Magnesium in PDB 5gg6: Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with 8- Oxo-Dgtp

The structure of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with 8- Oxo-Dgtp, PDB code: 5gg6 was solved by S.M.Arif, A.G.Patil, U.Varshney, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.36 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.109, 89.500, 59.930, 90.00, 99.07, 90.00
R / Rfree (%)	16.2 / 20.4

The structure of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with 8- Oxo-Dgtp also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with 8- Oxo-Dgtp (pdb code 5gg6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with 8- Oxo-Dgtp, PDB code: 5gg6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with 8- Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with 8- Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:21.6 occ:1.00 OE2 A:GLU85 2.1 31.6 1.0 O1G A:8DG401 2.2 26.2 1.0 O A:HOH555 2.2 26.8 1.0 O A:HOH682 2.3 34.0 1.0 O A:LYS65 2.4 23.9 1.0 OE2 A:GLU127 2.5 43.6 1.0 OE1 A:GLU127 2.9 58.0 1.0 CD A:GLU85 3.1 34.6 1.0 CD A:GLU127 3.1 52.9 1.0 OE1 A:GLU85 3.4 33.6 1.0 PG A:8DG401 3.5 31.4 1.0 C A:LYS65 3.6 24.4 1.0 O3G A:8DG401 3.8 33.3 1.0 NZ A:LYS65 4.0 25.9 1.0 O3B A:8DG401 4.1 31.7 1.0 CA A:GLY66 4.2 24.5 1.0 NH2 A:ARG55 4.3 23.8 1.0 N A:GLY66 4.3 24.8 1.0 CG A:GLU85 4.4 32.3 1.0 O A:HOH564 4.4 32.6 1.0 N A:LYS65 4.5 22.4 1.0 O2G A:8DG401 4.6 30.0 1.0 O A:HOH582 4.6 39.6 1.0 CG A:GLU127 4.6 46.2 1.0 O A:HOH534 4.7 22.7 1.0 CA A:LYS65 4.7 22.7 1.0 CG A:LYS65 4.8 22.0 1.0 CD A:LYS65 4.8 24.8 1.0 CE A:LYS65 5.0 25.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with 8- Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with 8- Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:15.7 occ:1.00 OE2 B:GLU85 2.1 32.4 1.0 O1G B:8DG401 2.1 27.5 1.0 O B:LYS65 2.3 23.5 1.0 O B:HOH695 2.4 25.9 1.0 O B:HOH534 2.4 25.7 1.0 OE2 B:GLU127 2.6 32.0 1.0 OE1 B:GLU127 2.7 43.3 1.0 CD B:GLU127 3.0 37.3 1.0 CD B:GLU85 3.2 32.5 1.0 PG B:8DG401 3.5 30.7 1.0 C B:LYS65 3.6 22.2 1.0 OE1 B:GLU85 3.6 30.6 1.0 O3G B:8DG401 3.9 33.3 1.0 O B:HOH546 4.0 46.0 1.0 NZ B:LYS65 4.0 23.9 1.0 CA B:GLY66 4.2 22.5 1.0 O3B B:8DG401 4.2 29.0 1.0 N B:GLY66 4.3 21.6 1.0 NH2 B:ARG55 4.4 28.8 1.0 CG B:GLU127 4.5 36.1 1.0 CG B:GLU85 4.5 27.8 1.0 O B:HOH574 4.5 32.4 1.0 O B:HOH542 4.5 30.6 1.0 N B:LYS65 4.5 19.3 1.0 O B:HOH684 4.6 35.5 1.0 CA B:LYS65 4.7 21.6 1.0 O2G B:8DG401 4.7 29.9 1.0 O B:HOH561 4.7 22.3 1.0 CG B:LYS65 4.8 19.6 1.0

S.M.Arif, A.G.Patil, U.Varshney, M.Vijayan. Biochemical and Structural Studies of Mycobacterium Smegmatis MUTT1, A Sanitization Enzyme with Unusual Modes of Association Acta Crystallogr D Struct V. 73 349 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28375146
DOI: 10.1107/S2059798317002534