Magnesium in PDB 7u79: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 140S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 140S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 140S, PDB code: 7u79 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)	42.73 / 1.69
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.687, 98.687, 82.28, 90, 90, 120
R / Rfree (%)	17.6 / 22.1

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 140S (pdb code 7u79). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 140S, PDB code: 7u79:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 140S


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 140S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:29.3 occ:0.60 OP1 P:DG9 1.9 27.1 0.2 OE1 A:GLU116 2.0 43.5 0.6 OD1 A:ASP13 2.2 38.1 0.4 O1A A:DGT506 2.2 26.3 0.6 OD1 A:ASP115 2.3 30.8 1.0 OE2 A:GLU116 2.3 41.6 0.4 O P:HOH210 2.3 41.4 1.0 OD1 A:ASP13 2.4 38.4 0.6 O A:HOH908 2.4 30.0 0.4 O3' P:DT8 2.4 30.9 0.1 O3' P:DT8 2.4 30.2 0.2 P P:DG9 2.7 27.5 0.2 CD A:GLU116 3.0 41.2 0.4 CD A:GLU116 3.1 41.4 0.6 CG A:ASP115 3.2 29.5 1.0 CG A:ASP13 3.4 31.7 0.6 CG A:ASP13 3.4 31.7 0.4 C3' P:DT8 3.4 33.8 0.1 OD2 A:ASP115 3.4 29.5 1.0 PA A:DGT506 3.5 30.8 0.6 MG A:MG502 3.5 18.8 1.0 OE1 A:GLU116 3.6 43.3 0.4 C3' P:DT8 3.7 33.5 0.2 OG A:SER113 3.7 36.5 1.0 OP2 P:DG9 3.7 31.8 0.2 O2A A:DGT506 3.8 32.0 0.6 CG A:GLU116 3.9 35.0 0.4 CB A:GLU116 3.9 32.2 0.6 OE2 A:GLU116 3.9 45.2 0.6 O5' P:DG9 3.9 27.3 0.2 CG A:GLU116 3.9 35.1 0.6 CB A:GLU116 3.9 32.2 0.4 OD2 A:ASP13 3.9 39.1 0.6 O5' A:DGT506 4.0 27.3 0.6 OD2 A:ASP13 4.0 35.9 0.4 C4' P:DT8 4.0 35.5 0.2 C5' P:DG9 4.1 25.5 0.2 C4' P:DT8 4.1 35.6 0.1 C5' A:DGT506 4.2 25.5 0.6 C5' P:DT8 4.3 36.3 0.2 C A:ASP115 4.4 24.8 1.0 O A:HOH690 4.5 42.9 1.0 NZ A:LYS224 4.5 38.6 0.8 C5' P:DT8 4.5 36.7 0.1 N A:GLU116 4.5 26.2 1.0 CB A:ASP13 4.5 26.3 0.4 CB A:ASP13 4.5 26.3 0.6 CB A:ASP115 4.6 22.6 1.0 O A:ASP115 4.6 25.4 1.0 C2' P:DT8 4.7 33.4 0.2 C2' P:DT8 4.7 32.8 0.1 O3A A:DGT506 4.7 29.2 0.6 O2G A:DGT506 4.8 25.2 0.6 CA A:GLU116 4.8 24.9 0.6 CA A:GLU116 4.8 24.9 0.4 O1 A:DPO507 4.8 22.5 0.2 CB A:SER113 4.8 26.6 1.0 O2B A:DGT506 4.9 21.4 0.6 CA A:ASP115 4.9 24.2 1.0 O5 A:DPO507 4.9 25.2 0.2

