ASP13 4.5 28.8 1.0 O A:ASP115 4.5 27.9 1.0 O A:HOH761 4.5 48.1 1.0 N A:GLU116 4.6 27.1 1.0 O3G A:0KX501 4.7 24.2 1.0 O1B A:0KX501 4.7 20.8 1.0 C5' P:DT8 4.8 37.8 1.0 N3A A:0KX501 4.8 31.4 1.0 CA A:GLU116 4.9 26.8 1.0 CA A:ASP115 4.9 24.3 1.0 CB A:SER113 5.0 29.9 1.0

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