Manganese in PDB 5kfi: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S, PDB code: 5kfi 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)	19.90 / 1.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.530, 98.530, 81.840, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.1

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S 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 10 Mm MN2+ For 120S (pdb code 5kfi). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S, PDB code: 5kfi:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S


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 10 Mm MN2+ For 120S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:12.2 occ:1.00 OP1 P:DA9 2.1 14.3 0.4 OD2 A:ASP13 2.1 14.8 1.0 OD1 A:ASP115 2.1 12.9 1.0 OE2 A:GLU116 2.2 13.2 1.0 O A:HOH780 2.2 14.0 1.0 O1A A:DTP507 2.4 14.4 0.6 O3' P:DT8 2.4 12.8 0.6 O3' P:DT8 2.5 12.4 0.4 P P:DA9 2.8 11.3 0.4 CG A:ASP115 3.1 12.1 1.0 CD A:GLU116 3.1 15.4 1.0 CG A:ASP13 3.2 13.6 1.0 C3' P:DT8 3.2 17.3 0.6 OD2 A:ASP115 3.3 10.8 1.0 C3' P:DT8 3.4 17.1 0.4 PA A:DTP507 3.5 10.2 0.6 CA A:CA502 3.5 12.7 0.2 MN A:MN503 3.6 12.7 0.8 OD1 A:ASP13 3.6 12.3 1.0 OG A:SER113 3.8 12.5 1.0 OE1 A:GLU116 3.8 16.5 1.0 OP2 P:DA9 3.8 14.9 0.4 O2A A:DTP507 4.0 13.4 0.6 C4' P:DT8 4.0 17.7 0.4 O5' P:DA9 4.0 11.5 0.4 O5' A:DTP507 4.0 9.9 0.6 C4' P:DT8 4.0 17.1 0.6 CG A:GLU116 4.1 10.1 1.0 CB A:GLU116 4.1 12.4 1.0 C5' A:DTP507 4.2 12.4 0.6 NZ A:LYS224 4.2 8.8 0.6 C5' P:DA9 4.3 11.7 0.4 C2' P:DT8 4.3 18.3 0.4 O A:HOH796 4.4 13.2 0.6 CB A:ASP13 4.4 11.3 1.0 O A:HOH796 4.5 11.2 0.4 CB A:ASP115 4.5 10.0 1.0 C2' P:DT8 4.5 16.6 0.6 O P:HOH203 4.5 11.5 0.6 C A:ASP115 4.6 12.5 1.0 C5' P:DT8 4.6 19.4 0.4 O A:ASP115 4.6 11.7 1.0 C5' P:DT8 4.7 19.5 0.6 O5 A:DPO508 4.7 11.8 0.4 N A:GLU116 4.8 7.5 1.0 CB A:SER113 4.8 14.2 1.0 O3A A:DTP507 4.8 10.8 0.6 O A:HOH627 4.9 23.7 1.0 O1G A:DTP507 4.9 11.9 0.6 CA A:ASP115 5.0 10.9 1.0 O1 A:DPO508 5.0 10.9 0.4

