Manganese in PDB 6vde: Full-Length M. Smegmatis POL1

All present enzymatic activity of Full-Length M. Smegmatis POL1:
2.7.7.7;

The structure of Full-Length M. Smegmatis POL1, PDB code: 6vde was solved by S.Shuman, Y.Goldgur, S.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.37 / 2.71
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.004, 80.940, 117.912, 98.68, 105.13, 109.36
R / Rfree (%)	23.4 / 30.4

The binding sites of Manganese atom in the Full-Length M. Smegmatis POL1 (pdb code 6vde). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Full-Length M. Smegmatis POL1, PDB code: 6vde:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Full-Length M. Smegmatis POL1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Full-Length M. Smegmatis POL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:0.5 occ:1.00 OD1 A:ASP130 1.7 0.6 1.0 CG A:ASP130 2.2 0.3 1.0 OD2 A:ASP130 2.3 0.6 1.0 OD2 A:ASP26 2.9 0.8 1.0 OD2 A:ASP153 2.9 0.4 1.0 CG A:ASP153 3.1 1.0 1.0 OD1 A:ASP153 3.2 0.4 1.0 MN A:MN1002 3.3 0.6 0.6 CB A:ASP130 3.7 0.9 1.0 CG A:ASP26 3.9 0.3 1.0 CB A:ASP153 3.9 0.4 1.0 OD1 A:ASP26 4.2 0.2 1.0 CA A:ASP130 4.5 0.4 1.0 CB A:SER29 4.7 0.7 1.0 N A:ASP130 4.7 0.1 1.0 OG1 A:THR151 5.0 93.5 1.0

Manganese binding site 2 out of 6 in the Full-Length M. Smegmatis POL1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Full-Length M. Smegmatis POL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:0.6 occ:0.61 OD1 A:ASP155 2.2 0.3 1.0 OD2 A:ASP153 2.2 0.4 1.0 CG A:ASP155 3.2 0.4 1.0 CG A:ASP153 3.2 1.0 1.0 MN A:MN1001 3.3 0.5 1.0 CB A:ASP153 3.6 0.4 1.0 OD2 A:ASP130 3.7 0.6 1.0 CB A:ASP155 3.9 0.6 1.0 OD2 A:ASP155 4.0 0.1 1.0 CG A:ASP130 4.1 0.3 1.0 OD1 A:ASP130 4.1 0.6 1.0 OD1 A:ASP153 4.3 0.4 1.0

Manganese binding site 3 out of 6 in the Full-Length M. Smegmatis POL1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Full-Length M. Smegmatis POL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1003 b:0.4 occ:1.00 OD2 A:ASP465 1.9 0.0 1.0 CG A:ASP465 2.4 0.7 1.0 OD1 A:ASP465 2.4 0.8 1.0 O A:ALA123 2.5 0.2 1.0 OE1 A:GLN473 3.3 0.0 1.0 OD2 A:ASP471 3.5 97.1 1.0 C A:ALA123 3.7 81.7 1.0 CB A:ASP465 3.8 0.6 1.0 N A:ALA123 4.0 85.3 1.0 OD1 A:ASP471 4.0 94.2 1.0 CG A:ASP471 4.1 88.6 1.0 CA A:ASP465 4.2 0.2 1.0 CA A:ALA123 4.3 80.3 1.0 OE1 A:GLU124 4.4 78.0 1.0 O A:ASP466 4.4 0.4 1.0 CD A:GLN473 4.5 95.2 1.0 N A:ASP466 4.5 0.4 1.0 CB A:ALA123 4.6 79.8 1.0 C A:ASP465 4.7 0.1 1.0 N A:GLU124 4.7 81.6 1.0 CA A:GLU124 5.0 87.2 1.0 C A:LEU122 5.0 87.0 1.0 C A:ASP466 5.0 0.8 1.0

Manganese binding site 4 out of 6 in the Full-Length M. Smegmatis POL1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Full-Length M. Smegmatis POL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:0.9 occ:0.86 OD2 B:ASP26 1.9 0.5 1.0 OD1 B:ASP130 2.3 0.2 1.0 CG B:ASP26 2.8 0.4 1.0 OD2 B:ASP153 2.9 0.9 1.0 OD1 B:ASP153 3.1 0.5 1.0 OD1 B:ASP26 3.1 0.1 1.0 CG B:ASP130 3.2 0.9 1.0 CG B:ASP153 3.2 0.3 1.0 OD2 B:ASP130 3.3 0.4 1.0 CB B:SER29 4.0 93.3 1.0 CB B:ASP26 4.2 0.8 1.0 CB B:ASP153 4.4 0.4 1.0 CB B:ASP130 4.5 99.7 1.0 OG1 B:THR151 4.6 1.0 1.0 OG B:SER29 4.7 95.9 1.0 N B:ASP130 4.7 95.0 1.0 CA B:ASP130 4.9 97.2 1.0

Manganese binding site 5 out of 6 in the Full-Length M. Smegmatis POL1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Full-Length M. Smegmatis POL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:0.3 occ:1.00 OD2 B:ASP155 2.6 1.0 1.0 OD1 B:ASP153 3.0 0.5 1.0 CG B:ASP155 3.5 0.1 1.0 CB B:ASP153 3.7 0.4 1.0 CG B:ASP153 3.8 0.3 1.0 OD1 B:ASP155 4.1 0.8 1.0 OD2 B:ASP130 4.4 0.4 1.0 CB B:ASP155 4.5 0.1 1.0 OD2 B:ASP153 5.0 0.9 1.0

Manganese binding site 6 out of 6 in the Full-Length M. Smegmatis POL1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Full-Length M. Smegmatis POL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1003 b:95.3 occ:1.00 OD2 B:ASP465 2.0 0.1 1.0 CG B:ASP465 2.6 1.0 1.0 OD1 B:ASP465 2.7 0.4 1.0 O B:ALA123 2.9 0.6 1.0 OD2 B:ASP471 3.3 0.2 1.0 OE1 B:GLN473 3.6 73.0 1.0 CB B:ASP465 3.9 0.5 1.0 CG B:ASP471 4.0 0.9 1.0 C B:ALA123 4.0 87.4 1.0 OD1 B:ASP471 4.1 99.0 1.0 CA B:ASP465 4.2 98.0 1.0 O B:ASP466 4.2 91.2 1.0 OE1 B:GLU124 4.3 95.3 1.0 N B:ALA123 4.4 79.6 1.0 N B:ASP466 4.4 84.8 1.0 C B:ASP466 4.5 79.2 1.0 C B:ASP465 4.6 89.2 1.0 CA B:ALA123 4.7 87.0 1.0 CD B:GLN473 4.8 78.5 1.0 N B:SER467 4.9 82.0 1.0

S.Ghosh, Y.Goldgur, S.Shuman. Mycobacterial Dna Polymerase I: Activities and Crystal Structures of the Pol Domain As Apoenzyme and in Complex with A Dna Primer-Template and of the Full-Length Fen/Exo-Pol Enzyme Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962