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

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

The structure of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 10 Mm MN2+ For 600S, PDB code: 5kfq 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 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.620, 98.620, 81.840, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.3

The structure of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 10 Mm MN2+ For 600S 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 with Sp-Datp-Alpha-S: Reaction with 10 Mm MN2+ For 600S (pdb code 5kfq). 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 with Sp-Datp-Alpha-S: Reaction with 10 Mm MN2+ For 600S, PDB code: 5kfq:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: 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 with Sp-Datp-Alpha-S: Reaction with 10 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:19.7 occ:0.90 OP1 P:AS9 2.0 21.0 0.1 OD2 A:ASP13 2.1 19.0 0.8 O2A A:STP507 2.2 21.3 0.8 OE2 A:GLU116 2.2 25.0 1.0 OD1 A:ASP115 2.2 19.3 1.0 O3' P:DT8 2.2 24.3 0.8 O P:HOH110 2.3 24.3 1.0 O3' P:DT8 2.4 24.3 0.1 OD1 A:ASP13 2.5 23.0 0.2 P P:AS9 2.7 19.5 0.1 CG A:ASP13 3.2 19.5 0.8 CD A:GLU116 3.2 26.8 1.0 CG A:ASP115 3.2 20.2 1.0 CG A:ASP13 3.2 19.7 0.2 C3' P:DT8 3.2 27.0 0.8 OD2 A:ASP13 3.3 21.6 0.2 PA A:STP507 3.4 19.4 0.8 OD2 A:ASP115 3.5 19.1 1.0 OD1 A:ASP13 3.6 18.0 0.8 MN A:MN503 3.6 16.6 0.8 CA A:CA502 3.6 16.8 0.1 C3' P:DT8 3.7 26.9 0.1 OG A:SER113 3.8 22.1 1.0 OE1 A:GLU116 3.9 27.4 1.0 O5' P:AS9 3.9 20.6 0.1 O5' A:STP507 3.9 19.9 0.8 C4' P:DT8 4.0 28.0 0.1 C4' P:DT8 4.0 28.2 0.8 S2P P:AS9 4.1 26.4 0.1 CG A:GLU116 4.1 19.6 1.0 S1A A:STP507 4.1 25.5 0.8 C5' A:STP507 4.1 21.2 0.8 CB A:GLU116 4.1 20.5 1.0 O A:HOH636 4.2 25.8 1.0 NZ A:LYS224 4.2 27.0 1.0 C5' P:DT8 4.2 32.4 0.1 C5' P:AS9 4.3 20.9 0.1 O P:HOH102 4.3 24.8 0.8 CB A:ASP13 4.5 15.9 0.8 C5' P:DT8 4.5 33.6 0.8 C2' P:DT8 4.5 28.6 0.8 CB A:ASP115 4.6 17.1 1.0 O5 A:DPO508 4.6 21.1 0.1 CB A:ASP13 4.6 16.5 0.2 O3A A:STP507 4.7 21.4 0.8 O1G A:STP507 4.7 21.2 0.8 C A:ASP115 4.7 17.8 1.0 O A:ASP115 4.7 17.0 1.0 C2' P:DT8 4.8 25.9 0.1 O2 A:DPO508 4.8 21.7 0.1 O1 A:DPO508 4.9 17.9 0.1 CB A:SER113 4.9 20.1 1.0 N A:GLU116 4.9 15.4 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: 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 with Sp-Datp-Alpha-S: Reaction with 10 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:16.6 occ:0.85 CA A:CA502 0.0 16.8 0.1 OD2 A:ASP115 2.1 19.1 1.0 OD1 A:ASP13 2.1 18.0 0.8 O1 A:DPO508 2.1 17.9 0.1 O1B A:STP507 2.2 16.6 0.8 O5 A:DPO508 2.2 21.1 0.1 O A:MET14 2.2 17.8 1.0 O1G A:STP507 2.2 21.2 0.8 O2A A:STP507 2.4 21.3 0.8 OP1 P:AS9 2.6 21.0 0.1 CG A:ASP13 3.1 19.5 0.8 OD1 A:ASP13 3.1 23.0 0.2 PB A:STP507 3.1 19.6 0.8 CG A:ASP115 3.2 20.2 1.0 P1 A:DPO508 3.3 20.0 0.1 OD2 A:ASP13 3.3 21.6 0.2 C A:MET14 3.3 16.4 1.0 CG A:ASP13 3.3 19.7 0.2 P2 A:DPO508 3.4 22.0 0.1 PG A:STP507 3.4 20.6 0.8 PA A:STP507 3.4 19.4 0.8 O3A A:STP507 3.4 21.4 0.8 OD2 A:ASP13 3.5 19.0 0.8 OD1 A:ASP115 3.6 19.3 1.0 O2 A:DPO508 3.6 21.7 0.1 O3B A:STP507 3.6 20.1 0.8 MN A:MN501 3.6 19.7 0.9 O4 A:DPO508 3.7 20.6 0.1 NZ A:LYS231 3.9 21.1 1.0 N A:MET14 3.9 14.9 1.0 O7 A:DPO508 4.0 20.7 0.1 P P:AS9 4.0 19.5 0.1 C5' A:STP507 4.0 21.2 0.8 O A:HOH636 4.0 25.8 1.0 O3G A:STP507 4.1 20.7 0.8 CA A:MET14 4.1 14.2 1.0 C5' P:AS9 4.2 20.9 0.1 C A:ASP13 4.2 15.9 1.0 O5' A:STP507 4.2 19.9 0.8 N A:ASP15 4.3 15.0 1.0 N A:CYS16 4.3 17.2 1.0 CB A:ASP13 4.4 15.9 0.8 O5' P:AS9 4.4 20.6 0.1 CB A:ASP13 4.4 16.5 0.2 CB A:ASP115 4.4 17.1 1.0 CA A:ASP15 4.5 16.2 1.0 O2B A:STP507 4.5 19.4 0.8 O3 A:DPO508 4.5 19.9 0.1 O P:HOH110 4.5 24.3 1.0 C A:ASP15 4.6 17.7 1.0 CB A:MET14 4.6 17.8 1.0 O6 A:DPO508 4.6 23.4 0.1 O A:ASP13 4.6 17.0 1.0 O2G A:STP507 4.6 23.6 0.8 N A:PHE17 4.7 16.1 1.0 CA A:ASP13 4.8 16.4 0.2 CA A:ASP13 4.8 16.4 0.8 CE A:LYS231 4.8 30.0 1.0 CB A:PHE17 4.9 16.5 1.0 O A:ASP115 4.9 17.0 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