Manganese in PDB 5kfd: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 300S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 300S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 300S, PDB code: 5kfd 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)	19.73 / 1.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.390, 98.390, 82.310, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 22

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 300S also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 300S (pdb code 5kfd). 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 300S, PDB code: 5kfd:
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 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:13.2 occ:0.90 OD2 A:ASP13 2.1 13.7 0.8 O A:HOH732 2.2 14.2 1.0 OE2 A:GLU116 2.2 16.1 1.0 OD1 A:ASP115 2.2 11.2 1.0 O3' P:DT8 2.3 14.6 1.0 O1A A:DTP506 2.3 13.0 1.0 OD2 A:ASP13 2.5 12.9 0.2 OD1 A:ASP13 2.9 11.7 0.2 CG A:ASP13 3.0 12.5 0.2 CG A:ASP115 3.2 11.7 1.0 CD A:GLU116 3.2 17.2 1.0 CG A:ASP13 3.2 11.7 0.8 C3' P:DT8 3.3 16.6 1.0 OD2 A:ASP115 3.4 9.6 1.0 PA A:DTP506 3.5 12.5 1.0 CA A:CA502 3.6 12.4 0.2 MN A:MN503 3.6 12.3 0.8 OD1 A:ASP13 3.8 15.8 0.8 OG A:SER113 3.8 15.5 1.0 OE1 A:GLU116 3.9 20.2 1.0 O2A A:DTP506 3.9 14.8 1.0 O5' A:DTP506 4.0 12.1 1.0 C4' P:DT8 4.1 17.1 1.0 CB A:GLU116 4.1 11.9 1.0 CG A:GLU116 4.1 9.8 1.0 C5' A:DTP506 4.2 14.0 1.0 O A:HOH714 4.2 20.1 1.0 NZ A:LYS224 4.2 10.0 0.6 O P:HOH105 4.4 11.9 0.7 CB A:ASP13 4.4 11.3 0.8 CB A:ASP13 4.5 11.4 0.2 C5' P:DT8 4.5 19.2 0.4 C2' P:DT8 4.6 18.4 1.0 CB A:ASP115 4.6 9.0 1.0 C A:ASP115 4.6 11.9 1.0 C5' P:DT8 4.7 20.8 0.6 O A:ASP115 4.7 11.1 1.0 O1G A:DTP506 4.8 11.6 1.0 N A:GLU116 4.8 8.3 1.0 O3A A:DTP506 4.9 12.3 1.0 CB A:SER113 4.9 13.2 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:12.3 occ:0.75 CA A:CA502 0.1 12.4 0.2 OD1 A:ASP13 2.2 11.7 0.2 O A:MET14 2.2 10.3 1.0 OD1 A:ASP13 2.2 15.8 0.8 OD2 A:ASP115 2.2 9.6 1.0 O1G A:DTP506 2.3 11.6 1.0 O1B A:DTP506 2.3 11.3 1.0 O1A A:DTP506 2.4 13.0 1.0 CG A:ASP13 3.0 11.7 0.8 OD2 A:ASP13 3.2 13.7 0.8 CG A:ASP115 3.3 11.7 1.0 PB A:DTP506 3.3 11.5 1.0 CG A:ASP13 3.4 12.5 0.2 C A:MET14 3.4 10.5 1.0 PG A:DTP506 3.5 12.9 1.0 PA A:DTP506 3.5 12.5 1.0 MN A:MN501 3.6 13.2 0.9 O3A A:DTP506 3.7 12.3 1.0 OD1 A:ASP115 3.7 11.2 1.0 NZ A:LYS231 3.8 11.7 0.5 O3B A:DTP506 3.8 10.3 1.0 N A:MET14 3.9 7.1 1.0 O A:HOH714 3.9 20.1 1.0 OD2 A:ASP13 4.1 12.9 0.2 O2G A:DTP506 4.1 11.2 1.0 CA A:MET14 4.1 11.2 1.0 C5' A:DTP506 4.1 14.0 1.0 C A:ASP13 4.2 8.5 1.0 CB A:ASP13 4.3 11.3 0.8 O5' A:DTP506 4.3 12.1 1.0 CB A:ASP13 4.4 11.4 0.2 O A:HOH732 4.4 14.2 1.0 N A:ASP15 4.4 8.4 1.0 N A:CYS16 4.5 9.8 1.0 CA A:ASP15 4.6 8.8 1.0 O A:ASP13 4.6 10.6 1.0 CB A:ASP115 4.6 9.0 1.0 CB A:MET14 4.7 12.5 1.0 O2B A:DTP506 4.7 10.3 1.0 O2A A:DTP506 4.7 14.8 1.0 CE A:LYS231 4.7 18.4 0.5 O3G A:DTP506 4.7 12.1 1.0 CA A:ASP13 4.7 12.2 0.2 CA A:ASP13 4.7 12.2 0.8 C A:ASP15 4.7 9.7 1.0 N A:PHE17 4.8 12.0 1.0 CB A:PHE17 4.9 9.6 1.0 O A:ASP115 4.9 11.1 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