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 140S


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 140S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:18.8 occ:1.00 O2G A:DGT506 2.1 25.2 0.6 O2B A:DGT506 2.2 21.4 0.6 OD2 A:ASP13 2.2 35.9 0.4 O1 A:DPO507 2.2 22.5 0.2 O A:MET14 2.3 24.3 1.0 O1A A:DGT506 2.3 26.3 0.6 OD2 A:ASP13 2.3 39.1 0.6 OD2 A:ASP115 2.4 29.5 1.0 O5 A:DPO507 2.4 25.2 0.2 OP1 P:DG9 2.5 27.1 0.2 OD1 A:ASP13 2.7 38.4 0.6 CG A:ASP13 2.8 31.7 0.6 CG A:ASP13 2.8 31.7 0.4 OD1 A:ASP13 2.9 38.1 0.4 PB A:DGT506 3.1 23.4 0.6 P1 A:DPO507 3.3 22.6 0.2 CG A:ASP115 3.3 29.5 1.0 O3A A:DGT506 3.4 29.2 0.6 PG A:DGT506 3.4 23.2 0.6 PA A:DGT506 3.4 30.8 0.6 C A:MET14 3.4 20.8 1.0 P2 A:DPO507 3.5 24.0 0.2 MG A:MG501 3.5 29.3 0.6 O3B A:DGT506 3.6 23.2 0.6 OD1 A:ASP115 3.7 30.8 1.0 P P:DG9 3.8 27.5 0.2 O4 A:DPO507 3.8 23.2 0.2 O2 A:DPO507 3.8 25.6 0.2 N A:MET14 4.0 21.0 1.0 O A:HOH690 4.0 42.9 1.0 O7 A:DPO507 4.1 23.1 0.2 O1G A:DGT506 4.1 22.5 0.6 C5' A:DGT506 4.2 25.5 0.6 C5' P:DG9 4.2 25.5 0.2 NZ A:LYS231 4.2 35.2 1.0 CB A:ASP13 4.2 26.3 0.6 CB A:ASP13 4.2 26.3 0.4 O5' A:DGT506 4.3 27.3 0.6 CA A:MET14 4.3 18.6 1.0 O5' P:DG9 4.3 27.3 0.2 C A:ASP13 4.3 19.3 1.0 O P:HOH210 4.3 41.4 1.0 N A:ASP15 4.4 20.8 1.0 N A:CYS16 4.5 22.8 1.0 CA A:ASP15 4.5 18.6 1.0 OP2 P:DG9 4.5 31.8 0.2 O2A A:DGT506 4.5 32.0 0.6 O1B A:DGT506 4.6 21.0 0.6 O3G A:DGT506 4.6 23.6 0.6 CB A:ASP115 4.6 22.6 1.0 O3 A:DPO507 4.6 21.1 0.2 C A:ASP15 4.6 21.8 1.0 O A:ASP13 4.7 21.6 1.0 CA A:ASP13 4.7 21.8 0.6 CA A:ASP13 4.7 21.9 0.4 N A:PHE17 4.8 18.2 1.0 O6 A:DPO507 4.8 27.0 0.2 CB A:MET14 4.8 19.4 1.0 O3' P:DT8 4.9 30.2 0.2 O A:ASP115 4.9 25.4 1.0 CB A:PHE17 4.9 15.5 1.0 CE A:LYS231 5.0 43.1 1.0

Magnesium binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 140S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 140S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:29.1 occ:0.35 O A:HOH935 2.0 45.8 1.0 O A:HOH850 2.1 31.1 0.5 O2A A:DGT506 2.1 32.0 0.6 OP2 P:DG9 2.2 31.8 0.2 O A:HOH605 2.2 35.5 1.0 O2 A:DPO507 2.3 25.6 0.2 O3A A:DGT506 2.5 29.2 0.6 NH1 A:ARG61 2.6 29.9 0.2 PA A:DGT506 2.8 30.8 0.6 O A:HOH690 2.8 42.9 1.0 O3' P:DT8 3.2 37.5 0.7 P P:DG9 3.5 27.5 0.2 CZ A:ARG61 3.6 28.5 0.2 C3' P:DT8 3.7 35.5 0.7 O3G A:DGT506 3.7 23.6 0.6 P1 A:DPO507 3.7 22.6 0.2 O A:HOH932 3.8 31.8 1.0 NH2 A:ARG61 3.8 25.6 0.2 O A:HOH797 3.8 26.4 0.8 O1A A:DGT506 3.8 26.3 0.6 PB A:DGT506 3.9 23.4 0.6 O3B A:DGT506 4.0 23.2 0.6 O5' A:DGT506 4.0 27.3 0.6 OP1 P:DG9 4.0 27.1 0.2 O5' P:DG9 4.1 27.3 0.2 O4 A:DPO507 4.1 23.2 0.2 O6 A:DPO507 4.1 27.0 0.2 O5 A:DPO507 4.2 25.2 0.2 PG A:DGT506 4.2 23.2 0.6 O2G A:DGT506 4.2 25.2 0.6 C4' P:DT8 4.4 35.0 0.7 P2 A:DPO507 4.4 24.0 0.2 O P:HOH210 4.5 41.4 1.0 O1B A:DGT506 4.6 21.0 0.6 O3 A:DPO507 4.6 21.1 0.2 O3' P:DT8 4.7 30.2 0.2 O1 A:DPO507 4.7 22.5 0.2 C3' P:DT8 4.7 33.8 0.1 O A:HOH643 4.8 43.1 1.0 NE A:ARG61 4.8 25.3 0.2 C5' P:DT8 4.8 37.4 0.7 C2' P:DT8 4.9 32.8 0.1 C3' P:DT8 4.9 33.5 0.2 O2B A:DGT506 5.0 21.4 0.6 C2' P:DT8 5.0 39.5 0.7

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