Magnesium in PDB 7u77: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S, PDB code: 7u77 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)	42.53 / 1.58
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.219, 98.219, 82.291, 90, 90, 120
R / Rfree (%)	18.4 / 20.3

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S (pdb code 7u77). 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 Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S, PDB code: 7u77:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S


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 Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:24.4 occ:0.60 OE1 A:GLU116 2.0 40.9 0.6 OD1 A:ASP13 2.1 31.0 0.4 OD2 A:ASP13 2.1 34.5 0.6 OD1 A:ASP115 2.2 27.6 0.5 OD1 A:ASP115 2.3 28.3 0.5 O1A A:DGT506 2.3 23.8 0.8 OE1 A:GLU116 2.3 39.1 0.4 O A:HOH670 2.4 39.3 1.0 O3' P:DT8 2.5 28.9 0.3 O A:HOH862 2.5 28.9 0.3 CG A:ASP115 3.1 24.4 0.5 CG A:ASP115 3.1 24.3 0.5 CD A:GLU116 3.1 36.9 0.4 CG A:ASP13 3.1 26.6 0.4 OD2 A:ASP115 3.2 26.9 0.5 CD A:GLU116 3.2 37.6 0.6 CG A:ASP13 3.3 26.7 0.6 OD2 A:ASP115 3.3 26.3 0.5 CA A:CA502 3.5 20.1 0.5 CG A:GLU116 3.5 32.4 0.4 MG A:MG503 3.5 20.2 0.5 C3' P:DT8 3.5 28.3 0.3 PA A:DGT506 3.5 23.0 0.8 OD2 A:ASP13 3.6 33.6 0.4 CB A:GLU116 3.6 26.3 0.6 OG A:SER113 3.7 31.0 1.0 OD1 A:ASP13 3.9 33.6 0.6 CG A:GLU116 3.9 29.6 0.6 CB A:GLU116 3.9 22.5 0.4 O2A A:DGT506 4.0 27.0 0.8 O A:HOH695 4.1 40.0 1.0 O5' A:DGT506 4.1 21.1 0.8 OE2 A:GLU116 4.1 37.0 0.4 OE2 A:GLU116 4.2 40.7 0.6 C5' A:DGT506 4.2 19.9 0.8 CB A:ASP13 4.3 21.1 0.4 C A:ASP115 4.4 24.2 0.5 CB A:ASP13 4.4 20.8 0.6 C A:ASP115 4.4 24.2 0.5 CB A:ASP115 4.4 23.5 0.5 C4' P:DT8 4.5 29.7 0.3 CB A:ASP115 4.5 23.5 0.5 N A:GLU116 4.5 20.8 0.6 N A:GLU116 4.5 20.9 0.4 NZ A:LYS224 4.5 37.5 0.7 O A:ASP115 4.5 24.7 0.5 O A:ASP115 4.6 24.8 0.5 CA A:GLU116 4.7 24.3 0.4 CA A:GLU116 4.7 24.2 0.6 C2' P:DT8 4.8 27.0 0.3 C5' P:DT8 4.8 35.5 0.3 O1G A:DGT506 4.8 22.7 0.8 CA A:ASP115 4.9 21.2 0.5 O3A A:DGT506 4.9 21.4 0.8 CA A:ASP115 4.9 21.2 0.5 O2B A:DGT506 4.9 19.5 0.8 CB A:SER113 4.9 25.3 1.0 O P:HOH117 4.9 30.1 0.5

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S


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 Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 40S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:20.2 occ:0.50 CA A:CA502 0.1 20.1 0.5 OD1 A:ASP13 2.1 33.6 0.6 OD2 A:ASP13 2.1 33.6 0.4 OD2 A:ASP115 2.1 26.9 0.5 O1G A:DGT506 2.2 22.7 0.8 OD2 A:ASP115 2.2 26.3 0.5 O2B A:DGT506 2.2 19.5 0.8 O1A A:DGT506 2.3 23.8 0.8 O A:MET14 2.3 21.7 1.0 CG A:ASP13 2.7 26.6 0.4 CG A:ASP13 2.8 26.7 0.6 OD1 A:ASP13 2.8 31.0 0.4 OD2 A:ASP13 3.0 34.5 0.6 PB A:DGT506 3.2 19.3 0.8 CG A:ASP115 3.3 24.4 0.5 CG A:ASP115 3.3 24.3 0.5 PG A:DGT506 3.4 21.2 0.8 PA A:DGT506 3.4 23.0 0.8 C A:MET14 3.4 19.0 1.0 MG A:MG501 3.5 24.4 0.6 O3A A:DGT506 3.5 21.4 0.8 O3B A:DGT506 3.6 18.2 0.8 O A:HOH695 3.7 40.0 1.0 OD1 A:ASP115 3.7 27.6 0.5 OD1 A:ASP115 3.8 28.3 0.5 N A:MET14 3.9 17.5 1.0 NZ A:LYS231 4.0 24.7 1.0 O3G A:DGT506 4.0 20.3 0.8 CB A:ASP13 4.1 21.1 0.4 CB A:ASP13 4.2 20.8 0.6 C5' A:DGT506 4.2 19.9 0.8 CA A:MET14 4.2 19.1 1.0 C A:ASP13 4.3 19.9 1.0 O5' A:DGT506 4.3 21.1 0.8 O A:HOH670 4.3 39.3 1.0 N A:ASP15 4.4 17.5 1.0 N A:CYS16 4.5 18.2 1.0 CB A:ASP115 4.5 23.5 0.5 CB A:ASP115 4.5 23.5 0.5 CA A:ASP15 4.6 16.3 1.0 O2A A:DGT506 4.6 27.0 0.8 O2G A:DGT506 4.6 22.9 0.8 O1B A:DGT506 4.7 19.1 0.8 C A:ASP15 4.7 18.7 1.0 CA A:ASP13 4.7 20.4 0.6 CA A:ASP13 4.7 20.5 0.4 O A:ASP13 4.7 22.7 1.0 N A:PHE17 4.8 15.7 1.0 CE A:LYS231 4.8 36.9 1.0 CB A:MET14 4.8 20.6 1.0 O A:ASP115 4.9 24.7 0.5 CB A:PHE17 5.0 14.2 1.0 O A:ASP115 5.0 24.8 0.5

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