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

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

The structure of The Crystal Structure of Dgtpalphase-Rp:Dnapre-II:Pol X Substrate Ternary Complex, PDB code: 8ile 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)	29.74 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.481, 77.382, 111.353, 90, 90, 90
R / Rfree (%)	22 / 28.4

The binding sites of Manganese atom in the The Crystal Structure of Dgtpalphase-Rp:Dnapre-II:Pol X Substrate Ternary Complex (pdb code 8ile). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Crystal Structure of Dgtpalphase-Rp:Dnapre-II:Pol X Substrate Ternary Complex, PDB code: 8ile:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Crystal Structure of Dgtpalphase-Rp: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-Rp:Dnapre-II:Pol X Substrate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:76.6 occ:1.00 OD2 A:ASP51 2.0 29.5 1.0 O A:HOH301 2.0 36.1 1.0 O1G A:7Q6203 2.0 61.6 1.0 OD1 A:ASP49 2.1 29.5 1.0 O2B A:7Q6203 2.2 66.9 1.0 SEA A:7Q6203 2.5 107.2 1.0 CG A:ASP51 3.0 30.2 1.0 CG A:ASP49 3.2 31.7 1.0 PG A:7Q6203 3.3 73.1 1.0 PB A:7Q6203 3.3 81.3 1.0 OD1 A:ASP51 3.3 32.0 1.0 O3B A:7Q6203 3.6 70.4 1.0 OG A:SER39 3.6 28.8 1.0 OD2 A:ASP49 3.7 33.3 1.0 O A:ASP49 3.7 30.1 1.0 MN A:MN202 3.8 57.7 1.0 O3A A:7Q6203 3.8 69.8 1.0 PA A:7Q6203 3.8 85.7 1.0 O2G A:7Q6203 4.0 63.2 1.0 O A:HOH302 4.2 47.1 1.0 C5' A:7Q6203 4.2 87.1 1.0 N A:SER39 4.3 25.2 1.0 C A:ASP49 4.3 28.6 1.0 CB A:ASP51 4.3 28.9 1.0 N A:ASP49 4.4 27.0 1.0 O3G A:7Q6203 4.4 65.5 1.0 O5' A:7Q6203 4.5 66.4 1.0 CB A:ASP49 4.5 28.6 1.0 O1B A:7Q6203 4.6 69.9 1.0 CA A:ASP49 4.6 28.0 1.0 CB A:SER39 4.6 26.4 1.0 CA A:GLY38 4.7 23.9 1.0 N A:ASP51 4.8 28.1 1.0

Manganese binding site 2 out of 4 in the The Crystal Structure of Dgtpalphase-Rp: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-Rp:Dnapre-II:Pol X Substrate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:57.7 occ:1.00 OD2 A:ASP49 2.1 33.3 1.0 OD2 A:ASP100 2.1 16.6 1.0 SEA A:7Q6203 2.3 107.2 1.0 OD1 A:ASP51 2.4 32.0 1.0 CG A:ASP49 3.1 31.7 1.0 CG A:ASP100 3.3 21.6 1.0 OD1 A:ASP49 3.4 29.5 1.0 CG A:ASP51 3.5 30.2 1.0 C3' E:DA8 3.6 15.5 1.0 MN A:MN201 3.8 76.6 1.0 CB A:ASP100 3.8 21.8 1.0 OD2 A:ASP51 3.8 29.5 1.0 PA A:7Q6203 3.9 85.7 1.0 O5' A:7Q6203 4.2 66.4 1.0 C4' E:DA8 4.2 15.7 1.0 O1A A:7Q6203 4.2 34.9 1.0 C5' E:DA8 4.3 17.3 1.0 C5' A:7Q6203 4.3 87.1 1.0 OD1 A:ASP100 4.3 25.4 1.0 NE2 A:GLN98 4.4 25.9 1.0 CB A:ASP49 4.4 28.6 1.0 O1G A:7Q6203 4.7 61.6 1.0 CB A:ASP51 4.8 28.9 1.0 CZ A:PHE102 4.8 27.3 1.0 C2' E:DA8 4.9 15.2 1.0

