Manganese in PDB 7u7i: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 180S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 180S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 180S, PDB code: 7u7i 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)	42.46 / 1.57
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.067, 98.067, 81.813, 90, 90, 120
R / Rfree (%)	18.1 / 21.9

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 180S (pdb code 7u7i). 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 180S, PDB code: 7u7i:
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 180S


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 180S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:22.0 occ:0.70 OE1 A:GLU116 2.0 28.3 0.7 OE1 A:GLU116 2.0 30.3 0.3 OP1 P:DG9 2.0 25.6 0.2 O P:HOH219 2.0 22.9 0.6 OD1 A:ASP115 2.1 24.9 1.0 OD1 A:ASP13 2.1 29.1 0.3 OD2 A:ASP13 2.1 28.2 0.7 O A:HOH795 2.2 23.6 0.2 O1A A:DGT507 2.3 25.8 0.5 O A:HOH755 2.3 32.8 1.0 O3' P:DT8 2.4 27.1 0.2 O3' P:DT8 2.5 27.2 0.2 P P:DG9 2.8 20.9 0.2 CD A:GLU116 3.0 30.6 0.7 CG A:ASP115 3.0 24.6 1.0 CD A:GLU116 3.1 30.3 0.3 CG A:ASP13 3.1 25.1 0.7 CG A:ASP13 3.2 24.5 0.3 OD2 A:ASP115 3.3 28.6 1.0 OD1 A:ASP13 3.4 24.6 0.7 C3' P:DT8 3.5 29.9 0.2 C3' P:DT8 3.5 29.3 0.2 PA A:DGT507 3.5 22.6 0.5 MN A:MN502 3.6 20.9 0.9 OG A:SER113 3.7 29.1 1.0 OE2 A:GLU116 3.8 32.8 0.7 OD2 A:ASP13 3.8 28.1 0.3 CG A:GLU116 3.8 22.9 0.3 CB A:GLU116 3.9 23.3 0.7 CB A:GLU116 3.9 23.2 0.3 OP2 P:DG9 3.9 28.2 0.2 OP1 P:DG9 3.9 25.5 0.1 O5' P:DG9 3.9 23.7 0.2 CG A:GLU116 3.9 22.6 0.7 O2A A:DGT507 4.0 29.5 0.5 OE2 A:GLU116 4.0 30.8 0.3 O A:HOH894 4.1 29.1 0.6 O5' A:DGT507 4.1 20.5 0.5 O3' P:DT8 4.1 27.5 0.1 NZ A:LYS224 4.1 28.9 0.7 C5' P:DG9 4.2 22.1 0.1 C4' P:DT8 4.2 31.5 0.2 C4' P:DT8 4.2 30.4 0.2 C5' A:DGT507 4.3 21.4 0.5 C5' P:DG9 4.4 21.4 0.2 CB A:ASP115 4.4 21.8 1.0 CB A:ASP13 4.4 20.8 0.3 O P:HOH216 4.4 31.4 0.6 P P:DG9 4.4 30.0 0.1 CB A:ASP13 4.4 20.8 0.7 O5' P:DG9 4.5 22.9 0.1 C A:ASP115 4.5 19.8 1.0 C5' P:DT8 4.5 33.5 0.2 O A:HOH894 4.5 29.2 0.5 C2' P:DT8 4.6 28.4 0.2 O A:ASP115 4.6 22.6 1.0 C4' P:DT8 4.6 31.7 0.1 C3' P:DT8 4.6 30.8 0.1 N A:GLU116 4.7 17.4 1.0 O3G A:DGT507 4.7 21.4 0.5 O5 A:DPO506 4.7 22.1 0.3 CB A:SER113 4.8 25.1 1.0 O3A A:DGT507 4.8 21.7 0.5 C2' P:DT8 4.8 29.4 0.2 O1 A:DPO506 4.9 18.6 0.3 CA A:GLU116 4.9 21.8 0.7 CA A:ASP115 4.9 20.1 1.0 CA A:GLU116 4.9 21.8 0.3 O5' P:DT8 4.9 34.6 0.2 C5' P:DT8 4.9 33.7 0.2 O5' P:DT8 5.0 36.3 0.2

