Magnesium in PDB 7u7b: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 250S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 250S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 250S, PDB code: 7u7b 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)	42.08 / 1.58
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.082, 98.082, 81.935, 90, 90, 120
R / Rfree (%)	17.8 / 20.6

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 250S (pdb code 7u7b). 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 250S, PDB code: 7u7b:
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 250S


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 250S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:17.4 occ:1.00 OD1 A:ASP13 1.9 25.3 0.6 OD2 A:ASP13 2.1 30.0 0.5 O A:MET14 2.2 20.8 1.0 O2G A:DGT505 2.2 21.1 0.3 OD2 A:ASP115 2.2 24.8 1.0 O2B A:DGT505 2.3 17.4 0.3 O1 A:DPO504 2.3 18.0 0.4 O5 A:DPO504 2.3 21.4 0.4 O1A A:DGT505 2.4 24.5 0.3 OP1 P:DG9 2.5 23.8 0.4 CG A:ASP13 2.8 23.8 0.5 OD1 A:ASP13 3.0 29.3 0.5 CG A:ASP13 3.0 25.2 0.6 PB A:DGT505 3.2 17.5 0.3 CG A:ASP115 3.3 24.6 1.0 P1 A:DPO504 3.4 18.6 0.4 C A:MET14 3.4 17.9 1.0 O3A A:DGT505 3.4 22.0 0.3 PG A:DGT505 3.5 19.1 0.3 PA A:DGT505 3.5 20.7 0.3 P2 A:DPO504 3.5 19.3 0.4 OD2 A:ASP13 3.5 35.9 0.6 MG A:MG506 3.6 25.1 0.6 O3B A:DGT505 3.6 17.9 0.3 OD1 A:ASP115 3.6 28.7 1.0 O2 A:DPO504 3.7 21.0 0.4 O4 A:DPO504 3.8 17.5 0.4 N A:MET14 3.8 17.3 1.0 P P:DG9 3.9 28.0 0.4 NZ A:LYS231 3.9 23.7 1.0 O A:HOH729 4.0 31.6 0.8 O3G A:DGT505 4.1 17.4 0.3 CA A:MET14 4.2 16.4 1.0 CB A:ASP13 4.2 18.7 0.5 C5' P:DG9 4.2 21.3 0.4 C A:ASP13 4.2 18.4 1.0 O7 A:DPO504 4.2 17.7 0.4 C5' A:DGT505 4.2 21.3 0.3 CB A:ASP13 4.3 18.6 0.6 O5' A:DGT505 4.3 21.6 0.3 O5' P:DG9 4.3 21.6 0.4 O A:HOH619 4.4 27.1 0.3 N A:ASP15 4.4 15.6 1.0 N A:CYS16 4.4 17.5 1.0 CA A:ASP15 4.5 15.2 1.0 CB A:ASP115 4.5 24.3 1.0 C A:ASP15 4.6 18.2 1.0 O1B A:DGT505 4.6 17.8 0.3 O1G A:DGT505 4.6 20.7 0.3 CA A:ASP13 4.7 18.5 0.6 CA A:ASP13 4.7 18.5 0.5 CB A:MET14 4.7 21.4 1.0 O A:ASP13 4.7 20.0 1.0 O2A A:DGT505 4.7 27.3 0.3 O A:ASP115 4.7 25.6 1.0 N A:PHE17 4.7 15.5 1.0 O6 A:DPO504 4.7 20.8 0.4 O3 A:DPO504 4.7 17.8 0.4 OP2 P:DG9 4.8 27.6 0.4 CE A:LYS231 4.8 39.6 1.0 O3' P:DT8 4.9 25.8 0.4 CB A:PHE17 4.9 12.9 1.0

