Manganese in PDB 7u7g: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 120S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 120S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 120S, PDB code: 7u7g 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)	42.35 / 1.77
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	97.792, 97.792, 82.081, 90, 90, 120
R / Rfree (%)	17.5 / 21

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 120S (pdb code 7u7g). 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 120S, PDB code: 7u7g:
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 120S


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 120S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:28.6 occ:0.80 OE1 A:GLU116 2.0 37.2 0.8 OD2 A:ASP13 2.0 40.2 0.8 OP1 P:DG9 2.1 29.3 0.1 OD1 A:ASP115 2.1 27.6 1.0 OD2 A:ASP13 2.1 32.4 0.2 O A:HOH763 2.2 26.9 0.6 O P:HOH203 2.2 30.8 0.5 O A:HOH782 2.3 23.8 0.2 O1A A:DGT507 2.3 29.6 0.6 OE2 A:GLU116 2.3 31.5 0.2 O3' P:DT8 2.4 28.0 0.2 O3' P:DT8 2.6 31.4 0.1 P P:DG9 2.9 26.9 0.1 CG A:ASP115 3.0 28.7 1.0 CD A:GLU116 3.1 37.8 0.2 CG A:ASP13 3.1 31.4 0.2 CG A:ASP13 3.2 31.5 0.8 CD A:GLU116 3.2 38.4 0.8 OD2 A:ASP115 3.2 34.6 1.0 OD1 A:ASP13 3.5 30.2 0.2 PA A:DGT507 3.6 31.8 0.6 C3' P:DT8 3.6 32.7 0.2 MN A:MN502 3.6 27.7 0.9 OG A:SER113 3.7 35.5 1.0 OD1 A:ASP13 3.7 32.6 0.8 OE1 A:GLU116 3.7 22.1 0.2 C3' P:DT8 3.7 33.0 0.1 CB A:GLU116 3.9 26.9 0.2 CG A:GLU116 3.9 32.3 0.2 CB A:GLU116 3.9 26.8 0.8 OP2 P:DG9 3.9 34.1 0.1 OP1 P:DG9 4.0 32.3 0.1 O5' P:DG9 4.0 29.7 0.1 CG A:GLU116 4.0 32.5 0.8 OE2 A:GLU116 4.1 38.6 0.8 O2A A:DGT507 4.1 37.2 0.6 O5' A:DGT507 4.1 30.2 0.6 O P:HOH208 4.1 37.2 0.6 C5' P:DG9 4.2 24.8 0.1 NZ A:LYS224 4.2 36.1 1.0 O A:HOH627 4.2 41.1 0.5 C5' A:DGT507 4.3 24.4 0.6 C4' P:DT8 4.3 39.8 0.1 C4' P:DT8 4.4 40.0 0.2 CB A:ASP115 4.4 23.6 1.0 CB A:ASP13 4.4 29.3 0.8 C5' P:DG9 4.4 27.8 0.1 CB A:ASP13 4.4 29.2 0.2 C A:ASP115 4.4 26.6 1.0 O A:ASP115 4.4 24.8 1.0 O P:HOH223 4.6 39.5 0.5 O1G A:DGT507 4.6 22.5 0.6 O5 A:DPO506 4.7 26.2 0.2 N A:GLU116 4.7 23.9 0.2 N A:GLU116 4.7 23.7 0.8 C2' P:DT8 4.7 33.0 0.1 O1 A:DPO506 4.8 27.4 0.2 CB A:SER113 4.8 33.8 1.0 C2' P:DT8 4.8 32.7 0.2 C5' P:DT8 4.8 39.1 0.1 O3A A:DGT507 4.8 31.5 0.6 CA A:ASP115 4.9 23.3 1.0 CA A:GLU116 4.9 25.1 0.2 CA A:GLU116 4.9 25.0 0.8 C5' P:DT8 5.0 39.2 0.2 O2B A:DGT507 5.0 22.8 0.6 P P:DG9 5.0 28.9 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 120S