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 180S


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 180S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:20.9 occ:0.90 OD1 A:ASP13 2.1 24.6 0.7 OD2 A:ASP115 2.1 28.6 1.0 O3G A:DGT507 2.1 21.4 0.5 O1 A:DPO506 2.1 18.6 0.3 O2B A:DGT507 2.2 18.4 0.5 O A:MET14 2.2 20.1 1.0 O5 A:DPO506 2.2 22.1 0.3 OD2 A:ASP13 2.3 28.1 0.3 O1A A:DGT507 2.3 25.8 0.5 OP1 P:DG9 2.6 25.6 0.2 O P:HOH219 2.6 22.9 0.6 CG A:ASP13 3.0 24.5 0.3 CG A:ASP13 3.1 25.1 0.7 PB A:DGT507 3.1 20.0 0.5 OD1 A:ASP13 3.1 29.1 0.3 CG A:ASP115 3.1 24.6 1.0 PG A:DGT507 3.2 22.2 0.5 P1 A:DPO506 3.3 20.6 0.3 O3A A:DGT507 3.3 21.7 0.5 P2 A:DPO506 3.4 22.1 0.3 PA A:DGT507 3.4 22.6 0.5 C A:MET14 3.4 19.8 1.0 OD2 A:ASP13 3.5 28.2 0.7 O3B A:DGT507 3.5 19.3 0.5 MN A:MN501 3.6 22.0 0.7 OD1 A:ASP115 3.7 24.9 1.0 O4 A:DPO506 3.7 19.4 0.3 O2 A:DPO506 3.8 24.5 0.3 O A:HOH894 3.9 29.1 0.6 NZ A:LYS231 3.9 23.0 1.0 P P:DG9 3.9 20.9 0.2 O7 A:DPO506 3.9 19.2 0.3 O2G A:DGT507 3.9 18.9 0.5 N A:MET14 3.9 19.1 1.0 OP1 P:DG9 4.1 25.5 0.1 O5' P:DG9 4.1 22.9 0.1 CA A:MET14 4.2 17.5 1.0 C5' A:DGT507 4.2 21.4 0.5 C5' P:DG9 4.2 21.4 0.2 O A:HOH894 4.2 29.2 0.5 C A:ASP13 4.2 18.2 1.0 C5' P:DG9 4.3 22.1 0.1 CB A:ASP13 4.3 20.8 0.7 O5' A:DGT507 4.3 20.5 0.5 CB A:ASP13 4.3 20.8 0.3 N A:CYS16 4.3 18.2 1.0 CB A:ASP115 4.3 21.8 1.0 N A:ASP15 4.4 16.6 1.0 O A:HOH755 4.4 32.8 1.0 O1B A:DGT507 4.5 19.3 0.5 CA A:ASP15 4.5 16.4 1.0 O1G A:DGT507 4.5 24.9 0.5 O2A A:DGT507 4.5 29.5 0.5 C A:ASP15 4.6 20.4 1.0 O3 A:DPO506 4.6 19.3 0.3 O5' P:DG9 4.6 23.7 0.2 N A:PHE17 4.6 17.1 1.0 OP2 P:DG9 4.6 28.2 0.2 O6 A:DPO506 4.6 25.2 0.3 O A:ASP13 4.7 21.6 1.0 CB A:MET14 4.7 19.5 1.0 CA A:ASP13 4.7 19.5 0.3 CA A:ASP13 4.7 19.4 0.7 P P:DG9 4.8 30.0 0.1 CE A:LYS231 4.8 35.1 1.0 CB A:PHE17 4.8 16.7 1.0 O A:ASP115 4.9 22.6 1.0 O3' P:DT8 5.0 27.1 0.2 O A:HOH795 5.0 23.6 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 180S


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 180S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:23.8 occ:0.20 OP1 P:DG9 1.5 25.5 0.1 O A:HOH741 1.9 25.2 0.5 P P:DG9 2.0 30.0 0.1 O2A A:DGT507 2.0 29.5 0.5 O P:HOH210 2.1 47.2 1.0 OP2 P:DG9 2.1 24.3 0.1 OP2 P:DG9 2.2 28.2 0.2 O2 A:DPO506 2.3 24.5 0.3 O A:HOH894 2.3 29.2 0.5 O3A A:DGT507 2.4 21.7 0.5 NH1 A:ARG61 2.5 24.5 0.1 O A:HOH695 2.5 34.3 1.0 PA A:DGT507 2.8 22.6 0.5 O5' P:DG9 3.1 22.9 0.1 O3' P:DT8 3.2 29.4 0.5 O3' P:DT8 3.4 27.5 0.1 CZ A:ARG61 3.5 24.2 0.1 P P:DG9 3.5 20.9 0.2 P1 A:DPO506 3.6 20.6 0.3 O P:HOH219 3.6 22.9 0.6 NH2 A:ARG61 3.7 20.9 0.1 O A:HOH873 3.7 32.5 1.0 PB A:DGT507 3.8 20.0 0.5 O1A A:DGT507 3.8 25.8 0.5 O1G A:DGT507 3.8 24.9 0.5 C3' P:DT8 3.8 32.5 0.5 O A:HOH894 3.8 29.1 0.6 C3' P:DT8 3.8 30.8 0.1 O4 A:DPO506 3.8 19.4 0.3 O A:HOH732 3.8 20.8 0.4 O3B A:DGT507 3.8 19.3 0.5 O6 A:DPO506 3.9 25.2 0.3 OP1 P:DG9 3.9 25.6 0.2 O5' A:DGT507 4.0 20.5 0.5 O5 A:DPO506 4.0 22.1 0.3 O3G A:DGT507 4.1 21.4 0.5 PG A:DGT507 4.1 22.2 0.5 P2 A:DPO506 4.2 22.1 0.3 O A:HOH956 4.3 42.8 0.7 C2' P:DT8 4.3 31.2 0.1 O A:HOH927 4.3 35.4 0.5 O5' P:DG9 4.3 23.7 0.2 C2' P:DT8 4.4 29.4 0.2 O1B A:DGT507 4.4 19.3 0.5 O A:HOH755 4.4 32.8 1.0 C5' P:DG9 4.5 22.1 0.1 O3 A:DPO506 4.5 19.3 0.3 O1 A:DPO506 4.5 18.6 0.3 C3' P:DT8 4.6 29.9 0.2 C4' P:DT8 4.6 32.8 0.5 O3' P:DT8 4.7 27.1 0.2 NE A:ARG61 4.7 24.6 0.1 O3' P:DT8 4.7 27.2 0.2 O2B A:DGT507 4.8 18.4 0.5 C3' P:DT8 4.8 29.3 0.2 C2' P:DT8 4.8 28.4 0.2 O A:HOH650 5.0 25.9 1.0 C5' P:DT8 5.0 31.8 0.5

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