Magnesium in PDB 7u7s: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.025 Mm MG2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.025 Mm MG2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.025 Mm MG2+ For 600S, PDB code: 7u7s 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)	42.63 / 1.60
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.452, 98.452, 82.203, 90, 90, 120
R / Rfree (%)	18.8 / 20.7

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.025 Mm MG2+ For 600S (pdb code 7u7s). 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 0.025 Mm MG2+ For 600S, PDB code: 7u7s:
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 0.025 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 0.025 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:33.0 occ:0.75 OD1 A:ASP115 2.1 29.7 0.3 OE1 A:GLU116 2.1 44.0 1.0 O A:HOH775 2.3 44.1 0.8 O3' P:DT8 2.3 35.0 0.1 OD1 A:ASP13 2.5 40.5 1.0 O1A A:XG4505 2.5 25.8 0.8 O A:HOH901 2.5 34.9 0.4 OD1 A:ASP115 2.5 34.6 0.7 CG A:ASP115 3.1 28.8 0.3 CD A:GLU116 3.3 45.8 1.0 CG A:ASP115 3.4 25.5 0.7 C3' P:DT8 3.4 34.6 0.1 CG A:ASP13 3.5 29.4 1.0 OG A:SER113 3.5 33.5 1.0 PA A:XG4505 3.6 24.9 0.8 MG A:MG502 3.6 20.0 1.0 OD2 A:ASP115 3.7 25.5 0.7 OD2 A:ASP115 3.8 29.3 0.3 CB A:GLU116 3.8 35.9 1.0 O2A A:XG4505 4.0 25.0 0.8 O5' A:XG4505 4.0 25.1 0.8 OD2 A:ASP13 4.0 46.1 1.0 CG A:GLU116 4.1 41.1 1.0 CB A:ASP115 4.2 25.9 0.3 OE2 A:GLU116 4.2 47.6 1.0 C5' A:XG4505 4.3 22.5 0.8 C4' P:DT8 4.3 35.4 0.1 O A:HOH689 4.4 37.1 1.0 C A:ASP115 4.5 26.9 1.0 N A:GLU116 4.5 24.0 1.0 C2' P:DT8 4.6 35.1 0.1 CB A:SER113 4.6 25.8 1.0 O5' P:DT8 4.6 37.5 0.1 CB A:ASP13 4.6 22.5 1.0 O A:ASP115 4.7 30.6 1.0 NZ A:LYS224 4.7 39.5 1.0 CB A:ASP115 4.7 25.3 0.7 CA A:GLU116 4.8 27.3 1.0 CA A:ASP115 4.8 24.9 0.3 O P:HOH114 4.9 34.1 0.5 C5' P:DT8 4.9 39.0 0.1 O1G A:XG4505 4.9 23.5 0.8 CA A:ASP115 5.0 24.6 0.7

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.025 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 0.025 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.0 occ:1.00 O A:MET14 2.2 26.7 1.0 OD2 A:ASP13 2.2 46.1 1.0 OD2 A:ASP115 2.2 25.5 0.7 O1G A:XG4505 2.3 23.5 0.8 O1B A:XG4505 2.4 19.9 0.8 O1A A:XG4505 2.4 25.8 0.8 OD1 A:ASP13 2.6 40.5 1.0 CG A:ASP13 2.7 29.4 1.0 CG A:ASP115 3.2 25.5 0.7 PB A:XG4505 3.3 22.8 0.8 C A:MET14 3.4 21.5 1.0 PG A:XG4505 3.5 22.7 0.8 PA A:XG4505 3.6 24.9 0.8 MG A:MG501 3.6 33.0 0.8 OD1 A:ASP115 3.6 34.6 0.7 O3B A:XG4505 3.8 19.6 0.8 N3A A:XG4505 3.8 22.0 0.8 N A:MET14 3.9 19.7 1.0 CG A:ASP115 3.9 28.8 0.3 O A:HOH689 4.0 37.1 1.0 OD1 A:ASP115 4.0 29.7 0.3 NZ A:LYS231 4.0 26.0 1.0 CB A:ASP115 4.1 25.9 0.3 CB A:ASP13 4.1 22.5 1.0 CA A:MET14 4.1 18.6 1.0 OD2 A:ASP115 4.1 29.3 0.3 O2G A:XG4505 4.2 23.5 0.8 C A:ASP13 4.2 21.2 1.0 C5' A:XG4505 4.2 22.5 0.8 O A:HOH775 4.3 44.1 0.8 N A:ASP15 4.4 19.4 1.0 O5' A:XG4505 4.4 25.1 0.8 CB A:ASP115 4.5 25.3 0.7 CA A:ASP15 4.6 19.4 1.0 N A:CYS16 4.6 22.0 1.0 CA A:ASP13 4.6 22.7 1.0 O A:ASP13 4.6 23.0 1.0 CB A:MET14 4.7 23.2 1.0 C A:ASP15 4.7 26.0 1.0 O2B A:XG4505 4.7 24.3 0.8 O3G A:XG4505 4.7 26.7 0.8 O A:ASP115 4.8 30.6 1.0 N A:PHE17 4.8 21.5 1.0 O2A A:XG4505 4.8 25.0 0.8 CB A:PHE17 5.0 16.1 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