Magnesium in PDB 6ime: RV2361C Complex with Substrate Analogues

All present enzymatic activity of RV2361C Complex with Substrate Analogues:
2.5.1.86; 2.5.1.87;

The structure of RV2361C Complex with Substrate Analogues, PDB code: 6ime was solved by T.-P.Ko, R.-T.Guo, C.-C.Chen, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.41 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.711, 89.120, 94.445, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 16.7

The structure of RV2361C Complex with Substrate Analogues also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the RV2361C Complex with Substrate Analogues (pdb code 6ime). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the RV2361C Complex with Substrate Analogues, PDB code: 6ime:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the RV2361C Complex with Substrate Analogues


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RV2361C Complex with Substrate Analogues within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:40.1 occ:1.00 O B:HOH422 1.8 25.3 1.0 O A:HOH401 1.9 29.1 0.5 O7 B:ISY307 2.1 16.3 1.0 CA A:GLY294 2.3 23.7 1.0 N A:GLY294 2.6 27.2 1.0 O2 B:ISY307 2.8 24.1 1.0 O5 B:ISY307 2.9 26.6 1.0 P3 B:ISY307 3.0 25.2 1.0 P1 B:ISY307 3.3 23.9 1.0 OH A:TYR261 3.3 20.5 0.7 O4 B:ISY307 3.6 26.9 1.0 C A:PHE293 3.6 29.7 1.0 C A:GLY294 3.7 24.3 1.0 CE1 A:TYR261 3.8 21.6 0.7 ND2 B:ASN124 3.9 18.0 1.0 O A:HOH401 3.9 20.9 0.5 O B:HOH417 4.0 22.6 1.0 CZ A:TYR261 4.1 19.3 0.7 OG B:SER121 4.1 22.1 1.0 O8 B:ISY307 4.2 24.5 1.0 O A:GLY294 4.2 23.3 1.0 O A:PHE293 4.2 27.6 1.0 C10 B:ISY307 4.2 28.8 1.0 CB B:GLU123 4.4 18.1 1.0 CA A:PHE293 4.5 30.4 1.0 S9 B:ISY307 4.6 30.9 1.0 CB B:SER252 4.6 16.7 1.0 C11 B:ISY307 4.6 27.6 1.0 N A:SER295 4.7 27.6 1.0 OG B:SER252 4.7 18.3 1.0 O6 B:ISY307 4.7 26.9 1.0 N A:PHE293 4.8 28.1 1.0 CB B:SER121 4.9 18.9 1.0 CG B:ASN124 4.9 16.9 1.0

Magnesium binding site 2 out of 2 in the RV2361C Complex with Substrate Analogues


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RV2361C Complex with Substrate Analogues within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg305 b:16.6 occ:1.00 O8 B:ISY307 2.0 24.5 1.0 O B:HOH497 2.1 27.2 1.0 O1A B:GST306 2.1 23.7 1.0 O B:HOH458 2.1 24.3 1.0 O3B B:GST306 2.2 22.8 1.0 OD1 B:ASP76 2.3 20.4 1.0 CG B:ASP76 3.3 19.1 1.0 PA B:GST306 3.3 24.2 1.0 PB B:GST306 3.3 23.2 1.0 P3 B:ISY307 3.4 25.2 1.0 OD2 B:ASP76 3.5 18.2 1.0 O1B B:GST306 3.7 22.8 1.0 O3A B:GST306 3.7 26.7 1.0 NH2 B:ARG127 4.0 18.9 1.0 NH2 B:ARG80 4.0 23.9 1.0 O6 B:ISY307 4.0 26.9 1.0 S9 B:ISY307 4.0 30.9 1.0 O B:HOH417 4.1 22.6 1.0 O B:HOH404 4.1 52.7 1.0 O2 B:ISY307 4.3 24.1 1.0 NE A:ARG292 4.3 35.2 1.0 NH2 A:ARG292 4.4 34.8 1.0 S1 B:GST306 4.4 24.6 1.0 C1 B:GST306 4.5 32.8 1.0 O2B B:GST306 4.5 25.3 1.0 O7 B:ISY307 4.6 16.3 1.0 P1 B:ISY307 4.6 23.9 1.0 CB B:ASP76 4.6 17.6 1.0 O2A B:GST306 4.6 22.9 1.0 N B:GLY77 4.6 16.0 1.0 NH2 B:ARG244 4.7 19.4 1.0 O5 B:ISY307 4.8 26.6 1.0 CZ A:ARG292 4.8 42.6 1.0 CA B:ASP76 5.0 15.5 1.0

T.-P.Ko, X.Xiao, R.-T.Guo, J.-W.Huang, W.Liu, C.-C.Chen. Substrate-Analogue Complex Structure of Mycobacterium Tuberculosis Decaprenyl Diphosphate Synthase. Acta Crystallogr.,Sect.F V. 75 212 2019.
ISSN: ESSN 2053-230X
PubMed: 30950820
DOI: 10.1107/S2053230X19001213