Manganese in PDB 7u7y: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.06 Mm MN2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.06 Mm MN2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.06 Mm MN2+ For 600S, PDB code: 7u7y 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)	42.70 / 1.78
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.607, 98.607, 81.801, 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 0.06 Mm MN2+ For 600S (pdb code 7u7y). 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 0.06 Mm MN2+ For 600S, PDB code: 7u7y:
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 0.06 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 0.06 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:31.8 occ:0.60 O A:HOH811 2.1 31.4 0.5 O3' P:DT8 2.3 31.0 0.2 OD1 A:ASP115 2.3 27.8 0.8 OE1 A:GLU116 2.3 41.5 1.0 OD1 A:ASP115 2.3 24.9 0.2 O1A A:XG4505 2.4 24.5 0.8 OD1 A:ASP13 2.4 31.8 0.5 O A:HOH817 2.4 39.6 1.0 OD2 A:ASP13 2.5 34.5 0.5 CG A:ASP115 3.1 27.1 0.2 C3' P:DT8 3.2 36.4 0.2 CG A:ASP115 3.3 24.3 0.8 CD A:GLU116 3.4 44.5 1.0 PA A:XG4505 3.5 26.2 0.8 CG A:ASP13 3.5 26.6 0.5 CG A:ASP13 3.5 26.7 0.5 OD2 A:ASP115 3.6 23.7 0.8 OD2 A:ASP115 3.6 23.4 0.2 MN A:MN502 3.6 28.7 0.8 OG A:SER113 3.7 35.0 1.0 O5' A:XG4505 3.8 25.9 0.8 O2A A:XG4505 4.0 27.9 0.8 CB A:ASP115 4.0 23.9 0.2 CB A:GLU116 4.0 31.6 1.0 OD1 A:ASP13 4.1 30.9 0.5 OD2 A:ASP13 4.1 29.3 0.5 C5' A:XG4505 4.2 21.8 0.8 CG A:GLU116 4.2 34.4 1.0 C4' P:DT8 4.2 32.3 0.2 OE2 A:GLU116 4.3 40.0 1.0 C2' P:DT8 4.4 32.6 0.2 O A:HOH721 4.4 38.7 1.0 NZ A:LYS224 4.5 45.5 1.0 O5' P:DT8 4.6 38.3 0.2 C A:ASP115 4.6 29.2 1.0 CB A:ASP13 4.6 26.0 0.5 CB A:ASP115 4.7 23.0 0.8 N A:GLU116 4.7 27.5 1.0 CB A:ASP13 4.7 25.9 0.5 O A:ASP115 4.7 27.8 1.0 O2G A:XG4505 4.8 22.3 0.8 CB A:SER113 4.8 31.5 1.0 C5' P:DT8 4.8 40.5 0.2 CA A:ASP115 4.9 24.9 0.2 N3A A:XG4505 4.9 26.9 0.8 CA A:GLU116 5.0 25.3 1.0 O1B A:XG4505 5.0 21.8 0.8

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.06 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 0.06 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:28.7 occ:0.85 OD1 A:ASP13 2.0 30.9 0.5 OD2 A:ASP115 2.2 23.7 0.8 O2G A:XG4505 2.2 22.3 0.8 O A:MET14 2.2 23.6 1.0 O1B A:XG4505 2.3 21.8 0.8 OD2 A:ASP13 2.4 29.3 0.5 O1A A:XG4505 2.4 24.5 0.8 OD1 A:ASP13 2.7 31.8 0.5 CG A:ASP13 2.8 26.6 0.5 CG A:ASP13 2.9 26.7 0.5 OD2 A:ASP13 3.1 34.5 0.5 CG A:ASP115 3.2 24.3 0.8 PB A:XG4505 3.3 25.8 0.8 C A:MET14 3.4 20.8 1.0 PG A:XG4505 3.5 24.8 0.8 PA A:XG4505 3.6 26.2 0.8 MN A:MN501 3.6 31.8 0.6 OD1 A:ASP115 3.6 27.8 0.8 O3B A:XG4505 3.7 22.0 0.8 N3A A:XG4505 3.8 26.9 0.8 N A:MET14 3.9 21.8 1.0 OD2 A:ASP115 4.0 23.4 0.2 CG A:ASP115 4.0 27.1 0.2 O A:HOH668 4.0 29.1 0.8 O3G A:XG4505 4.0 25.0 0.8 O A:HOH721 4.1 38.7 1.0 CB A:ASP115 4.1 23.9 0.2 NZ A:LYS231 4.1 31.9 0.5 CA A:MET14 4.2 22.3 1.0 C5' A:XG4505 4.2 21.8 0.8 CB A:ASP13 4.2 26.0 0.5 CB A:ASP13 4.2 25.9 0.5 C A:ASP13 4.3 21.1 1.0 O5' A:XG4505 4.4 25.9 0.8 N A:ASP15 4.4 22.9 1.0 OD1 A:ASP115 4.5 24.9 0.2 CB A:ASP115 4.5 23.0 0.8 N A:CYS16 4.5 25.3 1.0 O A:HOH817 4.5 39.6 1.0 CA A:ASP15 4.6 21.2 1.0 C A:ASP15 4.7 26.0 1.0 O2B A:XG4505 4.7 23.7 0.8 CB A:MET14 4.7 23.5 1.0 O A:ASP13 4.7 22.6 1.0 CA A:ASP13 4.7 23.8 0.5 CA A:ASP13 4.7 23.8 0.5 N A:PHE17 4.7 21.4 1.0 O1G A:XG4505 4.8 29.9 0.8 O A:ASP115 4.8 27.8 1.0 CB A:PHE17 4.9 19.9 1.0 O2A A:XG4505 4.9 27.9 0.8

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