Manganese in PDB 7u7f: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S, PDB code: 7u7f 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)	42.55 / 1.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.269, 98.269, 81.983, 90, 90, 120
R / Rfree (%)	20 / 24.6

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S (pdb code 7u7f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S, PDB code: 7u7f:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:28.4 occ:0.80 OP1 P:DG9 1.9 28.1 0.1 OD1 A:ASP115 2.0 25.5 0.6 OE1 A:GLU116 2.0 34.3 0.6 OD1 A:ASP13 2.1 28.2 0.5 O1A A:DGT505 2.2 28.1 0.6 OE2 A:GLU116 2.3 33.0 0.4 O3' P:DT8 2.3 29.1 0.1 OD1 A:ASP115 2.3 27.9 0.4 O A:HOH849 2.3 28.6 0.4 O A:HOH769 2.3 36.0 1.0 OD2 A:ASP13 2.4 31.1 0.5 O3' P:DT8 2.5 30.5 0.1 P P:DG9 2.7 28.4 0.1 CG A:ASP115 2.8 25.3 0.6 OD2 A:ASP115 3.0 32.5 0.6 CD A:GLU116 3.1 35.1 0.4 CD A:GLU116 3.2 35.4 0.6 CG A:ASP13 3.3 28.5 0.5 CG A:ASP13 3.3 28.0 0.5 C3' P:DT8 3.3 33.3 0.1 CG A:ASP115 3.4 22.1 0.4 PA A:DGT505 3.4 26.0 0.6 OD1 A:ASP13 3.5 24.4 0.5 MN A:MN506 3.6 23.8 0.8 OP1 P:DG9 3.6 30.0 0.1 C3' P:DT8 3.7 33.1 0.1 OE1 A:GLU116 3.7 29.7 0.4 OP2 P:DG9 3.7 31.7 0.1 OD2 A:ASP115 3.7 18.5 0.4 OG A:SER113 3.7 33.2 1.0 OD2 A:ASP13 3.8 27.9 0.5 CB A:GLU116 3.9 28.4 0.6 O2A A:DGT505 3.9 33.3 0.6 CB A:GLU116 3.9 28.3 0.4 O5' P:DG9 3.9 26.5 0.1 CG A:GLU116 3.9 28.3 0.4 O5' A:DGT505 4.0 26.4 0.6 CG A:GLU116 4.0 28.1 0.6 OE2 A:GLU116 4.1 34.3 0.6 C5' P:DG9 4.1 24.4 0.1 C4' P:DT8 4.2 34.3 0.1 C5' A:DGT505 4.2 23.5 0.6 C5' P:DG9 4.2 26.0 0.1 C4' P:DT8 4.2 34.4 0.1 O A:HOH717 4.2 39.2 1.0 CB A:ASP115 4.3 22.8 0.6 NZ A:LYS224 4.3 33.2 1.0 O A:ASP115 4.5 23.5 0.4 O A:HOH874 4.5 33.4 0.6 CB A:ASP13 4.5 21.2 0.5 C A:ASP115 4.5 22.9 0.4 C5' P:DT8 4.5 35.9 0.1 O P:HOH226 4.5 38.0 0.5 C A:ASP115 4.5 22.9 0.6 CB A:ASP13 4.6 21.2 0.5 C2' P:DT8 4.6 31.6 0.1 P P:DG9 4.6 29.4 0.1 O A:ASP115 4.6 23.9 0.6 N A:GLU116 4.7 20.6 0.6 O2G A:DGT505 4.7 24.5 0.6 N A:GLU116 4.7 20.7 0.4 O1 A:DPO504 4.7 25.3 0.2 O3A A:DGT505 4.7 28.5 0.6 CB A:ASP115 4.7 20.9 0.4 O3' P:DT8 4.8 30.9 0.1 C5' P:DT8 4.8 35.5 0.1 C2' P:DT8 4.8 32.2 0.1 O P:HOH223 4.8 32.8 0.5 O5' P:DG9 4.8 25.2 0.1 CA A:ASP115 4.9 21.5 0.6 CA A:GLU116 4.9 25.2 0.6 O2B A:DGT505 4.9 21.4 0.6 CA A:GLU116 4.9 25.2 0.4 O5 A:DPO504 4.9 26.5 0.2 CB A:SER113 5.0 27.3 1.0 O P:HOH205 5.0 43.1 1.0

