Manganese in PDB 5kff: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 1800S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 1800S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 1800S, PDB code: 5kff was solved by Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 1.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.410, 98.410, 81.990, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 22.1

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 1800S (pdb code 5kff). 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 Ternary Complex: Reaction with 1 Mm MN2+ For 1800S, PDB code: 5kff:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 1800S


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 Complex: Reaction with 1 Mm MN2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:10.4 occ:1.00 OD1 A:ASP115 2.1 9.3 1.0 OE2 A:GLU116 2.2 12.2 1.0 O A:HOH783 2.2 11.2 1.0 O1A A:DTP505 2.2 12.2 1.0 O3' P:DT8 2.3 11.9 1.0 OD2 A:ASP13 2.3 11.6 1.0 CG A:ASP115 3.1 9.7 1.0 CD A:GLU116 3.2 12.2 1.0 C3' P:DT8 3.2 13.3 1.0 CG A:ASP13 3.3 12.6 1.0 OD2 A:ASP115 3.4 8.8 1.0 PA A:DTP505 3.4 11.4 1.0 MN A:MN502 3.6 9.9 1.0 OD1 A:ASP13 3.8 11.2 1.0 O2A A:DTP505 3.8 13.6 1.0 OE1 A:GLU116 3.8 17.8 1.0 OG A:SER113 3.8 12.8 1.0 O5' A:DTP505 3.9 10.2 1.0 C4' P:DT8 4.0 13.6 1.0 CG A:GLU116 4.1 9.7 1.0 C5' A:DTP505 4.2 10.7 1.0 NZ A:LYS224 4.2 9.8 0.7 CB A:GLU116 4.2 12.1 1.0 O A:HOH667 4.2 18.3 1.0 O P:HOH104 4.4 12.5 1.0 C5' P:DT8 4.5 17.0 0.4 CB A:ASP13 4.5 8.7 1.0 CB A:ASP115 4.5 9.7 1.0 C2' P:DT8 4.5 15.2 1.0 C5' P:DT8 4.6 17.8 0.6 C A:ASP115 4.6 9.9 1.0 O A:ASP115 4.7 9.7 1.0 O1G A:DTP505 4.7 10.8 1.0 O3A A:DTP505 4.8 11.9 1.0 CB A:SER113 4.8 11.7 1.0 N A:GLU116 4.9 8.6 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 1800S


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 Complex: Reaction with 1 Mm MN2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:9.9 occ:1.00 O1G A:DTP505 2.2 10.8 1.0 OD2 A:ASP115 2.2 8.8 1.0 O A:MET14 2.2 10.6 1.0 O1B A:DTP505 2.2 9.9 1.0 OD1 A:ASP13 2.2 11.2 1.0 O1A A:DTP505 2.3 12.2 1.0 CG A:ASP13 3.0 12.6 1.0 PB A:DTP505 3.2 10.3 1.0 CG A:ASP115 3.3 9.7 1.0 OD2 A:ASP13 3.3 11.6 1.0 PA A:DTP505 3.4 11.4 1.0 C A:MET14 3.4 9.9 1.0 PG A:DTP505 3.4 13.1 1.0 O3A A:DTP505 3.5 11.9 1.0 MN A:MN501 3.6 10.4 1.0 O3B A:DTP505 3.7 9.6 1.0 OD1 A:ASP115 3.7 9.3 1.0 NZ A:LYS231 3.7 9.5 0.7 O A:HOH667 3.8 18.3 1.0 N A:MET14 3.9 8.6 1.0 O2G A:DTP505 4.0 10.2 1.0 C5' A:DTP505 4.1 10.7 1.0 CA A:MET14 4.1 10.1 1.0 O5' A:DTP505 4.2 10.2 1.0 C A:ASP13 4.2 9.7 1.0 CB A:ASP13 4.3 8.7 1.0 N A:ASP15 4.4 8.2 1.0 O A:HOH783 4.4 11.2 1.0 N A:CYS16 4.5 9.7 1.0 CB A:ASP115 4.5 9.7 1.0 O2B A:DTP505 4.6 9.2 1.0 O A:ASP13 4.6 10.7 1.0 CA A:ASP15 4.6 8.2 1.0 O2A A:DTP505 4.6 13.6 1.0 O3G A:DTP505 4.6 12.6 1.0 CB A:MET14 4.6 10.2 1.0 CE A:LYS231 4.6 15.9 0.7 N A:PHE17 4.7 7.7 1.0 C A:ASP15 4.8 11.8 1.0 CA A:ASP13 4.8 10.7 1.0 CB A:PHE17 4.9 7.2 1.0 O A:ASP115 4.9 9.7 1.0

Y.Gao, W.Yang. Capture of A Third MG2+ Is Essential For Catalyzing Dna Synthesis. Science V. 352 1334 2016.
ISSN: ESSN 1095-9203
PubMed: 27284197
DOI: 10.1126/SCIENCE.AAD9633