Manganese in PDB 7u80: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.25 Mm MN2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.25 Mm MN2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.25 Mm MN2+ For 600S, PDB code: 7u80 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)	42.75 / 1.83
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.731, 98.731, 82.026, 90, 90, 120
R / Rfree (%)	17.9 / 21.4

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.25 Mm MN2+ For 600S (pdb code 7u80). 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 0.25 Mm MN2+ For 600S, PDB code: 7u80:
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 0.25 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 0.25 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:30.3 occ:0.70 OD1 A:ASP115 2.0 28.2 0.9 OD2 A:ASP13 2.2 37.0 1.0 O A:HOH836 2.2 33.3 0.5 OE1 A:GLU116 2.2 35.6 1.0 O1A A:XG4505 2.4 26.6 0.8 O3' P:DT8 2.4 32.9 0.3 O A:HOH807 2.6 35.2 1.0 OD1 A:ASP115 2.6 28.9 0.1 CG A:ASP115 3.0 29.2 0.1 CG A:ASP115 3.0 32.0 0.9 CD A:GLU116 3.3 40.1 1.0 CG A:ASP13 3.3 31.1 1.0 OD2 A:ASP115 3.4 29.3 0.9 C3' P:DT8 3.4 34.5 0.3 OD2 A:ASP115 3.4 25.2 0.1 PA A:XG4505 3.5 28.3 0.8 MN A:MN502 3.6 28.9 0.8 OG A:SER113 3.7 33.8 1.0 OD1 A:ASP13 3.8 31.2 1.0 O5' A:XG4505 3.9 29.4 0.8 CB A:ASP115 3.9 28.1 0.1 CB A:GLU116 4.0 31.6 1.0 O2A A:XG4505 4.0 28.9 0.8 OE2 A:GLU116 4.1 42.3 1.0 CG A:GLU116 4.1 31.1 1.0 C5' A:XG4505 4.1 25.1 0.8 NZ A:LYS224 4.3 43.1 1.0 C4' P:DT8 4.3 31.6 0.3 O A:HOH761 4.4 41.0 1.0 CB A:ASP115 4.4 27.1 0.9 C A:ASP115 4.4 33.9 1.0 O A:ASP115 4.5 31.9 1.0 CB A:ASP13 4.5 29.0 1.0 C2' P:DT8 4.6 32.2 0.3 O A:HOH762 4.6 44.8 0.5 N A:GLU116 4.6 32.7 1.0 CA A:ASP115 4.7 29.7 0.1 O2G A:XG4505 4.7 23.9 0.8 CB A:SER113 4.8 31.4 1.0 CA A:ASP115 4.8 29.9 0.9 C5' P:DT8 4.8 38.9 0.3 O5' P:DT8 4.9 43.0 0.3 N3A A:XG4505 4.9 31.6 0.8 CA A:GLU116 4.9 28.9 1.0 N A:ASP115 5.0 24.9 1.0 O1B A:XG4505 5.0 23.7 0.8

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.25 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 0.25 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:28.9 occ:0.85 OD1 A:ASP13 2.1 31.2 1.0 O2G A:XG4505 2.2 23.9 0.8 OD2 A:ASP115 2.2 29.3 0.9 O A:MET14 2.2 25.5 1.0 O1B A:XG4505 2.3 23.7 0.8 O1A A:XG4505 2.4 26.6 0.8 CG A:ASP13 2.9 31.1 1.0 OD2 A:ASP13 3.1 37.0 1.0 PB A:XG4505 3.2 28.3 0.8 CG A:ASP115 3.3 32.0 0.9 C A:MET14 3.4 25.1 1.0 PG A:XG4505 3.4 28.6 0.8 PA A:XG4505 3.6 28.3 0.8 MN A:MN501 3.6 30.3 0.7 O3B A:XG4505 3.6 27.8 0.8 OD1 A:ASP115 3.7 28.2 0.9 N3A A:XG4505 3.7 31.6 0.8 N A:MET14 3.9 26.6 1.0 OD2 A:ASP115 3.9 25.2 0.1 O3G A:XG4505 3.9 25.7 0.8 NZ A:LYS231 4.0 29.9 1.0 O A:HOH761 4.0 41.0 1.0 CG A:ASP115 4.1 29.2 0.1 CA A:MET14 4.2 24.8 1.0 CB A:ASP115 4.2 28.1 0.1 C A:ASP13 4.2 24.6 1.0 C5' A:XG4505 4.2 25.1 0.8 CB A:ASP13 4.2 29.0 1.0 N A:ASP15 4.4 24.8 1.0 O5' A:XG4505 4.4 29.4 0.8 N A:CYS16 4.5 27.3 1.0 CB A:ASP115 4.5 27.1 0.9 CA A:ASP15 4.5 26.6 1.0 CE A:LYS231 4.5 46.3 1.0 C A:ASP15 4.6 30.7 1.0 O A:HOH807 4.6 35.2 1.0 O2B A:XG4505 4.7 27.7 0.8 O A:ASP13 4.7 24.4 1.0 CB A:MET14 4.7 29.8 1.0 CA A:ASP13 4.7 27.8 1.0 O1G A:XG4505 4.7 31.3 0.8 N A:PHE17 4.7 26.0 1.0 OD1 A:ASP115 4.8 28.9 0.1 O2A A:XG4505 4.8 28.9 0.8 O A:ASP115 4.8 31.9 1.0 CB A:PHE17 5.0 25.4 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