Manganese in PDB 5kfl: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 600S, PDB code: 5kfl 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)	19.92 / 1.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.450, 98.450, 81.960, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 20.8

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 600S (pdb code 5kfl). 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 600S, PDB code: 5kfl:
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 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 Ternary Complex: Reaction with 10 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:16.4 occ:1.00 OD2 A:ASP13 2.1 16.1 1.0 OD1 A:ASP115 2.1 15.8 1.0 OP1 P:DA9 2.1 17.4 0.6 OE2 A:GLU116 2.2 18.7 1.0 O3' P:DT8 2.2 18.4 0.4 O P:HOH214 2.3 16.7 1.0 O1A A:DTP506 2.4 17.9 0.4 O3' P:DT8 2.5 13.5 0.6 P P:DA9 2.8 16.8 0.6 CG A:ASP115 3.1 17.8 1.0 CG A:ASP13 3.1 15.2 1.0 CD A:GLU116 3.1 20.9 1.0 OD2 A:ASP115 3.4 13.5 1.0 OD1 A:ASP13 3.5 15.4 1.0 C3' P:DT8 3.5 23.0 0.4 MN A:MN502 3.6 15.5 1.0 PA A:DTP506 3.6 14.3 0.4 C3' P:DT8 3.7 23.1 0.6 OE1 A:GLU116 3.8 23.2 1.0 OG A:SER113 3.8 18.8 1.0 OP2 P:DA9 3.9 18.9 0.6 C4' P:DT8 4.0 24.7 0.4 O2A A:DTP506 4.0 16.9 0.4 C4' P:DT8 4.0 24.7 0.6 O5' P:DA9 4.0 16.3 0.6 CB A:GLU116 4.0 15.4 1.0 CG A:GLU116 4.1 15.7 1.0 C5' P:DT8 4.1 26.4 0.4 C5' P:DT8 4.2 26.2 0.6 O5' A:DTP506 4.2 15.4 0.4 O A:HOH651 4.2 25.4 1.0 NZ A:LYS224 4.2 21.9 0.8 C5' P:DA9 4.3 15.5 0.6 C5' A:DTP506 4.3 17.0 0.4 CB A:ASP13 4.4 14.3 1.0 O P:HOH206 4.4 21.8 0.5 CB A:ASP115 4.5 14.7 1.0 O A:ASP115 4.5 15.1 1.0 C A:ASP115 4.6 16.0 1.0 O5 A:DPO507 4.6 13.0 0.6 N A:GLU116 4.8 12.8 1.0 C2' P:DT8 4.8 19.9 0.6 O3A A:DTP506 4.8 15.8 0.4 O5' P:DT8 4.9 28.1 0.4 CB A:SER113 4.9 18.1 1.0 O1 A:DPO507 5.0 14.4 0.6 O1G A:DTP506 5.0 13.9 0.4 CA A:ASP115 5.0 15.6 1.0

