Magnesium in PDB 6aq4: Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa

The structure of Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa, PDB code: 6aq4 was solved by A.A.Fedorov, E.V.Fedorov, H.Wang, J.B.Bonanno, L.Carvalho, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.28 / 1.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.541, 88.365, 81.252, 90.00, 108.54, 90.00
R / Rfree (%)	19.1 / 23.3

The structure of Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa (pdb code 6aq4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa, PDB code: 6aq4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa


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 Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:34.9 occ:1.00 O A:HOH410 2.2 28.4 1.0 OD2 A:ASP146 2.2 41.0 1.0 O7 A:CQM302 2.2 34.5 1.0 OE1 A:GLU120 2.2 28.6 1.0 O A:HOH401 2.3 31.0 1.0 O3 A:CQM302 2.4 32.1 1.0 CD A:GLU120 3.1 29.7 1.0 CG A:ASP146 3.2 37.8 1.0 C4 A:CQM302 3.2 33.1 1.0 C3 A:CQM302 3.2 42.0 1.0 OE2 A:GLU120 3.4 26.1 1.0 CB A:ASP146 3.5 31.9 1.0 OD2 A:ASP45 3.8 33.4 1.0 O2 A:CQM302 4.0 37.0 1.0 C2 A:CQM302 4.1 50.4 1.0 NZ A:LYS100 4.1 35.2 1.0 NH1 A:ARG72 4.2 27.3 1.0 OD1 A:ASP146 4.3 37.3 1.0 CG A:GLU120 4.4 24.6 1.0 OE1 A:GLU44 4.4 29.2 1.0 O4 A:CQM302 4.4 29.9 1.0 N A:ASP146 4.4 26.2 1.0 C6 A:CQM302 4.4 46.4 1.0 CA A:ASP146 4.5 27.4 1.0 C1 A:CQM302 4.6 49.4 1.0 CE A:LYS100 4.6 36.5 1.0 CG C:PRO263 4.6 32.7 1.0 CD2 A:LEU118 4.7 26.8 1.0 CB A:GLU120 4.8 23.4 1.0 CG A:ASP45 4.8 33.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa


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 Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:34.5 occ:1.00 OD2 B:ASP146 2.2 27.6 1.0 OE1 B:GLU120 2.2 26.8 1.0 O7 B:CQM302 2.2 31.9 1.0 O B:HOH412 2.2 28.3 1.0 O3 B:CQM302 2.3 32.6 1.0 O B:HOH403 2.3 33.7 1.0 C4 B:CQM302 3.0 38.5 1.0 CD B:GLU120 3.0 26.5 1.0 C3 B:CQM302 3.1 41.5 1.0 CG B:ASP146 3.1 34.7 1.0 OE2 B:GLU120 3.3 27.4 1.0 CB B:ASP146 3.6 28.9 1.0 OD2 B:ASP45 3.9 33.9 1.0 O2 B:CQM302 4.0 38.7 1.0 NZ B:LYS100 4.0 28.4 1.0 C2 B:CQM302 4.1 46.9 1.0 C6 B:CQM302 4.2 43.5 1.0 O4 B:CQM302 4.2 36.9 1.0 NH1 B:ARG72 4.2 30.4 1.0 OD1 B:ASP146 4.2 32.9 1.0 CG B:GLU120 4.3 25.2 1.0 OE1 B:GLU44 4.5 27.9 1.0 C1 B:CQM302 4.5 52.1 1.0 N B:ASP146 4.5 25.7 1.0 CG A:PRO263 4.6 34.6 1.0 CA B:ASP146 4.6 23.5 1.0 CB B:GLU120 4.7 25.2 1.0 CD2 B:LEU118 4.7 31.4 1.0 CG B:ASP45 4.8 36.9 1.0 CE B:LYS100 4.9 35.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Citramalyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:36.2 occ:1.00 OD2 C:ASP146 2.1 32.8 1.0 OE1 C:GLU120 2.2 27.1 1.0 O C:HOH430 2.2 26.2 1.0 O C:HOH411 2.2 29.1 1.0 O2 C:PYR302 2.3 30.9 1.0 O3 C:PYR302 2.4 31.0 1.0 C1 C:PYR302 3.0 30.6 1.0 C2 C:PYR302 3.1 37.5 1.0 CD C:GLU120 3.1 29.2 1.0 CG C:ASP146 3.1 33.1 1.0 OE2 C:GLU120 3.4 28.4 1.0 CB C:ASP146 3.5 26.1 1.0 OD2 C:ASP45 3.8 44.0 1.0 NZ C:LYS100 4.1 28.8 1.0 NH1 C:ARG72 4.2 32.2 1.0 OD1 C:ASP146 4.2 33.4 1.0 O1 C:PYR302 4.3 34.5 1.0 CG C:GLU120 4.4 30.8 1.0 OE1 C:GLU44 4.4 29.5 1.0 N C:ASP146 4.5 29.1 1.0 CG B:PRO263 4.5 36.7 1.0 O B:HOH442 4.5 35.9 1.0 C3 C:PYR302 4.5 42.6 1.0 CA C:ASP146 4.6 28.8 1.0 CE C:LYS100 4.6 34.6 1.0 CD2 C:LEU118 4.7 26.1 1.0 CB C:GLU120 4.7 24.2 1.0 CG C:ASP45 4.8 43.2 1.0 O B:HOH496 4.8 46.1 1.0 CD C:LYS100 4.8 51.4 1.0 CD B:PRO263 4.9 36.9 1.0 O C:HOH453 5.0 39.8 1.0

H.Wang, A.A.Fedorov, E.V.Fedorov, D.M.Hunt, A.Rodgers, H.L.Douglas, A.Garza-Garcia, J.B.Bonanno, S.C.Almo, L.P.S.De Carvalho. An Essential Bifunctional Enzyme Inmycobacterium Tuberculosisfor Itaconate Dissimilation and Leucine Catabolism. Proc.Natl.Acad.Sci.Usa V. 116 15907 2019.
ISSN: ESSN 1091-6490
PubMed: 31320588
DOI: 10.1073/PNAS.1906606116