Magnesium in PDB 7u7w: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MG2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MG2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MG2+ For 600S, PDB code: 7u7w 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)	42.42 / 1.66
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	97.969, 97.969, 81.761, 90, 90, 120
R / Rfree (%)	18.4 / 20.8

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MG2+ For 600S (pdb code 7u7w). 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 1.0 Mm MG2+ For 600S, PDB code: 7u7w:
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 1.0 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 1.0 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:23.5 occ:1.00 OE1 A:GLU116 1.9 33.5 1.0 OD1 A:ASP115 2.1 21.5 0.8 OD2 A:ASP13 2.2 30.3 1.0 O A:HOH732 2.3 28.4 0.8 O A:HOH779 2.3 32.8 1.0 O1A A:XG4505 2.4 22.0 0.8 O3' P:DT8 2.4 27.9 0.1 OD1 A:ASP115 2.5 24.1 0.2 CG A:ASP115 3.1 20.0 0.8 CD A:GLU116 3.1 34.2 1.0 C3' P:DT8 3.2 25.5 0.1 CG A:ASP13 3.3 23.8 1.0 CG A:ASP115 3.3 22.9 0.2 OD2 A:ASP115 3.5 22.6 0.8 PA A:XG4505 3.5 21.2 0.8 MG A:MG502 3.7 19.1 0.9 OG A:SER113 3.7 31.2 1.0 OD1 A:ASP13 3.7 30.2 1.0 O2A A:XG4505 3.8 23.6 0.8 OD2 A:ASP115 3.9 22.2 0.2 O5' A:XG4505 3.9 23.0 0.8 CG A:GLU116 3.9 26.5 1.0 OE2 A:GLU116 4.0 31.8 1.0 CB A:GLU116 4.0 27.2 1.0 O A:HOH723 4.1 33.4 1.0 C4' P:DT8 4.1 31.2 0.1 CB A:ASP115 4.2 25.2 0.2 C5' A:XG4505 4.2 18.5 0.8 NZ A:LYS224 4.2 39.0 1.0 CB A:ASP115 4.4 25.7 0.8 C2' P:DT8 4.5 26.9 0.1 CB A:ASP13 4.5 21.0 1.0 O A:HOH931 4.5 28.8 0.5 C A:ASP115 4.5 25.1 1.0 C5' P:DT8 4.6 33.8 0.1 N A:GLU116 4.6 21.6 1.0 O A:ASP115 4.7 25.5 1.0 O1G A:XG4505 4.8 21.8 0.8 CB A:SER113 4.8 25.6 1.0 CA A:ASP115 4.8 23.4 0.2 CA A:ASP115 4.9 23.4 0.8 N3A A:XG4505 4.9 22.4 0.8 CA A:GLU116 4.9 25.5 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 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 1.0 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:19.1 occ:0.90 OD1 A:ASP13 1.8 30.2 1.0 OD2 A:ASP115 2.0 22.6 0.8 O1G A:XG4505 2.1 21.8 0.8 O A:MET14 2.1 25.0 1.0 O1B A:XG4505 2.2 21.4 0.8 O1A A:XG4505 2.4 22.0 0.8 CG A:ASP13 2.8 23.8 1.0 CG A:ASP115 3.1 20.0 0.8 OD2 A:ASP13 3.1 30.3 1.0 PB A:XG4505 3.1 21.8 0.8 PG A:XG4505 3.3 20.9 0.8 C A:MET14 3.3 19.6 1.0 PA A:XG4505 3.5 21.2 0.8 OD1 A:ASP115 3.5 21.5 0.8 O3B A:XG4505 3.6 17.7 0.8 N3A A:XG4505 3.6 22.4 0.8 MG A:MG501 3.7 23.5 1.0 NZ A:LYS231 3.8 23.3 1.0 N A:MET14 3.8 20.1 1.0 O A:HOH723 3.8 33.4 1.0 O2G A:XG4505 3.9 21.6 0.8 CG A:ASP115 4.0 22.9 0.2 OD2 A:ASP115 4.1 22.2 0.2 CA A:MET14 4.1 17.1 1.0 CB A:ASP13 4.1 21.0 1.0 C A:ASP13 4.2 18.4 1.0 CB A:ASP115 4.2 25.2 0.2 C5' A:XG4505 4.2 18.5 0.8 N A:ASP15 4.3 19.3 1.0 CB A:ASP115 4.3 25.7 0.8 O5' A:XG4505 4.4 23.0 0.8 OD1 A:ASP115 4.5 24.1 0.2 N A:CYS16 4.5 20.8 1.0 CA A:ASP15 4.5 17.7 1.0 O2B A:XG4505 4.5 19.5 0.8 O3G A:XG4505 4.5 24.6 0.8 O A:HOH779 4.6 32.8 1.0 C A:ASP15 4.6 19.9 1.0 CB A:MET14 4.6 23.6 1.0 CE A:LYS231 4.6 28.4 1.0 O A:ASP13 4.6 21.3 1.0 CA A:ASP13 4.6 19.5 1.0 O2A A:XG4505 4.7 23.6 0.8 N A:PHE17 4.7 21.5 1.0 CB A:PHE17 4.9 15.1 1.0 O A:ASP115 4.9 25.5 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