Manganese binding site 3 out of 4 in the The Crystal Structure of Dgtpalphase-Rp: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 3 of The Crystal Structure of Dgtpalphase-Rp:Dnapre-II:Pol X Substrate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:68.1 occ:1.00 OD2 B:ASP51 1.9 34.7 1.0 O1G B:7Q6203 2.0 54.1 1.0 O B:HOH301 2.0 45.3 1.0 OD1 B:ASP49 2.1 33.1 1.0 O2B B:7Q6203 2.2 45.7 1.0 CG B:ASP51 2.8 36.0 1.0 SEA B:7Q6203 2.9 106.3 1.0 OD1 B:ASP51 3.1 43.3 1.0 PB B:7Q6203 3.1 66.9 1.0 CG B:ASP49 3.2 36.9 1.0 PG B:7Q6203 3.2 61.2 1.0 O3A B:7Q6203 3.4 63.5 1.0 O3B B:7Q6203 3.4 48.3 1.0 MN B:MN202 3.4 152.3 1.0 OD2 B:ASP49 3.5 46.1 1.0 PA B:7Q6203 3.8 88.0 1.0 O3G B:7Q6203 3.9 46.8 1.0 OG B:SER39 3.9 26.6 1.0 O B:ASP49 3.9 32.9 1.0 C5' B:7Q6203 4.1 83.6 1.0 CB B:ASP51 4.2 34.1 1.0 N B:SER39 4.3 25.2 1.0 O2G B:7Q6203 4.4 52.8 1.0 O5' B:7Q6203 4.4 62.4 1.0 O B:HOH302 4.4 37.9 1.0 C B:ASP49 4.4 32.1 1.0 CB B:ASP49 4.5 34.2 1.0 O1B B:7Q6203 4.5 38.2 1.0 N B:ASP49 4.6 33.0 1.0 CA B:GLY38 4.7 22.1 1.0 CA B:ASP49 4.8 31.1 1.0 N B:ASP51 4.8 32.7 1.0 CB B:SER39 4.8 26.4 1.0

Manganese binding site 4 out of 4 in the The Crystal Structure of Dgtpalphase-Rp: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 4 of The Crystal Structure of Dgtpalphase-Rp:Dnapre-II:Pol X Substrate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:152.3 occ:1.00 OD2 B:ASP100 2.0 24.1 1.0 OD2 B:ASP49 2.1 46.1 1.0 OD1 B:ASP51 2.1 43.3 1.0 SEA B:7Q6203 2.3 106.3 1.0 CG B:ASP49 3.0 36.9 1.0 CG B:ASP100 3.1 26.9 1.0 CG B:ASP51 3.2 36.0 1.0 OD1 B:ASP49 3.3 33.1 1.0 MN B:MN201 3.4 68.1 1.0 CB B:ASP100 3.6 25.7 1.0 OD2 B:ASP51 3.6 34.7 1.0 C5' G:DA10 3.7 25.2 1.0 C3' G:DA10 4.0 18.3 1.0 PA B:7Q6203 4.1 88.0 1.0 OD1 B:ASP100 4.2 26.0 1.0 C5' B:7Q6203 4.3 83.6 1.0 CB B:ASP49 4.3 34.2 1.0 C4' G:DA10 4.3 19.3 1.0 NE2 B:GLN98 4.4 39.4 1.0 CB B:ASP51 4.5 34.1 1.0 O1G B:7Q6203 4.5 54.1 1.0 O5' B:7Q6203 4.5 62.4 1.0 CZ B:PHE102 4.7 28.0 1.0 O1A B:7Q6203 4.9 40.3 1.0 O5' G:DA10 4.9 32.8 1.0 CA B:ASP100 4.9 26.2 1.0 O2B B:7Q6203 4.9 45.7 1.0 O3A B:7Q6203 5.0 63.5 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