Magnesium in PDB 5l1l: Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dt Site

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

The structure of Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dt Site, PDB code: 5l1l 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 / 1.62
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.355, 98.355, 82.034, 90.00, 90.00, 120.00
R / Rfree (%)	15.7 / 19.3

The binding sites of Magnesium atom in the Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dt Site (pdb code 5l1l). 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 : Dt Site, PDB code: 5l1l:
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 : Dt 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 : Dt Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:8.5 occ:1.00 OD1 A:ASP13 2.0 11.9 1.0 OD2 A:ASP115 2.1 11.1 1.0 O1G A:0KX501 2.1 10.7 1.0 O2A A:0KX501 2.1 12.7 1.0 O1B A:0KX501 2.1 10.8 1.0 O A:MET14 2.1 10.6 1.0 CG A:ASP13 3.0 11.4 1.0 CG A:ASP115 3.1 11.5 1.0 PB A:0KX501 3.2 11.6 1.0 PA A:0KX501 3.3 12.8 1.0 C A:MET14 3.3 10.2 1.0 PG A:0KX501 3.3 12.0 1.0 OD2 A:ASP13 3.4 13.7 1.0 N3A A:0KX501 3.5 13.5 1.0 MG A:MG503 3.5 13.4 1.0 OD1 A:ASP115 3.6 11.8 1.0 O3B A:0KX501 3.6 11.3 1.0 NZ A:LYS231 3.8 12.5 1.0 N A:MET14 3.8 10.3 1.0 O A:HOH807 3.8 17.2 1.0 C5' A:0KX501 4.0 12.7 1.0 O3G A:0KX501 4.0 11.4 1.0 CA A:MET14 4.1 10.4 1.0 O5' A:0KX501 4.1 13.0 1.0 C A:ASP13 4.2 10.5 1.0 CB A:ASP13 4.2 10.9 1.0 N A:ASP15 4.4 9.4 1.0 O A:HOH827 4.4 14.7 1.0 CB A:ASP115 4.4 10.8 1.0 CE A:LYS231 4.5 14.8 1.0 N A:CYS16 4.5 9.6 1.0 O2B A:0KX501 4.5 10.7 1.0 CB A:MET14 4.6 12.0 1.0 O2G A:0KX501 4.6 12.2 1.0 O1A A:0KX501 4.6 15.7 1.0 O A:ASP13 4.6 10.5 1.0 CA A:ASP15 4.6 9.8 1.0 CA A:ASP13 4.7 11.2 1.0 C A:ASP15 4.7 9.9 1.0 N A:PHE17 4.7 9.7 1.0 CB A:PHE17 4.8 9.8 1.0 O A:ASP115 5.0 11.2 1.0

Magnesium binding site 2 out of 2 in the Postinsertion Complex of Human Dna Polymerase Eta Bypassing An O6- Methyl-2'-Deoxyguanosine : Dt 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 : Dt Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:13.4 occ:1.00 OD1 A:ASP115 2.0 11.8 1.0 OD2 A:ASP13 2.0 13.7 1.0 OE2 A:GLU116 2.1 16.4 1.0 O A:HOH827 2.2 14.7 1.0 O3' P:DT8 2.2 19.3 1.0 O2A A:0KX501 2.2 12.7 1.0 CG A:ASP115 3.1 11.5 1.0 CG A:ASP13 3.1 11.4 1.0 C3' P:DT8 3.1 36.1 1.0 CD A:GLU116 3.2 18.0 1.0 PA A:0KX501 3.3 12.8 1.0 OD2 A:ASP115 3.4 11.1 1.0 OD1 A:ASP13 3.5 11.9 1.0 MG A:MG502 3.5 8.5 1.0 OG A:SER113 3.7 14.1 1.0 O1A A:0KX501 3.8 15.7 1.0 O5' A:0KX501 3.8 13.0 1.0 OE1 A:GLU116 3.9 18.9 1.0 C4' P:DT8 4.0 38.4 1.0 O A:HOH807 4.0 17.2 1.0 C5' A:0KX501 4.1 12.7 1.0 CG A:GLU116 4.1 13.4 1.0 CB A:GLU116 4.2 14.0 1.0 CB A:ASP13 4.4 10.9 1.0 NZ A:LYS224 4.4 16.6 1.0 C2' P:DT8 4.4 35.4 1.0 CB A:ASP115 4.5 10.8 1.0 C5' P:DT8 4.5 44.0 1.0 C A:ASP115 4.6 11.2 1.0 O P:HOH105 4.6 21.2 1.0 O A:ASP115 4.6 11.2 1.0 O5' P:DT8 4.6 53.7 1.0 O1G A:0KX501 4.7 10.7 1.0 CB A:SER113 4.7 14.8 1.0 N3A A:0KX501 4.8 13.5 1.0 N A:GLU116 4.8 11.1 1.0 CA A:ASP115 4.9 10.7 1.0 O1B A:0KX501 4.9 10.8 1.0 O A:HOH828 5.0 20.3 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