Manganese in PDB 8ild: The Crystal Structure of Native Dgtp:Dnapre-I:Pol X Substrate Ternary Complex

All present enzymatic activity of The Crystal Structure of Native Dgtp:Dnapre-I:Pol X Substrate Ternary Complex:
2.7.7.7;

The structure of The Crystal Structure of Native Dgtp:Dnapre-I:Pol X Substrate Ternary Complex, PDB code: 8ild was solved by T.Qin, Y.Q.Chen, J.H.Gan, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.52 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.706, 75.441, 108.45, 90, 90, 90
R / Rfree (%)	21.2 / 26.3

The binding sites of Manganese atom in the The Crystal Structure of Native Dgtp:Dnapre-I:Pol X Substrate Ternary Complex (pdb code 8ild). 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 Native Dgtp:Dnapre-I:Pol X Substrate Ternary Complex, PDB code: 8ild:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The Crystal Structure of Native Dgtp:Dnapre-I: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 Native Dgtp:Dnapre-I:Pol X Substrate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:51.9 occ:1.00 OD1 A:ASP49 2.0 43.8 1.0 O1B A:GTP201 2.0 41.5 1.0 O1A A:GTP201 2.0 43.1 1.0 O3G A:GTP201 2.0 41.6 1.0 OD2 A:ASP51 2.0 40.3 1.0 O A:HOH302 2.0 44.9 1.0 CG A:ASP51 3.0 36.9 1.0 CG A:ASP49 3.1 43.0 1.0 PB A:GTP201 3.2 36.5 1.0 PA A:GTP201 3.3 37.9 1.0 PG A:GTP201 3.3 36.3 1.0 OD1 A:ASP51 3.3 40.8 1.0 OD2 A:ASP49 3.5 52.4 1.0 O3A A:GTP201 3.5 37.0 1.0 O3B A:GTP201 3.6 35.6 1.0 O A:ASP49 3.8 36.2 1.0 OG A:SER39 4.1 31.0 1.0 O2G A:GTP201 4.1 34.9 1.0 C5' A:GTP201 4.1 37.4 1.0 O5' A:GTP201 4.2 37.5 1.0 C A:ASP49 4.3 38.7 1.0 CB A:ASP49 4.3 39.2 1.0 CB A:ASP51 4.4 34.7 1.0 O2A A:GTP201 4.4 39.4 1.0 O1G A:GTP201 4.4 39.4 1.0 N A:ASP49 4.5 37.2 1.0 N A:SER39 4.5 33.4 1.0 OD2 A:ASP100 4.5 36.1 1.0 O A:HOH312 4.5 43.1 1.0 O2B A:GTP201 4.6 35.2 1.0 CA A:ASP49 4.6 37.8 1.0 CA A:GLY38 4.8 33.6 1.0 N A:ASP51 4.9 31.3 1.0

Manganese binding site 2 out of 2 in the The Crystal Structure of Native Dgtp:Dnapre-I: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 Native Dgtp:Dnapre-I:Pol X Substrate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:56.7 occ:1.00 O1B B:GTP201 2.0 42.7 1.0 O1A B:GTP201 2.0 52.9 1.0 O B:HOH301 2.0 55.3 1.0 O3G B:GTP201 2.0 44.2 1.0 OD1 B:ASP49 2.0 46.7 1.0 OD2 B:ASP51 2.1 42.9 1.0 CG B:ASP51 3.0 44.8 1.0 CG B:ASP49 3.1 49.3 1.0 OD1 B:ASP51 3.3 46.7 1.0 PB B:GTP201 3.3 43.3 1.0 PA B:GTP201 3.4 40.8 1.0 OD2 B:ASP49 3.5 53.5 1.0 PG B:GTP201 3.5 46.5 1.0 O3A B:GTP201 3.7 39.6 1.0 O3B B:GTP201 3.8 42.8 1.0 O B:HOH314 3.9 61.7 1.0 O B:ASP49 3.9 48.9 1.0 O B:HOH317 4.0 60.4 1.0 C5' B:GTP201 4.1 39.9 1.0 O2G B:GTP201 4.2 45.8 1.0 O5' B:GTP201 4.2 40.6 1.0 OG B:SER39 4.2 44.7 1.0 C B:ASP49 4.4 45.8 1.0 CB B:ASP49 4.4 47.3 1.0 CB B:ASP51 4.4 45.3 1.0 N B:ASP49 4.5 43.1 1.0 OD2 B:ASP100 4.5 49.5 1.0 O2A B:GTP201 4.5 41.4 1.0 O1G B:GTP201 4.6 48.8 1.0 O2B B:GTP201 4.6 44.4 1.0 N B:SER39 4.6 42.6 1.0 CA B:ASP49 4.7 45.9 1.0 CA B:GLY38 4.9 41.9 1.0 N B:ASP51 5.0 43.8 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