Manganese in PDB 8ilf: The Crystal Structure of Dgtpalphase-Sp:Dnapre-II:Pol X Substrate Ternary Complex

All present enzymatic activity of The Crystal Structure of Dgtpalphase-Sp:Dnapre-II:Pol X Substrate Ternary Complex:
2.7.7.7;

The structure of The Crystal Structure of Dgtpalphase-Sp:Dnapre-II:Pol X Substrate Ternary Complex, PDB code: 8ilf was solved by T.Qin, Q.W.Zhao, J.H.Gan, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.666, 78.19, 101.304, 90, 90, 90
R / Rfree (%)	20.4 / 24.5

The binding sites of Manganese atom in the The Crystal Structure of Dgtpalphase-Sp:Dnapre-II:Pol X Substrate Ternary Complex (pdb code 8ilf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Crystal Structure of Dgtpalphase-Sp:Dnapre-II:Pol X Substrate Ternary Complex, PDB code: 8ilf:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The Crystal Structure of Dgtpalphase-Sp:Dnapre-II:Pol X Substrate Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Dgtpalphase-Sp:Dnapre-II:Pol X Substrate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:19.3 occ:1.00 O3G A:7Q6202 2.0 23.9 1.0 OD1 A:ASP49 2.1 23.0 1.0 O1A A:7Q6202 2.1 21.7 1.0 OD2 A:ASP51 2.1 20.3 1.0 O2B A:7Q6202 2.2 20.9 1.0 O A:HOH303 2.3 12.5 1.0 CG A:ASP49 3.1 23.6 1.0 CG A:ASP51 3.1 21.2 1.0 PB A:7Q6202 3.2 21.9 1.0 PA A:7Q6202 3.3 23.0 1.0 PG A:7Q6202 3.3 26.2 1.0 OD1 A:ASP51 3.4 22.6 1.0 OD2 A:ASP49 3.5 24.4 1.0 O3A A:7Q6202 3.5 22.9 1.0 O3B A:7Q6202 3.6 22.7 1.0 C5' A:7Q6202 3.9 21.2 1.0 OG A:SER39 4.0 21.0 1.0 O5' A:7Q6202 4.1 21.5 1.0 O A:ASP49 4.2 24.3 1.0 O1G A:7Q6202 4.2 25.3 1.0 N A:SER39 4.3 20.4 1.0 CB A:ASP49 4.4 23.4 1.0 O2G A:7Q6202 4.4 27.5 1.0 O A:HOH313 4.4 18.2 1.0 CB A:ASP51 4.5 20.3 1.0 C A:ASP49 4.5 23.1 1.0 O1B A:7Q6202 4.6 21.6 1.0 CA A:GLY38 4.7 19.1 1.0 N A:ASP49 4.7 23.8 1.0 CA A:ASP49 4.8 23.4 1.0 OD2 A:ASP100 4.9 24.3 1.0 CB A:SER39 4.9 20.5 1.0 N A:ASP51 5.0 20.2 1.0 SEA A:7Q6202 5.0 30.4 1.0

Manganese binding site 2 out of 2 in the The Crystal Structure of Dgtpalphase-Sp:Dnapre-II:Pol X Substrate Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Dgtpalphase-Sp:Dnapre-II:Pol X Substrate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:22.1 occ:1.00 O3G B:7Q6202 1.9 25.2 1.0 OD2 B:ASP51 2.1 22.8 1.0 OD1 B:ASP49 2.1 18.5 1.0 O2B B:7Q6202 2.2 23.4 1.0 O1A B:7Q6202 2.2 22.9 1.0 O B:HOH301 2.3 27.4 1.0 CG B:ASP51 3.1 24.8 1.0 CG B:ASP49 3.1 19.5 1.0 PB B:7Q6202 3.2 23.6 1.0 PG B:7Q6202 3.3 28.0 1.0 PA B:7Q6202 3.4 24.7 1.0 OD1 B:ASP51 3.6 23.6 1.0 O3A B:7Q6202 3.6 23.8 1.0 OD2 B:ASP49 3.6 19.9 1.0 O3B B:7Q6202 3.6 25.7 1.0 O2G B:7Q6202 4.0 26.8 1.0 C5' B:7Q6202 4.0 24.0 1.0 OG B:SER39 4.0 21.2 1.0 O B:HOH305 4.2 21.6 1.0 O B:ASP49 4.2 22.6 1.0 O5' B:7Q6202 4.2 24.4 1.0 O B:HOH313 4.3 25.2 1.0 OD2 B:ASP100 4.3 25.8 1.0 CB B:ASP49 4.4 20.5 1.0 O1G B:7Q6202 4.4 24.2 1.0 C B:ASP49 4.4 21.7 1.0 CB B:ASP51 4.4 23.5 1.0 N B:SER39 4.5 21.5 1.0 N B:ASP49 4.6 21.6 1.0 O1B B:7Q6202 4.6 23.6 1.0 CA B:ASP49 4.7 21.3 1.0 CA B:GLY38 4.8 19.3 1.0 N B:ASP51 4.9 22.0 1.0

T.Qin, B.Hu, Q.Zhao, Y.Wang, S.Wang, D.Luo, J.Lyu, Y.Chen, J.Gan, Z.Huang. Structural Insight Into Polymerase Mechanism Via A Chiral Center Generated with A Single Selenium Atom. Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
PubMed: 37958741
DOI: 10.3390/IJMS242115758