Magnesium in PDB 7u7v: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.4 Mm MG2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.4 Mm MG2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.4 Mm MG2+ For 600S, PDB code: 7u7v 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)	42.25 / 1.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.618, 98.618, 81.963, 90, 90, 120
R / Rfree (%)	18.6 / 21.8

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.4 Mm MG2+ For 600S (pdb code 7u7v). 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 0.4 Mm MG2+ For 600S, PDB code: 7u7v:
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 0.4 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 0.4 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:25.2 occ:1.00 OD1 A:ASP115 2.1 25.6 0.8 OE1 A:GLU116 2.2 32.2 1.0 O A:HOH835 2.2 33.1 0.8 OD2 A:ASP13 2.2 35.8 0.8 O A:HOH830 2.3 34.8 1.0 OD1 A:ASP13 2.3 33.2 0.2 O1A A:XG4505 2.3 21.1 0.8 O3' P:DT8 2.3 32.4 0.1 OD1 A:ASP115 2.6 23.2 0.2 CG A:ASP115 3.1 25.7 0.8 CG A:ASP115 3.2 23.6 0.2 CD A:GLU116 3.3 35.8 1.0 CG A:ASP13 3.4 24.6 0.8 C3' P:DT8 3.4 33.0 0.1 OD2 A:ASP115 3.4 27.5 0.8 PA A:XG4505 3.4 21.8 0.8 CG A:ASP13 3.4 24.9 0.2 OD2 A:ASP115 3.6 22.7 0.2 MG A:MG502 3.6 20.7 1.0 OG A:SER113 3.7 29.3 1.0 O2A A:XG4505 3.8 23.9 0.8 O5' A:XG4505 3.9 21.6 0.8 OD1 A:ASP13 3.9 32.9 0.8 CB A:GLU116 4.0 27.0 1.0 OD2 A:ASP13 4.0 31.5 0.2 CB A:ASP115 4.1 24.0 0.2 OE2 A:GLU116 4.1 36.5 1.0 C5' A:XG4505 4.2 19.5 0.8 CG A:GLU116 4.2 27.6 1.0 O A:HOH643 4.2 34.7 1.0 C2' P:DT8 4.4 33.0 0.1 CB A:ASP115 4.5 23.0 0.8 C4' P:DT8 4.5 34.2 0.1 CB A:ASP13 4.5 22.8 0.2 CB A:ASP13 4.5 22.7 0.8 NZ A:LYS224 4.5 43.3 1.0 C A:ASP115 4.6 27.0 1.0 N A:GLU116 4.6 23.4 1.0 O1G A:XG4505 4.7 20.6 0.8 O A:ASP115 4.8 26.5 1.0 CB A:SER113 4.8 27.2 1.0 CA A:ASP115 4.8 22.8 0.2 O5' P:DT8 4.8 37.4 0.1 N3A A:XG4505 4.9 23.6 0.8 CA A:GLU116 4.9 26.7 1.0 CA A:ASP115 4.9 22.5 0.8 O1B A:XG4505 5.0 18.8 0.8

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.4 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 0.4 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.7 occ:1.00 OD1 A:ASP13 1.8 32.9 0.8 OD2 A:ASP13 2.0 31.5 0.2 OD2 A:ASP115 2.0 27.5 0.8 O A:MET14 2.1 24.9 1.0 O1G A:XG4505 2.1 20.6 0.8 O1B A:XG4505 2.3 18.8 0.8 O1A A:XG4505 2.3 21.1 0.8 CG A:ASP13 2.6 24.6 0.8 CG A:ASP13 2.6 24.9 0.2 OD1 A:ASP13 2.7 33.2 0.2 OD2 A:ASP13 2.8 35.8 0.8 CG A:ASP115 3.1 25.7 0.8 PB A:XG4505 3.2 21.6 0.8 C A:MET14 3.3 19.6 1.0 PG A:XG4505 3.3 21.6 0.8 PA A:XG4505 3.5 21.8 0.8 OD1 A:ASP115 3.6 25.6 0.8 MG A:MG501 3.6 25.2 1.0 O3B A:XG4505 3.6 19.4 0.8 N3A A:XG4505 3.7 23.6 0.8 N A:MET14 3.8 19.5 1.0 OD2 A:ASP115 3.8 22.7 0.2 O A:HOH643 3.9 34.7 1.0 NZ A:LYS231 3.9 23.4 1.0 O2G A:XG4505 4.0 20.8 0.8 CG A:ASP115 4.0 23.6 0.2 CB A:ASP13 4.0 22.7 0.8 CA A:MET14 4.1 19.9 1.0 CB A:ASP13 4.1 22.8 0.2 CB A:ASP115 4.1 24.0 0.2 C A:ASP13 4.2 20.5 1.0 C5' A:XG4505 4.2 19.5 0.8 N A:ASP15 4.3 19.0 1.0 CB A:ASP115 4.4 23.0 0.8 O5' A:XG4505 4.4 21.6 0.8 O A:HOH830 4.4 34.8 1.0 CA A:ASP15 4.5 19.3 1.0 N A:CYS16 4.6 20.9 1.0 CB A:MET14 4.6 24.6 1.0 CA A:ASP13 4.6 21.9 0.8 CA A:ASP13 4.6 22.0 0.2 O3G A:XG4505 4.6 24.2 0.8 O A:ASP13 4.6 19.8 1.0 O2B A:XG4505 4.6 19.3 0.8 OD1 A:ASP115 4.6 23.2 0.2 C A:ASP15 4.7 25.2 1.0 O2A A:XG4505 4.7 23.9 0.8 CE A:LYS231 4.8 33.8 1.0 N A:PHE17 4.8 19.5 1.0 O A:ASP115 4.9 26.5 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