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn506 b:23.8 occ:0.85 OD2 A:ASP115 2.0 32.5 0.6 OD1 A:ASP13 2.0 24.4 0.5 O2G A:DGT505 2.1 24.5 0.6 OD2 A:ASP13 2.1 27.9 0.5 O2B A:DGT505 2.2 21.4 0.6 O A:MET14 2.2 23.3 1.0 OD2 A:ASP115 2.2 18.5 0.4 O1 A:DPO504 2.3 25.3 0.2 O1A A:DGT505 2.4 28.1 0.6 O5 A:DPO504 2.4 26.5 0.2 OP1 P:DG9 2.5 28.1 0.1 CG A:ASP13 2.9 28.0 0.5 CG A:ASP13 3.1 28.5 0.5 OD1 A:ASP13 3.1 28.2 0.5 PB A:DGT505 3.1 24.7 0.6 CG A:ASP115 3.2 25.3 0.6 CG A:ASP115 3.2 22.1 0.4 C A:MET14 3.4 22.7 1.0 PG A:DGT505 3.4 27.0 0.6 P1 A:DPO504 3.4 24.3 0.2 O3A A:DGT505 3.4 28.5 0.6 OD1 A:ASP115 3.5 27.9 0.4 PA A:DGT505 3.5 26.0 0.6 P2 A:DPO504 3.5 22.4 0.2 OD2 A:ASP13 3.6 31.1 0.5 MN A:MN501 3.6 28.4 0.8 O3B A:DGT505 3.6 24.1 0.6 O4 A:DPO504 3.7 25.0 0.2 OD1 A:ASP115 3.8 25.5 0.6 N A:MET14 3.9 19.0 1.0 P P:DG9 3.9 28.4 0.1 NZ A:LYS231 3.9 27.0 1.0 O A:HOH717 4.0 39.2 1.0 O1G A:DGT505 4.0 21.4 0.6 OP1 P:DG9 4.0 30.0 0.1 O2 A:DPO504 4.1 25.9 0.2 CA A:MET14 4.1 19.8 1.0 C5' A:DGT505 4.2 23.5 0.6 C A:ASP13 4.2 19.3 0.5 C A:ASP13 4.2 19.3 0.5 O7 A:DPO504 4.2 24.8 0.2 CB A:ASP13 4.3 21.2 0.5 CB A:ASP115 4.3 22.8 0.6 C5' P:DG9 4.3 24.4 0.1 O5' A:DGT505 4.3 26.4 0.6 CB A:ASP13 4.3 21.2 0.5 N A:ASP15 4.4 19.1 1.0 N A:CYS16 4.4 21.3 1.0 C5' P:DG9 4.4 26.0 0.1 O5' P:DG9 4.4 26.5 0.1 CA A:ASP15 4.5 18.4 1.0 O1B A:DGT505 4.5 23.2 0.6 O3G A:DGT505 4.5 26.0 0.6 CB A:ASP115 4.6 20.9 0.4 O A:HOH769 4.6 36.0 1.0 O2A A:DGT505 4.6 33.3 0.6 C A:ASP15 4.6 21.7 1.0 O5' P:DG9 4.6 25.2 0.1 O A:ASP13 4.6 22.8 0.5 O A:ASP13 4.6 22.8 0.5 OP2 P:DG9 4.6 31.7 0.1 CB A:MET14 4.7 22.6 1.0 N A:PHE17 4.7 16.4 1.0 O3 A:DPO504 4.7 24.7 0.2 CA A:ASP13 4.7 22.0 0.5 CA A:ASP13 4.7 22.0 0.5 O A:ASP115 4.7 23.5 0.4 O6 A:DPO504 4.8 26.2 0.2 O A:ASP115 4.8 23.9 0.6 CB A:PHE17 4.9 17.4 1.0 CE A:LYS231 4.9 42.9 1.0 P P:DG9 5.0 29.4 0.1

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 90S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:27.6 occ:0.15 OP2 P:DG9 1.8 27.1 0.1 OP1 P:DG9 1.9 30.0 0.1 O2A A:DGT505 1.9 33.3 0.6 P P:DG9 1.9 29.4 0.1 O2 A:DPO504 2.0 25.9 0.2 O P:HOH201 2.0 26.9 0.1 O P:HOH205 2.1 43.1 1.0 OP2 P:DG9 2.1 31.7 0.1 O3A A:DGT505 2.2 28.5 0.6 NH1 A:ARG61 2.6 26.5 0.2 PA A:DGT505 2.6 26.0 0.6 O A:HOH677 2.7 30.6 1.0 O3' P:DT8 3.1 40.2 0.7 O5' P:DG9 3.1 25.2 0.1 O3' P:DT8 3.2 30.9 0.1 P P:DG9 3.3 28.4 0.1 P1 A:DPO504 3.4 24.3 0.2 C3' P:DT8 3.6 34.5 0.1 CZ A:ARG61 3.6 25.1 0.2 PB A:DGT505 3.6 24.7 0.6 O3B A:DGT505 3.7 24.1 0.6 O1A A:DGT505 3.7 28.1 0.6 O3G A:DGT505 3.7 26.0 0.6 NH2 A:ARG61 3.8 20.5 0.2 O A:HOH887 3.8 38.2 1.0 C3' P:DT8 3.9 36.2 0.7 O A:HOH687 3.9 22.3 0.6 O5' A:DGT505 3.9 26.4 0.6 OP1 P:DG9 3.9 28.1 0.1 O5' P:DG9 3.9 26.5 0.1 O4 A:DPO504 3.9 25.0 0.2 O6 A:DPO504 4.0 26.2 0.2 O A:HOH717 4.0 39.2 1.0 PG A:DGT505 4.1 27.0 0.6 O2G A:DGT505 4.1 24.5 0.6 O5 A:DPO504 4.2 26.5 0.2 O1 A:DPO504 4.2 25.3 0.2 O1B A:DGT505 4.3 23.2 0.6 C5' P:DG9 4.3 26.0 0.1 O3 A:DPO504 4.4 24.7 0.2 P2 A:DPO504 4.4 22.4 0.2 O A:HOH769 4.5 36.0 1.0 O A:HOH918 4.5 46.4 0.7 C2' P:DT8 4.6 31.6 0.1 O3' P:DT8 4.6 30.5 0.1 C2' P:DT8 4.6 34.8 0.1 C3' P:DT8 4.7 33.3 0.1 O2B A:DGT505 4.7 21.4 0.6 O P:HOH207 4.7 54.0 1.0 C4' P:DT8 4.7 35.1 0.1 C4' P:DT8 4.8 34.6 0.7 C3' P:DT8 4.8 33.1 0.1 NE A:ARG61 4.9 24.9 0.2 O A:HOH624 4.9 30.3 1.0 C5' P:DT8 4.9 36.4 0.1 C2' P:DT8 5.0 38.9 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