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S


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 10 Mm MN2+ For 120S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:12.7 occ:0.75 CA A:CA502 0.1 12.7 0.2 O5 A:DPO508 2.1 11.8 0.4 O1B A:DTP507 2.2 10.6 0.6 OD2 A:ASP115 2.2 10.8 1.0 O1A A:DTP507 2.3 14.4 0.6 OD1 A:ASP13 2.3 12.3 1.0 O1 A:DPO508 2.3 10.9 0.4 O A:MET14 2.3 11.7 1.0 O1G A:DTP507 2.3 11.9 0.6 OP1 P:DA9 2.5 14.3 0.4 CG A:ASP13 3.1 13.6 1.0 PB A:DTP507 3.2 12.0 0.6 OD2 A:ASP13 3.3 14.8 1.0 CG A:ASP115 3.3 12.1 1.0 P1 A:DPO508 3.3 11.8 0.4 P2 A:DPO508 3.3 11.7 0.4 PA A:DTP507 3.4 10.2 0.6 C A:MET14 3.4 9.6 1.0 O3A A:DTP507 3.5 10.8 0.6 PG A:DTP507 3.5 11.3 0.6 MN A:MN501 3.6 12.2 1.0 O2 A:DPO508 3.7 11.3 0.4 O4 A:DPO508 3.7 11.1 0.4 O3B A:DTP507 3.7 11.0 0.6 OD1 A:ASP115 3.8 12.9 1.0 P P:DA9 3.9 11.3 0.4 O7 A:DPO508 3.9 11.4 0.4 O2G A:DTP507 4.0 10.0 0.6 N A:MET14 4.0 8.7 1.0 C5' A:DTP507 4.0 12.4 0.6 NZ A:LYS231 4.1 12.6 0.5 O A:HOH796 4.1 13.2 0.6 O A:HOH796 4.1 11.2 0.4 O5' A:DTP507 4.2 9.9 0.6 CA A:MET14 4.2 10.7 1.0 C5' P:DA9 4.2 11.7 0.4 C A:ASP13 4.3 9.2 1.0 O A:HOH780 4.4 14.0 1.0 O5' P:DA9 4.4 11.5 0.4 CB A:ASP13 4.4 11.3 1.0 N A:ASP15 4.4 8.4 1.0 N A:CYS16 4.5 9.0 1.0 O2B A:DTP507 4.5 10.8 0.6 O6 A:DPO508 4.5 11.4 0.4 CA A:ASP15 4.6 7.7 1.0 CB A:ASP115 4.6 10.0 1.0 O2A A:DTP507 4.6 13.4 0.6 O3 A:DPO508 4.7 10.8 0.4 OP2 P:DA9 4.7 14.9 0.4 O A:ASP13 4.7 9.6 1.0 CE A:LYS231 4.7 14.8 0.5 O3G A:DTP507 4.8 11.3 0.6 C A:ASP15 4.8 10.3 1.0 N A:PHE17 4.8 11.5 1.0 CB A:MET14 4.8 13.9 1.0 CA A:ASP13 4.9 9.3 1.0 O3' P:DT8 4.9 12.4 0.4 CB A:PHE17 4.9 9.2 1.0 MN P:MN101 5.0 16.5 0.4

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 120S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:16.5 occ:0.40 O2A A:DTP507 1.7 13.4 0.6 OP2 P:DA9 2.1 14.9 0.4 O P:HOH222 2.1 17.2 0.4 O3A A:DTP507 2.2 10.8 0.6 O2 A:DPO508 2.3 11.3 0.4 O A:HOH650 2.3 27.0 1.0 O A:HOH796 2.4 11.2 0.4 PA A:DTP507 2.4 10.2 0.6 O A:HOH618 2.7 15.9 1.0 NH1 A:ARG61 2.8 21.4 0.6 P P:DA9 3.2 11.3 0.4 O1A A:DTP507 3.5 14.4 0.6 O5' A:DTP507 3.6 9.9 0.6 PB A:DTP507 3.7 12.0 0.6 P1 A:DPO508 3.7 11.8 0.4 OP1 P:DA9 3.7 14.3 0.4 O6 A:DPO508 3.7 11.4 0.4 CZ A:ARG61 3.7 17.1 0.6 NH2 A:ARG61 3.8 13.8 0.6 O A:HOH796 3.8 13.2 0.6 O5 A:DPO508 3.9 11.8 0.4 O5' P:DA9 3.9 11.5 0.4 O3B A:DTP507 4.0 11.0 0.6 O A:HOH621 4.0 26.9 0.5 O1G A:DTP507 4.1 11.9 0.6 O4 A:DPO508 4.1 11.1 0.4 P2 A:DPO508 4.1 11.7 0.4 O A:HOH705 4.1 13.8 0.4 O A:HOH914 4.2 21.5 1.0 O3G A:DTP507 4.2 11.3 0.6 O A:HOH780 4.3 14.0 1.0 PG A:DTP507 4.3 11.3 0.6 O2B A:DTP507 4.4 10.8 0.6 O3' P:DT8 4.4 12.4 0.4 O P:HOH213 4.5 18.8 1.0 O1 A:DPO508 4.6 10.9 0.4 O3 A:DPO508 4.6 10.8 0.4 C3' P:DT8 4.6 17.1 0.4 C2' P:DT8 4.7 16.6 0.6 O1B A:DTP507 4.7 10.6 0.6 O A:HOH791 4.8 24.8 1.0 C3' P:DT8 4.8 17.3 0.6 C5' A:DTP507 4.9 12.4 0.6 C8 A:DTP507 4.9 15.2 0.6 CA A:CA502 4.9 12.7 0.2 C2' P:DT8 5.0 18.3 0.4 MN A:MN503 5.0 12.7 0.8 NE A:ARG61 5.0 17.5 0.6

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