Manganese in PDB 7u81: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.5 Mm MN2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.5 Mm MN2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.5 Mm MN2+ For 600S, PDB code: 7u81 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)	42.57 / 1.60
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.311, 98.311, 82.088, 90, 90, 120
R / Rfree (%)	18.8 / 21.9

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.5 Mm MN2+ For 600S (pdb code 7u81). 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 0.5 Mm MN2+ For 600S, PDB code: 7u81:
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 0.5 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 0.5 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:22.6 occ:0.80 OD1 A:ASP115 2.1 23.8 0.9 OE1 A:GLU116 2.2 25.8 1.0 O A:HOH670 2.2 25.6 0.5 O1A A:XG4505 2.3 22.0 0.9 OD2 A:ASP13 2.3 28.2 1.0 O A:HOH773 2.3 28.5 1.0 O3' P:DT8 2.4 26.0 0.3 OD1 A:ASP115 2.5 21.1 0.1 CG A:ASP115 3.1 22.4 0.1 CG A:ASP115 3.1 21.6 0.9 CD A:GLU116 3.2 29.6 1.0 CG A:ASP13 3.3 25.0 1.0 C3' P:DT8 3.4 25.6 0.3 PA A:XG4505 3.4 21.8 0.9 OD2 A:ASP115 3.5 21.9 0.9 MN A:MN502 3.6 21.4 0.9 OD2 A:ASP115 3.6 21.9 0.1 OD1 A:ASP13 3.7 23.3 1.0 O5' A:XG4505 3.8 21.7 0.9 CB A:ASP115 3.8 22.4 0.1 OG A:SER113 3.9 27.8 1.0 O2A A:XG4505 3.9 22.6 0.9 OE2 A:GLU116 4.0 29.6 1.0 CB A:GLU116 4.0 22.2 1.0 C5' A:XG4505 4.1 19.4 0.9 CG A:GLU116 4.1 21.4 1.0 O A:HOH747 4.2 29.4 1.0 NZ A:LYS224 4.2 29.3 1.0 O A:HOH908 4.2 25.7 0.3 C4' P:DT8 4.4 26.4 0.3 CB A:ASP115 4.4 23.9 0.9 C A:ASP115 4.5 26.1 1.0 O A:ASP115 4.5 25.2 1.0 C2' P:DT8 4.6 25.5 0.3 CB A:ASP13 4.6 21.6 1.0 O2G A:XG4505 4.7 23.2 0.9 N A:GLU116 4.7 21.1 1.0 CA A:ASP115 4.7 21.8 0.1 O5' P:DT8 4.8 30.6 0.3 N3A A:XG4505 4.8 23.2 0.9 C5' P:DT8 4.8 30.3 0.3 CA A:ASP115 4.8 21.8 0.9 CB A:SER113 4.9 23.8 1.0 O1B A:XG4505 4.9 20.4 0.9 CA A:GLU116 5.0 22.5 1.0 N A:ASP115 5.0 18.6 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.5 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 0.5 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:21.4 occ:0.90 OD1 A:ASP13 2.1 23.3 1.0 O A:MET14 2.1 22.8 1.0 OD2 A:ASP115 2.2 21.9 0.9 O2G A:XG4505 2.2 23.2 0.9 O1B A:XG4505 2.2 20.4 0.9 O1A A:XG4505 2.4 22.0 0.9 CG A:ASP13 3.0 25.0 1.0 PB A:XG4505 3.2 21.7 0.9 CG A:ASP115 3.2 21.6 0.9 C A:MET14 3.3 17.6 1.0 OD2 A:ASP13 3.3 28.2 1.0 PG A:XG4505 3.4 23.6 0.9 PA A:XG4505 3.5 21.8 0.9 O3B A:XG4505 3.6 20.6 0.9 MN A:MN501 3.6 22.6 0.8 OD1 A:ASP115 3.6 23.8 0.9 N3A A:XG4505 3.6 23.2 0.9 N A:MET14 3.8 18.3 1.0 NZ A:LYS231 3.9 23.7 1.0 O3G A:XG4505 3.9 22.2 0.9 O A:HOH747 4.0 29.4 1.0 CA A:MET14 4.1 18.6 1.0 OD2 A:ASP115 4.1 21.9 0.1 CB A:ASP115 4.1 22.4 0.1 CG A:ASP115 4.1 22.4 0.1 C A:ASP13 4.1 16.8 1.0 C5' A:XG4505 4.2 19.4 0.9 CB A:ASP13 4.3 21.6 1.0 N A:ASP15 4.3 19.4 1.0 O5' A:XG4505 4.4 21.7 0.9 N A:CYS16 4.4 22.4 1.0 CA A:ASP15 4.4 19.1 1.0 CB A:ASP115 4.5 23.9 0.9 C A:ASP15 4.5 22.7 1.0 O A:HOH773 4.6 28.5 1.0 O A:ASP13 4.6 19.9 1.0 O2B A:XG4505 4.6 21.8 0.9 CE A:LYS231 4.6 29.4 1.0 O1G A:XG4505 4.6 24.4 0.9 CB A:MET14 4.7 22.3 1.0 N A:PHE17 4.7 21.0 1.0 CA A:ASP13 4.7 21.1 1.0 OD1 A:ASP115 4.7 21.1 0.1 O2A A:XG4505 4.8 22.6 0.9 O A:ASP115 4.8 25.2 1.0 CB A:PHE17 4.9 16.1 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