Manganese in PDB 7u7j: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 300S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 300S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 300S, PDB code: 7u7j 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)	42.54 / 1.58
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.249, 98.249, 82.161, 90, 90, 120
R / Rfree (%)	18.1 / 21.3

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 300S (pdb code 7u7j). 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 300S, PDB code: 7u7j:
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 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:19.7 occ:0.70 OP1 P:DG9 1.9 19.3 0.2 O1A A:DGT507 2.1 19.8 0.4 O A:HOH895 2.1 30.8 0.8 OD2 A:ASP13 2.1 27.0 0.3 OD1 A:ASP115 2.1 24.4 1.0 OE1 A:GLU116 2.1 29.0 0.7 OD2 A:ASP13 2.2 28.5 0.7 O A:HOH854 2.2 21.9 0.2 OE2 A:GLU116 2.3 29.2 0.3 O P:HOH205 2.3 29.3 0.7 O3' P:DT8 2.5 26.3 0.2 O3' P:DT8 2.5 24.2 0.2 P P:DG9 2.7 25.4 0.2 CG A:ASP115 3.0 21.6 1.0 CD A:GLU116 3.1 29.8 0.3 CD A:GLU116 3.1 30.1 0.7 CG A:ASP13 3.1 24.6 0.7 CG A:ASP13 3.2 24.4 0.3 OD2 A:ASP115 3.3 23.9 1.0 PA A:DGT507 3.4 20.0 0.4 OD1 A:ASP13 3.5 21.5 0.7 MN A:MN502 3.6 19.0 0.9 C3' P:DT8 3.6 26.6 0.2 OD1 A:ASP13 3.7 24.6 0.3 OG A:SER113 3.7 29.5 1.0 OE1 A:GLU116 3.8 31.5 0.3 C3' P:DT8 3.8 24.9 0.2 O5' P:DG9 3.8 22.4 0.2 OP2 P:DG9 3.9 25.7 0.2 CG A:GLU116 3.9 20.6 0.3 CB A:GLU116 3.9 21.6 0.3 O2A A:DGT507 3.9 25.6 0.4 CB A:GLU116 3.9 21.5 0.7 OE2 A:GLU116 3.9 31.6 0.7 O5' A:DGT507 4.0 21.9 0.4 CG A:GLU116 4.0 20.4 0.7 C5' P:DG9 4.0 17.1 0.2 O A:HOH766 4.1 38.0 1.0 C4' P:DT8 4.2 30.0 0.2 O A:HOH837 4.2 27.6 0.5 NZ A:LYS224 4.2 28.3 1.0 C5' P:DG9 4.2 19.6 0.1 C5' A:DGT507 4.3 16.6 0.4 C4' P:DT8 4.3 30.6 0.2 CB A:ASP115 4.4 20.2 1.0 CB A:ASP13 4.4 18.0 0.7 CB A:ASP13 4.4 18.2 0.3 C A:ASP115 4.5 18.6 1.0 C5' P:DT8 4.5 31.8 0.2 O A:ASP115 4.6 20.1 1.0 O3A A:DGT507 4.6 24.3 0.4 O3' P:DT8 4.6 24.5 0.1 O1G A:DGT507 4.6 21.0 0.4 N A:GLU116 4.7 16.1 1.0 O5 A:DPO506 4.7 21.4 0.4 CB A:SER113 4.8 24.8 1.0 C2' P:DT8 4.8 26.2 0.2 O1 A:DPO506 4.8 17.4 0.4 O5' P:DT8 4.8 30.7 0.2 O5' P:DG9 4.9 19.4 0.1 C2' P:DT8 4.9 29.2 0.2 CA A:ASP115 4.9 18.3 1.0 CA A:GLU116 4.9 20.0 0.3 CA A:GLU116 4.9 20.0 0.7 C5' P:DT8 4.9 30.2 0.1 O2B A:DGT507 4.9 16.2 0.4 OP1 P:DG9 5.0 24.6 0.1

