Magnesium in PDB 6as5: Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Acetoacetate and Coenzyme A

The structure of Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Acetoacetate and Coenzyme A, PDB code: 6as5 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)	31.27 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.579, 72.998, 85.788, 90.00, 98.83, 90.00
R / Rfree (%)	21.7 / 27.7

The binding sites of Magnesium atom in the Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Acetoacetate and Coenzyme A (pdb code 6as5). 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, Acetoacetate and Coenzyme A, PDB code: 6as5:
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, Acetoacetate 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, Acetoacetate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:29.6 occ:1.00 OE1 A:GLU120 2.2 25.2 1.0 O8 A:AAE303 2.3 27.1 1.0 O A:HOH411 2.3 16.9 1.0 O3 A:AAE303 2.4 23.8 1.0 OD2 A:ASP146 2.4 38.2 1.0 O A:HOH402 2.4 21.3 1.0 CD A:GLU120 3.1 25.7 1.0 C5 A:AAE303 3.1 35.0 1.0 C2 A:AAE303 3.2 32.4 1.0 C4 A:AAE303 3.3 37.4 1.0 CG A:ASP146 3.4 33.2 1.0 OE2 A:GLU120 3.4 19.7 1.0 CB A:ASP146 3.7 22.9 1.0 OD2 A:ASP45 3.8 31.7 1.0 NH1 A:ARG72 3.9 19.7 1.0 O C:HOH408 4.1 18.6 1.0 NZ A:LYS100 4.2 36.8 1.0 CD2 A:LEU118 4.3 27.6 1.0 O1 A:AAE303 4.4 27.7 1.0 CG A:GLU120 4.4 11.2 1.0 OE1 A:GLU44 4.5 27.2 1.0 OD1 A:ASP146 4.5 33.3 1.0 C9 A:AAE303 4.5 37.1 1.0 CG C:PRO263 4.7 25.1 1.0 CG A:ASP45 4.8 32.3 1.0 N A:ASP146 4.8 23.2 1.0 CB A:GLU120 4.8 21.8 1.0 CA A:ASP146 4.8 19.6 1.0 CZ A:ARG72 4.8 27.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Acetoacetate 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, Acetoacetate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:21.8 occ:1.00 O3 B:AAE303 2.2 18.5 1.0 O B:HOH414 2.3 21.5 1.0 OD2 B:ASP146 2.3 41.5 1.0 O8 B:AAE303 2.3 27.0 1.0 OE1 B:GLU120 2.3 24.5 1.0 O B:HOH407 2.4 28.5 1.0 CD B:GLU120 3.1 26.1 1.0 C5 B:AAE303 3.2 22.9 1.0 C2 B:AAE303 3.2 30.9 1.0 CG B:ASP146 3.2 30.8 1.0 OE2 B:GLU120 3.3 26.4 1.0 C4 B:AAE303 3.5 30.7 1.0 CB B:ASP146 3.6 15.4 1.0 OD2 B:ASP45 3.9 29.1 1.0 NZ B:LYS100 4.0 32.8 1.0 NH1 B:ARG72 4.1 24.9 1.0 O A:HOH443 4.2 14.2 1.0 O1 B:AAE303 4.3 24.3 1.0 CG B:GLU120 4.3 22.7 1.0 OD1 B:ASP146 4.3 39.3 1.0 C9 B:AAE303 4.5 14.5 1.0 N B:ASP146 4.6 22.1 1.0 CD2 B:LEU118 4.6 25.8 1.0 CE B:LYS100 4.6 43.6 1.0 CA B:ASP146 4.6 15.8 1.0 CG A:PRO263 4.6 26.9 1.0 OE1 B:GLU44 4.7 26.5 1.0 CB B:GLU120 4.7 18.0 1.0 CG B:ASP45 5.0 31.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Protein Cite From Mycobacterium Tuberculosis in Complex with Magnesium, Acetoacetate 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, Acetoacetate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:28.4 occ:1.00 O8 C:AAE303 2.2 28.3 1.0 O C:HOH418 2.2 14.7 1.0 O3 C:AAE303 2.3 22.6 1.0 OE1 C:GLU120 2.3 22.9 1.0 OD2 C:ASP146 2.3 31.8 1.0 O C:HOH405 2.3 25.9 1.0 C5 C:AAE303 3.0 34.4 1.0 C2 C:AAE303 3.1 34.2 1.0 CG C:ASP146 3.2 25.3 1.0 C4 C:AAE303 3.2 35.8 1.0 CD C:GLU120 3.3 27.5 1.0 OE2 C:GLU120 3.6 20.2 1.0 CB C:ASP146 3.6 17.5 1.0 NZ C:LYS100 3.9 42.0 1.0 OD2 C:ASP45 3.9 25.4 1.0 O B:HOH403 4.1 11.4 1.0 NH1 C:ARG72 4.1 30.2 1.0 OD1 C:ASP146 4.2 28.8 1.0 O1 C:AAE303 4.3 29.9 1.0 CD2 C:LEU118 4.4 21.0 1.0 CG B:PRO263 4.4 19.5 1.0 C9 C:AAE303 4.5 25.9 1.0 N C:ASP146 4.5 19.1 1.0 CG C:GLU120 4.6 22.0 1.0 CA C:ASP146 4.7 18.4 1.0 OE1 C:GLU44 4.7 32.0 1.0 CE C:LYS100 4.7 49.1 1.0 CB C:GLU120 4.8 21.0 1.0 CG C:ASP45 4.8 35.1 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