Magnesium in PDB 4q9d: X-Ray Structure of A Putative Thiamin Diphosphate-Dependent Enzyme Isolated From Mycobacterium Smegmatis

All present enzymatic activity of X-Ray Structure of A Putative Thiamin Diphosphate-Dependent Enzyme Isolated From Mycobacterium Smegmatis:
4.1.1.7;

The structure of X-Ray Structure of A Putative Thiamin Diphosphate-Dependent Enzyme Isolated From Mycobacterium Smegmatis, PDB code: 4q9d was solved by F.H.Andrews, J.D.Horton, H.J.Yoon, A.M.K.Malik, M.G.Logsdon, D.H.Shin, M.M.Kneen, S.W.Suh, M.J.Mcleish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.90 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	137.162, 137.162, 337.057, 90.00, 90.00, 120.00
R / Rfree (%)	15 / 18.5

The binding sites of Magnesium atom in the X-Ray Structure of A Putative Thiamin Diphosphate-Dependent Enzyme Isolated From Mycobacterium Smegmatis (pdb code 4q9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of A Putative Thiamin Diphosphate-Dependent Enzyme Isolated From Mycobacterium Smegmatis, PDB code: 4q9d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Structure of A Putative Thiamin Diphosphate-Dependent Enzyme Isolated From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of A Putative Thiamin Diphosphate-Dependent Enzyme Isolated From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:75.7 occ:1.00 OD1 A:ASN461 2.7 69.8 1.0 OD1 A:ASP434 2.9 43.7 1.0 O A:HOH943 3.2 47.4 1.0 O A:LEU459 3.3 38.5 1.0 CG A:ASN461 3.3 76.2 1.0 O1 A:FMT603 3.3 59.4 1.0 C A:FMT603 3.5 60.7 1.0 ND2 A:ASN461 3.5 79.7 1.0 O A:GLU463 3.6 79.2 1.0 N A:ASP434 3.7 32.5 1.0 CA A:GLY433 3.9 28.4 1.0 CG A:ASP434 3.9 42.2 1.0 O A:HOH1045 4.3 58.7 1.0 C A:GLY433 4.3 35.4 1.0 N A:ASN461 4.3 47.3 1.0 C A:LEU459 4.4 37.1 1.0 CB A:ASN461 4.6 64.2 1.0 O2 A:FMT603 4.6 53.7 1.0 OD2 A:ASP434 4.6 49.6 1.0 CA A:ASP434 4.7 35.1 1.0 C A:GLU463 4.8 87.8 1.0 CB A:ASP434 4.8 34.3 1.0 CB A:LEU459 4.8 37.0 1.0 CA A:ASN461 5.0 59.2 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of A Putative Thiamin Diphosphate-Dependent Enzyme Isolated From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of A Putative Thiamin Diphosphate-Dependent Enzyme Isolated From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:32.0 occ:1.00 O B:GLU463 2.2 32.3 1.0 OD1 B:ASN461 2.2 31.1 1.0 OD1 B:ASP434 2.3 32.8 1.0 O B:HOH1051 2.4 31.7 1.0 O2 B:FMT603 2.6 34.3 1.0 O B:HOH872 2.6 40.2 1.0 CG B:ASN461 3.2 40.0 1.0 C B:GLU463 3.5 35.1 1.0 CG B:ASP434 3.5 23.3 1.0 ND2 B:ASN461 3.5 39.1 1.0 C B:FMT603 3.5 32.0 1.0 N B:ASP434 4.0 19.8 1.0 OD2 B:ASP434 4.0 29.1 1.0 N B:GLU463 4.0 25.9 1.0 O B:LEU459 4.1 28.5 1.0 CA B:GLU463 4.3 35.1 1.0 O B:HOH1177 4.4 38.2 1.0 N B:ASN461 4.4 26.2 1.0 N B:GLY435 4.4 24.8 1.0 N B:TYR464 4.4 29.9 1.0 CA B:TYR464 4.5 40.7 1.0 CB B:ASN461 4.5 32.2 1.0 O B:HOH1179 4.6 52.8 1.0 O1 B:FMT603 4.6 36.7 1.0 CG B:GLU463 4.6 37.2 1.0 CB B:ASP434 4.7 18.6 1.0 C B:TYR464 4.7 43.9 1.0 N B:ALA465 4.7 48.8 1.0 N B:GLY462 4.7 30.1 1.0 CA B:ASP434 4.7 20.8 1.0 CA B:GLY433 4.8 18.6 1.0 C B:GLY433 4.8 23.9 1.0 CA B:ASN461 4.8 30.9 1.0 C B:ASN461 4.9 36.4 1.0 O B:HOH916 5.0 52.1 1.0

F.H.Andrews, J.D.Horton, D.Shin, H.J.Yoon, M.G.Logsdon, A.M.Malik, M.P.Rogers, M.M.Kneen, S.W.Suh, M.J.Mcleish. The Kinetic Characterization and X-Ray Structure of A Putative Benzoylformate Decarboxylase From M. Smegmatis Highlights the Difficulties in the Functional Annotation of Thdp-Dependent Enzymes. Biochim.Biophys.Acta 2015.
ISSN: ISSN 0006-3002
PubMed: 25936776
DOI: 10.1016/J.BBAPAP.2015.04.027