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 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 Ternary Complex: Reaction with 10 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:15.5 occ:1.00 O5 A:DPO507 2.1 13.0 0.6 O1 A:DPO507 2.1 14.4 0.6 OD2 A:ASP115 2.2 13.5 1.0 O1B A:DTP506 2.2 14.2 0.4 OD1 A:ASP13 2.2 15.4 1.0 O1A A:DTP506 2.2 17.9 0.4 O1G A:DTP506 2.3 13.9 0.4 O A:MET14 2.3 14.6 1.0 OP1 P:DA9 2.4 17.4 0.6 PB A:DTP506 3.1 16.4 0.4 CG A:ASP13 3.2 15.2 1.0 P1 A:DPO507 3.2 15.8 0.6 CG A:ASP115 3.2 17.8 1.0 P2 A:DPO507 3.3 16.6 0.6 O3A A:DTP506 3.3 15.8 0.4 PA A:DTP506 3.3 14.3 0.4 PG A:DTP506 3.4 12.9 0.4 C A:MET14 3.4 13.9 1.0 OD2 A:ASP13 3.5 16.1 1.0 MN A:MN501 3.6 16.4 1.0 O3B A:DTP506 3.6 14.5 0.4 O4 A:DPO507 3.6 14.4 0.6 O2 A:DPO507 3.7 14.8 0.6 OD1 A:ASP115 3.7 15.8 1.0 P P:DA9 3.8 16.8 0.6 O7 A:DPO507 3.8 15.8 0.6 NZ A:LYS231 3.9 17.3 1.0 O A:HOH651 3.9 25.4 1.0 C5' A:DTP506 3.9 17.0 0.4 N A:MET14 4.0 12.8 1.0 O5' A:DTP506 4.1 15.4 0.4 O2G A:DTP506 4.1 15.6 0.4 CA A:MET14 4.2 14.9 1.0 C5' P:DA9 4.2 15.5 0.6 O5' P:DA9 4.3 16.3 0.6 C A:ASP13 4.3 12.7 1.0 O P:HOH214 4.4 16.7 1.0 N A:CYS16 4.4 13.2 1.0 N A:ASP15 4.4 13.1 1.0 O2B A:DTP506 4.4 14.7 0.4 CB A:ASP13 4.4 14.3 1.0 O6 A:DPO507 4.5 15.1 0.6 CB A:ASP115 4.5 14.7 1.0 O3 A:DPO507 4.5 15.1 0.6 CA A:ASP15 4.5 14.3 1.0 CE A:LYS231 4.6 25.3 1.0 O2A A:DTP506 4.6 16.9 0.4 O3G A:DTP506 4.6 17.5 0.4 CB A:MET14 4.7 15.8 1.0 C A:ASP15 4.7 15.4 1.0 OP2 P:DA9 4.7 18.9 0.6 N A:PHE17 4.7 13.9 1.0 O A:ASP13 4.8 14.9 1.0 O3' P:DT8 4.8 13.5 0.6 MN P:MN101 4.8 19.8 0.6 CB A:PHE17 4.9 13.1 1.0 CA A:ASP13 4.9 14.4 1.0 O A:ASP115 5.0 15.1 1.0 O3' P:DT8 5.0 18.4 0.4

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 600S


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 600S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:19.8 occ:0.60 O2A A:DTP506 1.8 16.9 0.4 O A:HOH874 2.1 18.1 0.6 O3A A:DTP506 2.1 15.8 0.4 OP2 P:DA9 2.2 18.9 0.6 O A:HOH834 2.2 30.1 1.0 O2 A:DPO507 2.2 14.8 0.6 PA A:DTP506 2.4 14.3 0.4 O A:HOH651 2.5 25.4 1.0 O A:HOH623 2.6 23.5 1.0 NH1 A:ARG61 2.8 24.7 0.5 P P:DA9 3.2 16.8 0.6 O1A A:DTP506 3.3 17.9 0.4 OP1 P:DA9 3.6 17.4 0.6 O5' A:DTP506 3.6 15.4 0.4 PB A:DTP506 3.6 16.4 0.4 P1 A:DPO507 3.6 15.8 0.6 O6 A:DPO507 3.7 15.1 0.6 CZ A:ARG61 3.7 23.9 0.5 NH2 A:ARG61 3.8 20.4 0.5 O5 A:DPO507 3.8 13.0 0.6 O5' P:DA9 3.9 16.3 0.6 O A:HOH767 4.0 19.7 0.6 O4 A:DPO507 4.0 14.4 0.6 P2 A:DPO507 4.1 16.6 0.6 O A:HOH748 4.1 32.2 0.5 O3B A:DTP506 4.1 14.5 0.4 O A:HOH909 4.2 25.4 1.0 O P:HOH214 4.2 16.7 1.0 O3G A:DTP506 4.2 17.5 0.4 O A:HOH948 4.2 42.6 1.0 O1G A:DTP506 4.2 13.9 0.4 O P:HOH209 4.3 34.0 1.0 O2B A:DTP506 4.3 14.7 0.4 O P:HOH211 4.4 30.4 1.0 PG A:DTP506 4.4 12.9 0.4 O1 A:DPO507 4.5 14.4 0.6 O3' P:DT8 4.6 13.5 0.6 O3 A:DPO507 4.6 15.1 0.6 O1B A:DTP506 4.7 14.2 0.4 MN A:MN502 4.8 15.5 1.0 C5' A:DTP506 4.9 17.0 0.4 C3' P:DT8 4.9 23.1 0.6 C3' P:DT8 4.9 23.0 0.4 C8 A:DTP506 5.0 19.7 0.4 NE A:ARG61 5.0 24.6 0.5

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