Manganese in PDB 7u82: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MN2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MN2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MN2+ For 600S, PDB code: 7u82 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)	42.02 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	97.999, 97.999, 81.701, 90, 90, 120
R / Rfree (%)	19.2 / 22.1

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MN2+ For 600S (pdb code 7u82). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MN2+ For 600S, PDB code: 7u82:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MN2+ For 600S


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-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:22.8 occ:0.85 OD1 A:ASP115 2.0 20.1 0.8 O A:HOH651 2.1 23.3 0.5 OD2 A:ASP13 2.2 23.9 1.0 OE1 A:GLU116 2.2 25.5 1.0 O1A A:XG4505 2.3 21.7 0.9 O A:HOH801 2.3 29.3 1.0 OD1 A:ASP115 2.3 19.9 0.2 O3' P:DT8 2.3 23.1 0.3 CG A:ASP115 3.0 21.6 0.2 CG A:ASP115 3.1 20.4 0.8 CD A:GLU116 3.2 27.9 1.0 CG A:ASP13 3.2 24.7 1.0 C3' P:DT8 3.4 24.4 0.3 PA A:XG4505 3.4 21.4 0.9 OD2 A:ASP115 3.4 20.4 0.8 MN A:MN502 3.6 20.5 0.9 OD1 A:ASP13 3.6 22.1 1.0 OD2 A:ASP115 3.7 23.4 0.2 OG A:SER113 3.8 26.3 1.0 CB A:ASP115 3.8 21.1 0.2 O5' A:XG4505 3.8 22.2 0.9 O2A A:XG4505 3.8 23.4 0.9 OE2 A:GLU116 4.0 29.4 1.0 CB A:GLU116 4.0 23.0 1.0 O P:HOH102 4.0 25.4 0.3 C5' A:XG4505 4.1 20.0 0.9 CG A:GLU116 4.1 21.8 1.0 O A:HOH750 4.2 26.6 1.0 O A:HOH904 4.2 28.1 0.5 NZ A:LYS224 4.2 27.0 1.0 C4' P:DT8 4.3 24.1 0.3 CB A:ASP115 4.4 21.6 0.8 C A:ASP115 4.4 23.5 1.0 CB A:ASP13 4.5 21.1 1.0 O A:ASP115 4.5 24.6 1.0 C2' P:DT8 4.5 24.0 0.3 CA A:ASP115 4.6 19.6 0.2 N A:GLU116 4.7 20.2 1.0 O2G A:XG4505 4.7 23.4 0.9 O5' P:DT8 4.8 28.3 0.3 C5' P:DT8 4.8 26.7 0.3 N3A A:XG4505 4.8 23.4 0.9 CB A:SER113 4.8 21.4 1.0 CA A:ASP115 4.8 19.2 0.8 O1B A:XG4505 4.9 21.0 0.9 CA A:GLU116 4.9 23.4 1.0 N A:ASP115 5.0 18.7 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MN2+ For 600S


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-Dgmpnpp Ternary Mismatch Complex in 1.0 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:20.5 occ:0.90 OD1 A:ASP13 2.1 22.1 1.0 O A:MET14 2.1 22.6 1.0 OD2 A:ASP115 2.1 20.4 0.8 O2G A:XG4505 2.2 23.4 0.9 O1B A:XG4505 2.2 21.0 0.9 O1A A:XG4505 2.3 21.7 0.9 CG A:ASP13 3.0 24.7 1.0 CG A:ASP115 3.2 20.4 0.8 PB A:XG4505 3.2 20.9 0.9 C A:MET14 3.3 17.2 1.0 OD2 A:ASP13 3.4 23.9 1.0 PG A:XG4505 3.4 22.3 0.9 PA A:XG4505 3.4 21.4 0.9 OD1 A:ASP115 3.6 20.1 0.8 O3B A:XG4505 3.6 20.0 0.9 MN A:MN501 3.6 22.8 0.8 N3A A:XG4505 3.6 23.4 0.9 N A:MET14 3.8 18.1 1.0 NZ A:LYS231 3.9 21.7 1.0 O3G A:XG4505 3.9 22.2 0.9 O A:HOH750 4.0 26.6 1.0 CG A:ASP115 4.1 21.6 0.2 CA A:MET14 4.1 17.6 1.0 CB A:ASP115 4.1 21.1 0.2 OD2 A:ASP115 4.1 23.4 0.2 C5' A:XG4505 4.1 20.0 0.9 C A:ASP13 4.2 17.8 1.0 CB A:ASP13 4.3 21.1 1.0 N A:ASP15 4.3 20.0 1.0 O5' A:XG4505 4.3 22.2 0.9 N A:CYS16 4.4 20.4 1.0 CB A:ASP115 4.4 21.6 0.8 O A:HOH801 4.5 29.3 1.0 CA A:ASP15 4.5 19.6 1.0 OD1 A:ASP115 4.5 19.9 0.2 O2B A:XG4505 4.6 21.9 0.9 CB A:MET14 4.6 21.8 1.0 O A:ASP13 4.6 20.2 1.0 C A:ASP15 4.6 22.9 1.0 O1G A:XG4505 4.6 23.4 0.9 N A:PHE17 4.7 20.2 1.0 O2A A:XG4505 4.7 23.4 0.9 CE A:LYS231 4.7 26.9 1.0 CA A:ASP13 4.7 20.3 1.0 O A:ASP115 4.8 24.6 1.0 CB A:PHE17 4.8 18.6 1.0

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