Manganese in PDB 5l9x: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 60S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 60S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 60S, PDB code: 5l9x 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)	19.94 / 1.90
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.290, 98.290, 82.050, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 21.4

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 60S 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 60S (pdb code 5l9x). 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 60S, PDB code: 5l9x:
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 60S


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 60S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:13.9 occ:0.90 OP1 P:DA9 2.1 15.3 0.2 OD1 A:ASP115 2.1 10.5 1.0 OE2 A:GLU116 2.2 15.0 1.0 OD2 A:ASP13 2.2 17.8 1.0 O P:HOH214 2.2 13.3 1.0 O1A A:DTP507 2.3 15.5 0.8 O3' P:DT8 2.4 13.8 0.8 O3' P:DT8 2.4 16.3 0.2 P P:DA9 2.8 18.2 0.2 CG A:ASP115 3.1 13.8 1.0 CD A:GLU116 3.2 18.4 1.0 CG A:ASP13 3.2 17.0 1.0 C3' P:DT8 3.3 22.8 0.8 OD2 A:ASP115 3.3 13.6 1.0 C3' P:DT8 3.4 21.5 0.2 MN A:MN503 3.5 16.7 0.3 CA A:CA502 3.5 16.7 0.7 PA A:DTP507 3.6 15.6 0.8 OD1 A:ASP13 3.7 13.5 1.0 OG A:SER113 3.8 18.0 1.0 OE1 A:GLU116 3.8 18.7 1.0 OP2 P:DA9 3.9 17.3 0.2 O5' P:DA9 3.9 16.8 0.2 C4' P:DT8 4.0 20.7 0.2 O5' A:DTP507 4.0 16.8 0.8 O2A A:DTP507 4.0 16.4 0.8 C4' P:DT8 4.1 20.1 0.8 CB A:GLU116 4.1 15.5 1.0 CG A:GLU116 4.1 17.6 1.0 C5' A:DTP507 4.2 16.1 0.8 C5' P:DA9 4.2 16.1 0.2 NZ A:LYS224 4.3 14.6 0.6 O A:HOH715 4.3 23.1 1.0 C2' P:DT8 4.4 20.4 0.2 C5' P:DT8 4.5 24.5 0.2 CB A:ASP13 4.5 13.4 1.0 O P:HOH204 4.5 13.7 0.7 CB A:ASP115 4.5 11.2 1.0 C A:ASP115 4.6 16.2 1.0 O A:ASP115 4.6 13.3 1.0 C2' P:DT8 4.6 21.4 0.8 C5' P:DT8 4.7 24.2 0.8 N A:GLU116 4.8 10.2 1.0 O5 A:DPO508 4.8 14.7 0.2 O3A A:DTP507 4.9 17.2 0.8 O1G A:DTP507 4.9 14.2 0.8 CB A:SER113 5.0 16.9 1.0 CA A:ASP115 5.0 12.9 1.0

