Magnesium in PDB 5l1j: Crystal Structure of Human Dna Polymerase Eta Inserting Dtmpnpp Opposite O6-Methyl-2'-Deoxyguanosine

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Inserting Dtmpnpp Opposite O6-Methyl-2'-Deoxyguanosine:
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dtmpnpp Opposite O6-Methyl-2'-Deoxyguanosine, PDB code: 5l1j 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 / 1.94
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.004, 99.004, 81.704, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dtmpnpp Opposite O6-Methyl-2'-Deoxyguanosine (pdb code 5l1j). 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 Dtmpnpp Opposite O6-Methyl-2'-Deoxyguanosine, PDB code: 5l1j:
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 Dtmpnpp Opposite O6-Methyl-2'-Deoxyguanosine


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 Dtmpnpp Opposite O6-Methyl-2'-Deoxyguanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:26.1 occ:1.00 OD1 A:ASP13 2.0 34.4 1.0 O1B A:1FZ504 2.1 20.1 0.8 OD2 A:ASP115 2.1 32.1 1.0 O2A A:1FZ504 2.2 25.2 0.8 O1G A:1FZ504 2.3 20.0 0.8 O A:MET14 2.3 24.9 1.0 CG A:ASP13 3.0 32.4 1.0 PB A:1FZ504 3.1 26.6 0.8 CG A:ASP115 3.1 35.2 1.0 PA A:1FZ504 3.2 29.8 0.8 PG A:1FZ504 3.4 24.8 0.8 MG A:MG502 3.4 27.5 0.5 C A:MET14 3.4 18.8 1.0 OD2 A:ASP13 3.5 53.6 1.0 N3A A:1FZ504 3.5 29.6 0.8 O3B A:1FZ504 3.6 24.0 0.8 OD1 A:ASP115 3.6 33.9 1.0 C5' A:1FZ504 3.7 31.7 0.8 N A:MET14 3.8 18.1 1.0 O5' A:1FZ504 3.9 31.0 0.8 O2G A:1FZ504 4.1 21.5 0.8 NZ A:LYS231 4.1 34.5 1.0 O A:HOH603 4.2 39.6 1.0 C A:ASP13 4.2 21.0 1.0 CA A:MET14 4.2 18.8 1.0 CB A:ASP13 4.3 25.3 1.0 CB A:ASP115 4.4 27.9 1.0 N A:ASP15 4.4 18.2 1.0 O2B A:1FZ504 4.4 22.6 0.8 O1A A:1FZ504 4.4 33.8 0.8 N A:CYS16 4.5 19.8 1.0 O3G A:1FZ504 4.5 23.8 0.8 CA A:ASP15 4.6 19.2 1.0 CA A:ASP13 4.6 22.2 1.0 O A:ASP13 4.6 18.9 1.0 O A:ASP115 4.6 25.1 1.0 CB A:MET14 4.7 21.4 1.0 C A:ASP15 4.7 21.1 1.0 N A:PHE17 4.8 17.7 1.0 CB A:PHE17 4.9 17.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dtmpnpp Opposite O6-Methyl-2'-Deoxyguanosine


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 Dtmpnpp Opposite O6-Methyl-2'-Deoxyguanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.5 occ:0.48 O A:HOH603 2.2 39.6 1.0 OD1 A:ASP115 2.2 33.9 1.0 O2A A:1FZ504 2.4 25.2 0.8 O3' P:DT8 2.4 29.1 1.0 OD2 A:ASP13 2.5 53.6 1.0 CG A:GLU116 2.5 29.7 1.0 OE1 A:GLU116 2.6 39.6 1.0 CD A:GLU116 2.8 36.5 1.0 CG A:ASP115 3.1 35.2 1.0 C3' P:DT8 3.2 27.4 1.0 CG A:ASP13 3.3 32.4 1.0 PA A:1FZ504 3.4 29.8 0.8 OD2 A:ASP115 3.4 32.1 1.0 MG A:MG501 3.4 26.1 1.0 OD1 A:ASP13 3.5 34.4 1.0 O5' A:1FZ504 3.7 31.0 0.8 OG A:SER113 3.8 25.9 1.0 O1A A:1FZ504 3.8 33.8 0.8 CB A:GLU116 3.9 25.6 1.0 C5' A:1FZ504 4.0 31.7 0.8 OE2 A:GLU116 4.0 37.3 1.0 C4' P:DT8 4.1 29.6 1.0 C A:ASP115 4.3 25.5 1.0 N A:GLU116 4.3 24.4 1.0 O A:ASP115 4.4 25.1 1.0 C2' P:DT8 4.4 29.7 1.0 CB A:ASP115 4.5 27.9 1.0 CB A:ASP13 4.5 25.3 1.0 CA A:GLU116 4.6 23.5 1.0 C5' P:DT8 4.6 30.1 0.3 NZ A:LYS224 4.7 24.3 0.5 C5' P:DT8 4.7 29.2 0.7 N3A A:1FZ504 4.8 29.6 0.8 O1B A:1FZ504 4.8 20.1 0.8 CA A:ASP115 4.8 26.0 1.0 O1G A:1FZ504 4.8 20.0 0.8 CB A:SER113 5.0 27.5 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