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:19.0 occ:0.90 OD1 A:ASP13 2.0 21.5 0.7 OD2 A:ASP115 2.0 23.9 1.0 O2B A:DGT507 2.1 16.2 0.4 O1G A:DGT507 2.1 21.0 0.4 O1 A:DPO506 2.1 17.4 0.4 O A:MET14 2.2 19.7 1.0 O5 A:DPO506 2.3 21.4 0.4 OD1 A:ASP13 2.3 24.6 0.3 O A:HOH895 2.3 30.8 0.8 O1A A:DGT507 2.4 19.8 0.4 OP1 P:DG9 2.5 19.3 0.2 CG A:ASP13 3.0 24.6 0.7 CG A:ASP13 3.0 24.4 0.3 PB A:DGT507 3.1 18.4 0.4 CG A:ASP115 3.1 21.6 1.0 OD2 A:ASP13 3.2 27.0 0.3 P1 A:DPO506 3.2 18.9 0.4 O3A A:DGT507 3.3 24.3 0.4 PG A:DGT507 3.3 22.1 0.4 C A:MET14 3.4 17.6 1.0 OD2 A:ASP13 3.4 28.5 0.7 P2 A:DPO506 3.4 21.8 0.4 PA A:DGT507 3.4 20.0 0.4 O3B A:DGT507 3.5 19.5 0.4 MN A:MN501 3.6 19.7 0.7 OD1 A:ASP115 3.6 24.4 1.0 O4 A:DPO506 3.7 18.9 0.4 O2 A:DPO506 3.7 23.1 0.4 P P:DG9 3.8 25.4 0.2 N A:MET14 3.9 15.7 1.0 NZ A:LYS231 3.9 21.3 1.0 O3G A:DGT507 4.0 18.3 0.4 O7 A:DPO506 4.0 18.8 0.4 O A:HOH766 4.0 38.0 1.0 CA A:MET14 4.2 14.5 1.0 C5' A:DGT507 4.2 16.6 0.4 C5' P:DG9 4.2 17.1 0.2 C A:ASP13 4.2 16.9 1.0 O5' P:DG9 4.2 22.4 0.2 CB A:ASP13 4.3 18.0 0.7 O5' A:DGT507 4.3 21.9 0.4 CB A:ASP13 4.3 18.2 0.3 O P:HOH205 4.3 29.3 0.7 CB A:ASP115 4.3 20.2 1.0 N A:ASP15 4.4 15.5 1.0 C5' P:DG9 4.4 19.6 0.1 N A:CYS16 4.4 15.8 1.0 O1B A:DGT507 4.5 18.1 0.4 O5' P:DG9 4.5 19.4 0.1 CA A:ASP15 4.5 13.6 1.0 O3 A:DPO506 4.5 18.2 0.4 O2G A:DGT507 4.5 23.3 0.4 C A:ASP15 4.6 18.4 1.0 O2A A:DGT507 4.6 25.6 0.4 OP2 P:DG9 4.6 25.7 0.2 N A:PHE17 4.6 15.7 1.0 O A:ASP13 4.6 19.7 1.0 O6 A:DPO506 4.7 23.6 0.4 CB A:MET14 4.7 19.7 1.0 CA A:ASP13 4.7 17.4 0.7 CA A:ASP13 4.7 17.4 0.3 CB A:PHE17 4.8 13.8 1.0 O A:ASP115 4.8 20.1 1.0 OP1 P:DG9 4.8 24.6 0.1 CE A:LYS231 4.9 35.4 1.0 O3' P:DT8 5.0 26.3 0.2

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:25.2 occ:0.25 OP1 P:DG9 0.6 24.6 0.1 O2A A:DGT507 1.9 25.6 0.4 OP2 P:DG9 2.0 25.7 0.2 P P:DG9 2.0 21.4 0.1 O P:HOH218 2.0 29.4 0.8 O2 A:DPO506 2.3 23.1 0.4 O A:HOH683 2.3 34.8 1.0 O3A A:DGT507 2.5 24.3 0.4 NH1 A:ARG61 2.7 26.6 0.1 PA A:DGT507 2.8 20.0 0.4 O P:HOH224 2.8 62.8 1.0 OP2 P:DG9 2.8 24.9 0.1 O3' P:DT8 3.0 24.5 0.1 O5' P:DG9 3.0 19.4 0.1 O3' P:DT8 3.1 26.8 0.4 P P:DG9 3.3 25.4 0.2 O A:HOH766 3.5 38.0 1.0 CZ A:ARG61 3.6 22.7 0.1 C3' P:DT8 3.6 28.6 0.1 O A:HOH865 3.6 31.9 1.0 P1 A:DPO506 3.7 18.9 0.4 O A:HOH816 3.7 20.3 0.5 NH2 A:ARG61 3.7 20.8 0.1 O2G A:DGT507 3.8 23.3 0.4 O3B A:DGT507 3.8 19.5 0.4 PB A:DGT507 3.8 18.4 0.4 O1A A:DGT507 3.8 19.8 0.4 C3' P:DT8 3.8 30.9 0.4 O6 A:DPO506 3.8 23.6 0.4 O A:HOH895 3.8 30.8 0.8 OP1 P:DG9 3.9 19.3 0.2 O5' P:DG9 3.9 22.4 0.2 O4 A:DPO506 3.9 18.9 0.4 O5' A:DGT507 4.0 21.9 0.4 O5 A:DPO506 4.1 21.4 0.4 O1G A:DGT507 4.2 21.0 0.4 C5' P:DG9 4.2 19.6 0.1 PG A:DGT507 4.2 22.1 0.4 P2 A:DPO506 4.2 21.8 0.4 O P:HOH205 4.4 29.3 0.7 O1B A:DGT507 4.4 18.1 0.4 O3' P:DT8 4.5 26.3 0.2 O3 A:DPO506 4.5 18.2 0.4 O A:HOH949 4.5 41.0 0.5 C2' P:DT8 4.6 26.1 0.1 O1 A:DPO506 4.7 17.4 0.4 C3' P:DT8 4.7 24.9 0.2 C2' P:DT8 4.7 26.2 0.2 C3' P:DT8 4.7 26.6 0.2 C4' P:DT8 4.7 29.6 0.4 C4' P:DT8 4.8 28.7 0.1 NE A:ARG61 4.8 22.9 0.1 O2B A:DGT507 4.9 16.2 0.4 O5' P:DT8 5.0 31.3 0.1 C5' P:DT8 5.0 30.2 0.1

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