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 120S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:27.7 occ:0.90 OD1 A:ASP13 1.9 30.2 0.2 OD2 A:ASP115 2.0 34.6 1.0 OD1 A:ASP13 2.1 32.6 0.8 O1G A:DGT507 2.1 22.5 0.6 O2B A:DGT507 2.1 22.8 0.6 O1 A:DPO506 2.2 27.4 0.2 O A:MET14 2.2 24.7 1.0 O5 A:DPO506 2.3 26.2 0.2 O1A A:DGT507 2.4 29.6 0.6 OP1 P:DG9 2.6 29.3 0.1 O P:HOH203 2.7 30.8 0.5 CG A:ASP13 2.9 31.5 0.8 CG A:ASP13 3.0 31.4 0.2 PB A:DGT507 3.1 29.6 0.6 CG A:ASP115 3.1 28.7 1.0 OD2 A:ASP13 3.1 40.2 0.8 PG A:DGT507 3.3 26.9 0.6 P1 A:DPO506 3.3 27.2 0.2 P2 A:DPO506 3.3 27.5 0.2 C A:MET14 3.3 22.1 1.0 OD2 A:ASP13 3.4 32.4 0.2 O3A A:DGT507 3.4 31.5 0.6 PA A:DGT507 3.5 31.8 0.6 O3B A:DGT507 3.5 25.6 0.6 MN A:MN501 3.6 28.6 0.8 O4 A:DPO506 3.7 25.7 0.2 OD1 A:ASP115 3.7 27.6 1.0 O7 A:DPO506 3.8 27.1 0.2 O3G A:DGT507 3.8 25.2 0.6 N A:MET14 3.9 22.7 1.0 O2 A:DPO506 4.0 35.0 0.2 P P:DG9 4.0 26.9 0.1 NZ A:LYS231 4.0 25.9 1.0 O A:HOH627 4.1 41.1 0.5 OP1 P:DG9 4.2 32.3 0.1 CA A:MET14 4.2 22.1 1.0 C5' P:DG9 4.2 24.8 0.1 CB A:ASP13 4.2 29.2 0.2 CB A:ASP13 4.2 29.3 0.8 C A:ASP13 4.3 18.9 1.0 C5' A:DGT507 4.3 24.4 0.6 C5' P:DG9 4.3 27.8 0.1 CB A:ASP115 4.3 23.6 1.0 N A:ASP15 4.3 20.5 1.0 O5' A:DGT507 4.4 30.2 0.6 O A:HOH763 4.4 26.9 0.6 N A:CYS16 4.4 21.8 1.0 CA A:ASP15 4.5 21.4 1.0 O5' P:DG9 4.5 29.7 0.1 O1B A:DGT507 4.5 28.1 0.6 O2G A:DGT507 4.5 27.8 0.6 C A:ASP15 4.6 24.6 1.0 O3 A:DPO506 4.6 28.1 0.2 O2A A:DGT507 4.6 37.2 0.6 N A:PHE17 4.7 23.6 1.0 CB A:MET14 4.7 24.2 1.0 O A:ASP13 4.7 22.2 1.0 O A:ASP115 4.7 24.8 1.0 O6 A:DPO506 4.7 28.9 0.2 OP2 P:DG9 4.7 34.1 0.1 CA A:ASP13 4.7 24.4 0.2 CA A:ASP13 4.7 24.3 0.8 CE A:LYS231 4.7 44.2 1.0 O5' P:DG9 4.8 26.8 0.1 CB A:PHE17 4.9 17.9 1.0 O A:HOH782 5.0 23.8 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 120S


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 120S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:29.9 occ:0.18 OP1 P:DG9 1.8 32.3 0.1 OP2 P:DG9 1.9 30.1 0.1 O2A A:DGT507 2.0 37.2 0.6 O P:HOH218 2.0 34.2 0.3 O P:HOH212 2.0 29.0 0.4 P P:DG9 2.1 28.9 0.1 O2 A:DPO506 2.2 35.0 0.2 OP2 P:DG9 2.2 34.1 0.1 O A:HOH655 2.3 37.8 1.0 O3A A:DGT507 2.4 31.5 0.6 NH1 A:ARG61 2.5 29.8 0.1 PA A:DGT507 2.8 31.8 0.6 O A:HOH627 2.9 41.1 0.5 O3' P:DT8 3.1 35.0 0.5 O5' P:DG9 3.3 26.8 0.1 O3' P:DT8 3.4 32.3 0.1 CZ A:ARG61 3.4 27.8 0.1 P P:DG9 3.5 26.9 0.1 P1 A:DPO506 3.5 27.2 0.2 NH2 A:ARG61 3.6 26.1 0.1 O A:HOH849 3.6 35.4 1.0 O A:HOH774 3.7 25.1 0.5 C3' P:DT8 3.7 35.2 0.1 O P:HOH203 3.7 30.8 0.5 O1A A:DGT507 3.7 29.6 0.6 O2G A:DGT507 3.7 27.8 0.6 O3B A:DGT507 3.8 25.6 0.6 O4 A:DPO506 3.8 25.7 0.2 PB A:DGT507 3.8 29.6 0.6 C3' P:DT8 3.9 34.6 0.5 O6 A:DPO506 3.9 28.9 0.2 O5 A:DPO506 4.0 26.2 0.2 OP1 P:DG9 4.0 29.3 0.1 O5' A:DGT507 4.0 30.2 0.6 O1G A:DGT507 4.1 22.5 0.6 O5' P:DG9 4.1 29.7 0.1 P2 A:DPO506 4.2 27.5 0.2 PG A:DGT507 4.2 26.9 0.6 C5' P:DG9 4.3 27.8 0.1 O3 A:DPO506 4.4 28.1 0.2 O1B A:DGT507 4.4 28.1 0.6 O1 A:DPO506 4.5 27.4 0.2 O A:HOH859 4.5 60.4 1.0 O A:HOH935 4.5 41.3 0.5 NE A:ARG61 4.6 30.1 0.1 O A:HOH763 4.7 26.9 0.6 C2' P:DT8 4.7 35.1 0.1 C4' P:DT8 4.7 37.9 0.5 O3' P:DT8 4.7 31.4 0.1 C2' P:DT8 4.7 32.7 0.2 C3' P:DT8 4.8 33.0 0.1 O A:HOH659 4.8 30.8 1.0 O2B A:DGT507 4.8 22.8 0.6 C3' P:DT8 4.8 32.7 0.2 C4' P:DT8 4.9 36.5 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