Magnesium in PDB 5l1k: Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dc Site

All present enzymatic activity of Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dc Site:
2.7.7.7;

The structure of Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dc Site, PDB code: 5l1k 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)	50.00 / 1.82
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.459, 98.459, 82.112, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 18.8

The binding sites of Magnesium atom in the Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dc Site (pdb code 5l1k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dc Site, PDB code: 5l1k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dc Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dc Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:4.0 occ:1.00 OD1 A:ASP13 2.1 15.7 1.0 OD2 A:ASP115 2.2 11.5 1.0 O2G A:0KX501 2.2 10.7 1.0 O A:MET14 2.2 9.6 1.0 O2B A:0KX501 2.2 8.6 1.0 O1A A:0KX501 2.2 13.6 1.0 CG A:ASP13 3.1 15.7 1.0 CG A:ASP115 3.2 11.9 1.0 PB A:0KX501 3.3 10.6 1.0 MG A:MG503 3.3 13.0 0.5 C A:MET14 3.4 9.1 1.0 PA A:0KX501 3.4 12.9 1.0 OD2 A:ASP13 3.4 27.2 1.0 PG A:0KX501 3.5 11.4 1.0 OD1 A:ASP115 3.6 10.3 1.0 N3A A:0KX501 3.7 11.8 1.0 O3B A:0KX501 3.7 9.9 1.0 O A:HOH885 3.8 25.5 1.0 N A:MET14 3.9 9.6 1.0 NZ A:LYS231 3.9 14.3 1.0 C5' A:0KX501 4.0 11.3 1.0 O5' A:0KX501 4.1 11.5 1.0 CA A:MET14 4.1 10.0 1.0 O3G A:0KX501 4.2 10.7 1.0 C A:ASP13 4.2 10.6 1.0 CB A:ASP13 4.4 12.8 1.0 N A:ASP15 4.5 9.2 1.0 CB A:ASP115 4.5 10.9 1.0 CE A:LYS231 4.5 15.9 1.0 N A:CYS16 4.6 9.2 1.0 CB A:MET14 4.6 10.5 1.0 O1B A:0KX501 4.6 9.9 1.0 O A:ASP13 4.7 11.7 1.0 CA A:ASP15 4.7 9.7 1.0 O1G A:0KX501 4.7 10.8 1.0 O2A A:0KX501 4.7 13.2 1.0 N A:PHE17 4.8 8.2 1.0 CA A:ASP13 4.8 11.7 1.0 C A:ASP15 4.8 9.5 1.0 CB A:PHE17 4.8 8.3 1.0 O A:ASP115 4.9 11.6 1.0 O3' P:DC8 4.9 21.2 1.0 O A:HOH850 5.0 31.4 1.0

Magnesium binding site 2 out of 2 in the Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dc Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dc Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:13.0 occ:0.51 O3' P:DC8 2.0 21.2 1.0 OD1 A:ASP115 2.1 10.3 1.0 OE2 A:GLU116 2.1 29.4 1.0 OD2 A:ASP13 2.2 27.2 1.0 O1A A:0KX501 2.3 13.6 1.0 C3' P:DC8 2.7 24.8 1.0 CG A:ASP115 3.0 11.9 1.0 CG A:ASP13 3.2 15.7 1.0 CD A:GLU116 3.2 25.0 1.0 OD2 A:ASP115 3.3 11.5 1.0 MG A:MG502 3.3 4.0 1.0 OD1 A:ASP13 3.4 15.7 1.0 PA A:0KX501 3.5 12.9 1.0 O A:HOH885 3.7 25.5 1.0 C4' P:DC8 3.8 25.7 1.0 OG A:SER113 3.8 13.0 1.0 O5' A:0KX501 3.9 11.5 1.0 C2' P:DC8 3.9 27.4 1.0 OE1 A:GLU116 3.9 22.4 1.0 O2A A:0KX501 4.1 13.2 1.0 C5' A:0KX501 4.1 11.3 1.0 CB A:GLU116 4.2 16.6 1.0 CG A:GLU116 4.2 17.7 1.0 CB A:ASP115 4.4 10.9 1.0 C A:ASP115 4.4 11.7 1.0 C5' P:DC8 4.5 28.4 1.0 O A:ASP115 4.5 11.6 1.0 CB A:ASP13 4.5 12.8 1.0 O A:HOH720 4.6 39.6 1.0 N A:GLU116 4.7 11.2 1.0 O2G A:0KX501 4.8 10.7 1.0 CA A:ASP115 4.8 11.2 1.0 NZ A:LYS224 4.8 24.5 1.0 O2B A:0KX501 4.8 8.6 1.0 C1' P:DC8 4.9 26.3 1.0 N3A A:0KX501 4.9 11.8 1.0 CB A:SER113 4.9 13.1 1.0 O4' P:DC8 4.9 23.1 1.0 N A:ASP115 5.0 10.1 1.0 O5' P:DC8 5.0 36.4 1.0

A.Patra, Q.Zhang, F.P.Guengerich, M.Egli. Mechanisms of Insertion of Dctp and Dttp Opposite the Dna Lesion O6-Methyl-2'-Deoxyguanosine By Human Dna Polymerase Eta. J.Biol.Chem. V. 291 24304 2016.
ISSN: ESSN 1083-351X
PubMed: 27694439
DOI: 10.1074/JBC.M116.755462