Magnesium in PDB 6arb: Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Coenzyme A

The structure of Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Coenzyme A, PDB code: 6arb 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)	28.45 / 1.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.533, 73.491, 86.459, 90.00, 99.14, 90.00
R / Rfree (%)	21.9 / 26.2

The binding sites of Magnesium atom in the Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Pyruvate and Coenzyme A (pdb code 6arb). 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 Coenzyme A, PDB code: 6arb:
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 Coenzyme A


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 Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:17.8 occ:1.00 OD2 A:ASP146 2.2 21.7 1.0 O3 A:PYR302 2.2 23.8 1.0 OE1 A:GLU120 2.2 18.2 1.0 O A:HOH409 2.3 17.0 1.0 O2 A:PYR302 2.3 19.9 1.0 O A:HOH407 2.4 21.5 1.0 C2 A:PYR302 2.9 32.8 1.0 C1 A:PYR302 2.9 28.3 1.0 CD A:GLU120 3.2 19.0 1.0 CG A:ASP146 3.2 21.9 1.0 OE2 A:GLU120 3.5 16.9 1.0 CB A:ASP146 3.5 12.7 1.0 O C:HOH432 3.9 27.9 1.0 OD2 A:ASP45 4.0 26.1 1.0 NH1 A:ARG72 4.1 19.7 1.0 NZ A:LYS100 4.1 39.2 1.0 O1 A:PYR302 4.2 23.6 1.0 C3 A:PYR302 4.2 32.9 1.0 OD1 A:ASP146 4.3 24.9 1.0 OE1 A:GLU44 4.4 23.8 1.0 CG A:GLU120 4.4 9.9 1.0 O C:HOH452 4.5 35.6 1.0 CD2 A:LEU118 4.6 11.2 1.0 N A:ASP146 4.6 16.5 1.0 CG C:PRO263 4.6 25.3 1.0 CA A:ASP146 4.6 18.4 1.0 CB A:GLU120 4.8 14.8 1.0 O A:HOH416 4.9 34.2 1.0 CG A:ASP45 4.9 27.2 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 Coenzyme A


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 Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:16.8 occ:1.00 OD2 B:ASP146 2.2 25.0 1.0 O B:HOH410 2.2 17.5 1.0 O3 B:PYR302 2.2 26.7 1.0 O2 B:PYR302 2.3 15.8 1.0 OE1 B:GLU120 2.3 19.3 1.0 O B:HOH445 2.4 22.2 1.0 C2 B:PYR302 2.9 29.6 1.0 C1 B:PYR302 3.0 26.7 1.0 CD B:GLU120 3.2 21.8 1.0 CG B:ASP146 3.2 18.9 1.0 OE2 B:GLU120 3.5 16.3 1.0 CB B:ASP146 3.7 16.2 1.0 O B:HOH473 3.9 29.0 1.0 NH1 B:ARG72 3.9 20.8 1.0 OD2 B:ASP45 4.0 24.2 1.0 NZ B:LYS100 4.2 27.4 1.0 O1 B:PYR302 4.2 23.3 1.0 O B:HOH531 4.2 30.6 1.0 OD1 B:ASP146 4.3 25.0 1.0 C3 B:PYR302 4.3 28.1 1.0 OE1 B:GLU44 4.4 22.7 1.0 CG B:GLU120 4.4 11.2 1.0 N B:ASP146 4.6 17.3 1.0 CG A:PRO263 4.6 22.5 1.0 CD2 B:LEU118 4.6 12.3 1.0 CA B:ASP146 4.7 17.9 1.0 CB B:GLU120 4.8 13.3 1.0 CZ B:ARG72 4.9 21.4 1.0 CG B:ASP45 4.9 24.9 1.0 CE B:LYS100 5.0 32.1 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 Coenzyme A


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 Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:18.8 occ:1.00 O3 C:PYR302 2.2 21.9 1.0 OD2 C:ASP146 2.2 23.7 1.0 O2 C:PYR302 2.2 19.8 1.0 OE1 C:GLU120 2.2 19.2 1.0 O C:HOH423 2.3 19.6 1.0 O C:HOH406 2.3 22.8 1.0 C2 C:PYR302 2.9 30.0 1.0 C1 C:PYR302 2.9 23.4 1.0 CD C:GLU120 3.1 22.1 1.0 CG C:ASP146 3.1 21.4 1.0 OE2 C:GLU120 3.5 18.5 1.0 CB C:ASP146 3.5 17.3 1.0 OD2 C:ASP45 4.0 29.3 1.0 NH1 C:ARG72 4.1 17.6 1.0 O1 C:PYR302 4.1 20.7 1.0 OD1 C:ASP146 4.2 23.6 1.0 NZ C:LYS100 4.2 24.0 1.0 O B:HOH464 4.3 29.9 1.0 C3 C:PYR302 4.3 35.5 1.0 CG C:GLU120 4.4 12.7 1.0 N C:ASP146 4.5 16.8 1.0 CG B:PRO263 4.5 25.8 1.0 CD2 C:LEU118 4.5 14.2 1.0 OE1 C:GLU44 4.6 27.7 1.0 CA C:ASP146 4.6 17.1 1.0 CB C:GLU120 4.7 13.8 1.0 CG C:ASP45 5.0 30.7 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