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 60S


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 60S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:16.7 occ:0.35 CA A:CA502 0.0 16.7 0.7 O5 A:DPO508 2.2 14.7 0.2 O1G A:DTP507 2.3 14.2 0.8 O1A A:DTP507 2.3 15.5 0.8 O1B A:DTP507 2.3 14.1 0.8 OD1 A:ASP13 2.3 13.5 1.0 OD2 A:ASP115 2.3 13.6 1.0 O1 A:DPO508 2.4 14.5 0.2 O A:MET14 2.4 12.1 1.0 OP1 P:DA9 2.5 15.3 0.2 CG A:ASP13 3.1 17.0 1.0 OD2 A:ASP13 3.2 17.8 1.0 PB A:DTP507 3.3 16.1 0.8 CG A:ASP115 3.4 13.8 1.0 P2 A:DPO508 3.5 17.8 0.2 PG A:DTP507 3.5 18.0 0.8 P1 A:DPO508 3.5 16.1 0.2 PA A:DTP507 3.5 15.6 0.8 C A:MET14 3.5 13.3 1.0 MN A:MN501 3.5 13.9 0.9 O3A A:DTP507 3.6 17.2 0.8 O3B A:DTP507 3.8 14.6 0.8 O2 A:DPO508 3.8 17.1 0.2 OD1 A:ASP115 3.8 10.5 1.0 O A:HOH715 3.9 23.1 1.0 O4 A:DPO508 3.9 14.7 0.2 P P:DA9 4.0 18.2 0.2 O7 A:DPO508 4.0 13.2 0.2 O2G A:DTP507 4.0 12.8 0.8 N A:MET14 4.0 11.5 1.0 NZ A:LYS231 4.0 16.5 0.5 C5' A:DTP507 4.1 16.1 0.8 C5' P:DA9 4.2 16.1 0.2 C A:ASP13 4.3 9.8 1.0 O5' A:DTP507 4.3 16.8 0.8 O P:HOH214 4.3 13.3 1.0 CA A:MET14 4.3 14.4 1.0 N A:CYS16 4.4 12.4 1.0 CB A:ASP13 4.4 13.4 1.0 O5' P:DA9 4.4 16.8 0.2 N A:ASP15 4.5 10.6 1.0 CA A:ASP15 4.6 12.3 1.0 O A:HOH765 4.6 14.3 0.5 O2B A:DTP507 4.6 15.5 0.8 O6 A:DPO508 4.6 16.5 0.2 CB A:ASP115 4.7 11.2 1.0 C A:ASP15 4.7 16.4 1.0 O A:ASP13 4.7 11.6 1.0 O3G A:DTP507 4.7 16.7 0.8 O2A A:DTP507 4.8 16.4 0.8 N A:PHE17 4.8 9.4 1.0 O3 A:DPO508 4.8 15.6 0.2 CB A:MET14 4.8 12.0 1.0 OP2 P:DA9 4.8 17.3 0.2 CA A:ASP13 4.9 15.1 1.0 O3' P:DT8 4.9 16.3 0.2 CB A:PHE17 5.0 9.7 1.0

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 60S


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 60S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:18.6 occ:0.20 O2A A:DTP507 1.8 16.4 0.8 OP2 P:DA9 2.0 17.3 0.2 O A:HOH606 2.2 22.7 0.1 O3A A:DTP507 2.3 17.2 0.8 O2 A:DPO508 2.3 17.1 0.2 PA A:DTP507 2.5 15.6 0.8 NH1 A:ARG61 2.6 23.8 0.8 O A:HOH642 2.8 18.0 1.0 O P:HOH217 2.8 16.0 0.1 O A:HOH899 3.1 34.6 1.0 P P:DA9 3.2 18.2 0.2 O A:HOH715 3.4 23.1 1.0 O1A A:DTP507 3.5 15.5 0.8 CZ A:ARG61 3.6 28.5 0.8 OP1 P:DA9 3.6 15.3 0.2 NH2 A:ARG61 3.7 20.2 0.8 P1 A:DPO508 3.8 16.1 0.2 O5' A:DTP507 3.8 16.8 0.8 PB A:DTP507 3.8 16.1 0.8 O5' P:DA9 3.9 16.8 0.2 NH2 A:ARG61 3.9 27.7 0.2 O A:HOH771 4.0 27.6 0.6 O5 A:DPO508 4.0 14.7 0.2 O6 A:DPO508 4.0 16.5 0.2 O3B A:DTP507 4.1 14.6 0.8 O A:HOH701 4.1 18.9 0.1 O1G A:DTP507 4.1 14.2 0.8 O4 A:DPO508 4.2 14.7 0.2 O3G A:DTP507 4.3 16.7 0.8 O A:HOH921 4.3 25.5 1.0 P2 A:DPO508 4.3 17.8 0.2 O P:HOH214 4.4 13.3 1.0 NE A:ARG61 4.4 25.5 0.2 PG A:DTP507 4.4 18.0 0.8 O P:HOH215 4.4 27.9 1.0 O3' P:DT8 4.5 16.3 0.2 CZ A:ARG61 4.6 25.3 0.2 C2' P:DT8 4.6 21.4 0.8 O2B A:DTP507 4.6 15.5 0.8 O1 A:DPO508 4.6 14.5 0.2 C3' P:DT8 4.7 21.5 0.2 O3 A:DPO508 4.7 15.6 0.2 C3' P:DT8 4.7 22.8 0.8 O P:HOH220 4.7 32.1 1.0 NE A:ARG61 4.8 28.2 0.8 O1B A:DTP507 4.8 14.1 0.8 C8 A:DTP507 5.0 20.2 0.8 O3' P:DT8 5.0 13.8 0.8 C5' A:DTP507 5.0 16.1 0.8

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