Magnesium in PDB 7u7t: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.05 Mm MG2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.05 Mm MG2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.05 Mm MG2+ For 600S, PDB code: 7u7t was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.71 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.631, 98.631, 81.973, 90, 90, 120
R / Rfree (%)	18.8 / 20.2

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.05 Mm MG2+ For 600S (pdb code 7u7t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.05 Mm MG2+ For 600S, PDB code: 7u7t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.05 Mm MG2+ For 600S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.05 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:24.6 occ:0.75 O A:HOH773 2.1 39.6 0.8 OE1 A:GLU116 2.2 36.8 0.5 OD1 A:ASP13 2.2 26.7 0.4 OD2 A:ASP13 2.3 33.1 0.4 O3' P:DT8 2.3 36.5 0.1 OD1 A:ASP115 2.3 28.8 0.8 O A:HOH770 2.3 42.9 1.0 OE2 A:GLU116 2.4 38.3 0.5 O1A A:XG4505 2.4 21.8 0.8 OD1 A:ASP115 2.7 25.1 0.1 CG A:ASP115 3.2 24.5 0.8 OD2 A:ASP13 3.2 29.3 0.2 CD A:GLU116 3.3 38.0 0.5 C3' P:DT8 3.3 33.3 0.1 CG A:ASP13 3.3 22.8 0.4 CG A:ASP115 3.3 21.7 0.1 CD A:GLU116 3.3 38.0 0.5 CG A:ASP13 3.4 22.9 0.4 OD2 A:ASP115 3.4 27.6 0.8 OD1 A:ASP13 3.5 27.1 0.2 CG A:ASP13 3.5 23.9 0.2 PA A:XG4505 3.5 20.6 0.8 MG A:MG502 3.6 16.8 1.0 OG A:SER113 3.7 28.1 1.0 OD1 A:ASP13 3.8 30.2 0.4 CG A:GLU116 3.9 32.4 0.5 CB A:GLU116 3.9 29.9 0.5 CG A:GLU116 3.9 32.6 0.5 CB A:GLU116 3.9 29.7 0.5 O2A A:XG4505 4.0 22.2 0.8 OD2 A:ASP13 4.0 30.3 0.4 OD2 A:ASP115 4.0 25.8 0.1 O5' A:XG4505 4.0 19.2 0.8 CB A:ASP115 4.1 23.6 0.1 OE1 A:GLU116 4.2 34.3 0.5 O A:HOH667 4.3 33.0 1.0 C5' A:XG4505 4.3 19.1 0.8 OE2 A:GLU116 4.3 33.4 0.5 C2' P:DT8 4.4 30.7 0.1 C4' P:DT8 4.4 30.2 0.1 CB A:ASP13 4.5 19.5 0.4 O P:HOH113 4.5 27.9 0.2 CB A:ASP13 4.5 19.4 0.4 C A:ASP115 4.6 22.6 1.0 N A:GLU116 4.6 20.7 1.0 CB A:ASP115 4.6 21.1 0.8 CB A:ASP13 4.6 19.5 0.2 NZ A:LYS224 4.7 37.8 1.0 O5' P:DT8 4.7 35.8 0.1 O A:ASP115 4.8 25.5 1.0 O1G A:XG4505 4.8 21.4 0.8 CB A:SER113 4.8 22.7 1.0 CA A:GLU116 4.9 23.0 0.5 CA A:GLU116 4.9 23.0 0.5 CA A:ASP115 4.9 21.1 0.1 O A:HOH886 5.0 35.8 0.5 C5' P:DT8 5.0 35.2 0.1 N3A A:XG4505 5.0 17.1 0.8

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.05 Mm MG2+ For 600S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.05 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:16.8 occ:1.00 OD1 A:ASP13 1.8 30.2 0.4 OD1 A:ASP13 1.9 27.1 0.2 OD2 A:ASP115 2.0 27.6 0.8 O1G A:XG4505 2.3 21.4 0.8 O A:MET14 2.3 26.6 1.0 O1B A:XG4505 2.3 19.7 0.8 OD2 A:ASP13 2.4 30.3 0.4 O1A A:XG4505 2.4 21.8 0.8 CG A:ASP13 2.8 22.8 0.4 OD1 A:ASP13 2.8 26.7 0.4 CG A:ASP13 2.8 22.9 0.4 CG A:ASP13 3.0 23.9 0.2 OD2 A:ASP13 3.1 33.1 0.4 CG A:ASP115 3.1 24.5 0.8 PB A:XG4505 3.3 19.8 0.8 C A:MET14 3.4 19.8 1.0 PG A:XG4505 3.4 19.2 0.8 OD2 A:ASP13 3.4 29.3 0.2 PA A:XG4505 3.5 20.6 0.8 MG A:MG501 3.6 24.6 0.8 OD1 A:ASP115 3.6 28.8 0.8 O3B A:XG4505 3.7 17.7 0.8 N3A A:XG4505 3.7 17.1 0.8 N A:MET14 3.9 17.5 1.0 O A:HOH667 4.0 33.0 1.0 NZ A:LYS231 4.0 23.1 1.0 CG A:ASP115 4.0 21.7 0.1 O2G A:XG4505 4.1 18.7 0.8 CB A:ASP115 4.1 23.6 0.1 OD2 A:ASP115 4.1 25.8 0.1 CB A:ASP13 4.1 19.4 0.4 C5' A:XG4505 4.2 19.1 0.8 CA A:MET14 4.2 16.7 1.0 C A:ASP13 4.2 19.5 1.0 CB A:ASP13 4.2 19.5 0.4 CB A:ASP13 4.3 19.5 0.2 O5' A:XG4505 4.4 19.2 0.8 CB A:ASP115 4.4 21.1 0.8 N A:ASP15 4.4 17.1 1.0 O A:HOH770 4.5 42.9 1.0 OD1 A:ASP115 4.5 25.1 0.1 N A:CYS16 4.6 21.0 1.0 CA A:ASP15 4.6 16.0 1.0 CA A:ASP13 4.6 20.4 0.2 CA A:ASP13 4.6 20.3 0.4 CA A:ASP13 4.6 20.3 0.4 O A:ASP13 4.6 19.4 1.0 C A:ASP15 4.7 19.9 1.0 CB A:MET14 4.7 19.5 1.0 O2B A:XG4505 4.7 19.4 0.8 O3G A:XG4505 4.7 20.9 0.8 N A:PHE17 4.8 18.1 1.0 O2A A:XG4505 4.8 22.2 0.8 O A:ASP115 4.9 25.5 1.0 CB A:PHE17 5.0 17.2 1.0 CE A:LYS231 5.0 33.5 1.0

C.Chang, C.Lee Luo, Y.Gao. In Crystallo Observation of Three Metal Ion Promoted Dna Polymerase Misincorporation. Nat Commun V. 13 2346 2022.
ISSN: ESSN 2041-1723
PubMed: 35487947
DOI: 10.1038/S41467-022-30005-3