Manganese in PDB 8ilg: The Crystal Structure of Dg-Dna:Pol X Product Binary Complex

All present enzymatic activity of The Crystal Structure of Dg-Dna:Pol X Product Binary Complex:
2.7.7.7;

The structure of The Crystal Structure of Dg-Dna:Pol X Product Binary Complex, PDB code: 8ilg was solved by T.Qin, J.H.Gan, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.86 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.033, 81.422, 92.594, 90, 90, 90
R / Rfree (%)	22.2 / 25.5

The binding sites of Manganese atom in the The Crystal Structure of Dg-Dna:Pol X Product Binary Complex (pdb code 8ilg). 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 Dg-Dna:Pol X Product Binary Complex, PDB code: 8ilg:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The Crystal Structure of Dg-Dna:Pol X Product Binary 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 Dg-Dna:Pol X Product Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:21.4 occ:1.00 OP1 D:DG8 2.1 28.2 1.0 OD2 A:ASP51 2.1 21.3 1.0 OD1 A:ASP49 2.2 22.0 1.0 O1 A:FMT202 2.2 19.2 1.0 O A:HOH351 2.2 22.2 1.0 O A:HOH328 2.3 26.0 1.0 C A:FMT202 2.9 21.7 1.0 CG A:ASP51 3.0 20.6 1.0 CG A:ASP49 3.1 27.6 1.0 OD1 A:ASP51 3.3 21.9 1.0 OD2 A:ASP49 3.4 30.1 1.0 P D:DG8 3.5 24.3 1.0 O5' D:DG8 4.1 18.9 1.0 O A:HOH415 4.1 19.8 1.0 O2 A:FMT202 4.1 26.7 1.0 O A:HOH357 4.2 21.2 1.0 C5' D:DG8 4.2 15.9 1.0 OP2 D:DG8 4.2 21.3 1.0 O D:HOH119 4.3 41.2 1.0 OG A:SER39 4.3 23.1 1.0 O A:ASP49 4.3 19.5 1.0 OD2 A:ASP100 4.3 34.0 1.0 N A:SER39 4.4 15.5 1.0 CB A:ASP51 4.4 19.9 1.0 CB A:ASP49 4.5 23.3 1.0 O3' D:DC7 4.6 19.1 1.0 C A:ASP49 4.7 21.0 1.0 O A:HOH450 4.7 37.1 1.0 CA A:GLY38 4.7 14.6 1.0 CB A:SER39 4.9 20.7 1.0

Manganese binding site 2 out of 2 in the The Crystal Structure of Dg-Dna:Pol X Product Binary 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 Dg-Dna:Pol X Product Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:22.1 occ:1.00 OD2 B:ASP51 2.0 19.4 1.0 O B:HOH337 2.1 20.0 1.0 OP1 C:DG8 2.2 25.8 1.0 O1 B:FMT202 2.2 20.2 1.0 OD1 B:ASP49 2.3 24.8 1.0 O B:HOH328 2.4 24.7 1.0 CG B:ASP51 3.0 21.8 1.0 CG B:ASP49 3.1 27.1 1.0 C B:FMT202 3.2 25.9 1.0 OD2 B:ASP49 3.2 30.6 1.0 OD1 B:ASP51 3.2 25.0 1.0 P C:DG8 3.6 22.0 1.0 O5' C:DG8 4.1 21.2 1.0 O B:HOH448 4.2 38.0 1.0 O B:HOH364 4.2 17.2 1.0 C5' C:DG8 4.2 19.7 1.0 N B:SER39 4.2 17.6 1.0 O B:HOH342 4.2 25.4 1.0 OG B:SER39 4.3 23.4 1.0 O2 B:FMT202 4.3 25.8 1.0 O B:ASP49 4.3 21.8 1.0 CB B:ASP51 4.3 21.2 1.0 OP2 C:DG8 4.3 22.5 1.0 OD2 B:ASP100 4.4 30.2 1.0 CB B:ASP49 4.5 24.9 1.0 CA B:GLY38 4.6 16.6 1.0 O3' C:DC7 4.7 20.7 1.0 C B:ASP49 4.7 22.5 1.0 CB B:SER39 4.9 20.5 1.0 N B:ASP51 4.9 19.1 1.0 C B:GLY38 5.0 20.2 1.0 N B:ASP49 5.0 19.8 1.0 CA B:ASP49 5.0 21.3 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