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 250S


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 250S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:25.1 occ:0.55 OP1 P:DG9 2.1 23.8 0.4 OD1 A:ASP13 2.1 29.3 0.5 OE1 A:GLU116 2.2 39.1 0.6 OE2 A:GLU116 2.2 38.8 0.5 O A:HOH861 2.3 24.0 0.3 O1A A:DGT505 2.3 24.5 0.3 OD1 A:ASP115 2.3 28.7 1.0 O3' P:DT8 2.5 25.8 0.4 O A:HOH619 2.5 27.1 0.3 OD2 A:ASP13 2.6 35.9 0.6 P P:DG9 2.8 28.0 0.4 CD A:GLU116 2.9 38.1 0.5 CD A:GLU116 3.2 38.4 0.6 CG A:ASP115 3.3 24.6 1.0 CG A:ASP13 3.3 23.8 0.5 CG A:ASP13 3.3 25.2 0.6 OD1 A:ASP13 3.5 25.3 0.6 PA A:DGT505 3.5 20.7 0.3 OD2 A:ASP115 3.6 24.8 1.0 MG A:MG501 3.6 17.4 1.0 OG A:SER113 3.6 30.5 1.0 OE1 A:GLU116 3.7 36.8 0.5 CB A:GLU116 3.7 28.6 0.6 C3' P:DT8 3.7 26.2 0.4 CB A:GLU116 3.7 28.6 0.5 CG A:GLU116 3.7 31.1 0.5 CG A:GLU116 3.8 31.0 0.6 OP2 P:DG9 3.8 27.6 0.4 OD2 A:ASP13 3.8 30.0 0.5 O2A A:DGT505 3.9 27.3 0.3 C4' P:DT8 4.0 27.1 0.4 O5' P:DG9 4.0 21.6 0.4 O5' A:DGT505 4.1 21.6 0.3 OE2 A:GLU116 4.2 36.2 0.6 C5' P:DT8 4.2 32.0 0.4 C5' P:DG9 4.2 21.3 0.4 C5' A:DGT505 4.3 21.3 0.3 C A:ASP115 4.3 23.0 1.0 O A:ASP115 4.3 25.6 1.0 N A:GLU116 4.4 19.4 1.0 CB A:ASP13 4.5 18.7 0.5 NZ A:LYS224 4.5 28.6 0.2 CB A:ASP115 4.6 24.3 1.0 CB A:ASP13 4.6 18.6 0.6 O A:HOH729 4.6 31.6 0.8 CA A:GLU116 4.6 24.0 0.6 CA A:GLU116 4.7 24.0 0.5 C2' P:DT8 4.8 24.9 0.4 O A:HOH611 4.8 45.9 1.0 O3A A:DGT505 4.8 22.0 0.3 CB A:SER113 4.8 24.3 1.0 CA A:ASP115 4.8 19.2 1.0 O2G A:DGT505 4.9 21.1 0.3 C5' P:DT8 4.9 33.1 0.6 N A:ASP115 5.0 17.4 1.0 O1 A:DPO504 5.0 18.0 0.4

Magnesium binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 250S


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 250S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:32.1 occ:0.55 O A:HOH828 2.0 29.5 0.8 O A:HOH622 2.1 31.2 0.8 O2 A:DPO504 2.2 21.0 0.4 O P:HOH220 2.2 32.1 0.6 O2A A:DGT505 2.2 27.3 0.3 O A:HOH729 2.2 31.6 0.8 O3A A:DGT505 2.3 22.0 0.3 OP2 P:DG9 2.4 27.6 0.4 NH1 A:ARG61 2.7 26.6 0.1 PA A:DGT505 2.7 20.7 0.3 O3' P:DT8 3.1 33.5 0.6 P P:DG9 3.5 28.0 0.4 P1 A:DPO504 3.6 18.6 0.4 CZ A:ARG61 3.6 24.4 0.1 PB A:DGT505 3.7 17.5 0.3 O1G A:DGT505 3.7 20.7 0.3 O1A A:DGT505 3.7 24.5 0.3 O6 A:DPO504 3.8 20.8 0.4 O3B A:DGT505 3.8 17.9 0.3 O A:HOH919 3.8 29.2 1.0 NH2 A:ARG61 3.8 21.4 0.1 O A:HOH785 3.8 21.7 0.8 OP1 P:DG9 3.9 23.8 0.4 C3' P:DT8 3.9 33.5 0.6 O4 A:DPO504 3.9 17.5 0.4 O5' A:DGT505 4.0 21.6 0.3 O5' P:DG9 4.0 21.6 0.4 O2G A:DGT505 4.0 21.1 0.3 O5 A:DPO504 4.1 21.4 0.4 PG A:DGT505 4.2 19.1 0.3 P2 A:DPO504 4.2 19.3 0.4 O1B A:DGT505 4.4 17.8 0.3 O3 A:DPO504 4.4 17.8 0.4 O A:HOH619 4.4 27.1 0.3 O1 A:DPO504 4.6 18.0 0.4 C4' P:DT8 4.7 26.4 0.6 NE A:ARG61 4.7 23.8 0.1 O2B A:DGT505 4.8 17.4 0.3 O3' P:DT8 4.8 25.8 0.4 O5' P:DT8 4.9 40.0 0.6

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