Magnesium in PDB 9imq: Crystal Structure of A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis:
2.5.1.10; 2.5.1.29; 2.5.1.85;

The structure of Crystal Structure of A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis, PDB code: 9imq was solved by Q.Wang, Y.Yang, C.-C.Chen, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.92 / 2.54
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.882, 90.376, 59.032, 90, 101.21, 90
R / Rfree (%)	18.8 / 27.6

The binding sites of Magnesium atom in the Crystal Structure of A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis (pdb code 9imq). 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 A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis, PDB code: 9imq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis


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 A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:40.8 occ:1.00 NH2 A:ARG257 3.0 54.6 1.0 N A:ILE172 3.5 45.5 1.0 N A:GLU173 3.7 42.1 1.0 CB A:ILE172 3.9 34.8 1.0 OG A:SER171 4.1 45.1 1.0 CA A:ILE172 4.1 40.8 1.0 CB A:GLU173 4.2 41.2 1.0 C A:SER171 4.2 44.7 1.0 CZ A:ARG257 4.2 53.3 1.0 CA A:SER171 4.3 41.1 1.0 CG1 A:ILE172 4.3 47.3 1.0 C A:ILE172 4.4 43.4 1.0 CB A:SER171 4.6 42.8 1.0 CA A:GLU173 4.6 41.3 1.0 NE A:ARG257 4.7 46.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis


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 A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:38.0 occ:1.00 O A:VAL8 2.4 54.5 1.0 O A:HOH520 3.3 42.9 1.0 NH2 A:ARG58 3.4 57.1 1.0 C A:VAL8 3.5 46.1 1.0 NE A:ARG23 3.8 45.8 1.0 O A:VAL7 3.8 45.9 1.0 CA A:VAL8 3.9 46.8 1.0 CD A:ARG23 4.3 40.4 1.0 NH1 A:ARG58 4.3 60.1 1.0 CZ A:ARG58 4.3 65.5 1.0 CG A:ARG23 4.4 35.7 1.0 N A:ALA9 4.6 39.8 1.0 C A:VAL7 4.7 45.5 1.0 N A:VAL8 4.7 43.4 1.0 CZ A:ARG23 4.8 47.4 1.0 CG1 A:VAL8 4.8 42.0 1.0 NH2 A:ARG23 4.9 46.4 1.0 CB A:VAL8 5.0 43.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis


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 A C45 Isoprenyl Diphosphate Synthase, RV0562 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:28.0 occ:1.00 O A:HOH558 3.3 35.9 1.0 NH2 A:ARG107 3.4 43.6 1.0 NE A:ARG107 3.4 48.1 1.0 CZ A:ARG107 3.8 41.6 1.0 NE2 A:HIS90 3.9 37.8 1.0 N A:LYS57 3.9 46.0 1.0 O A:HOH517 4.0 37.2 1.0 CD1 A:LEU94 4.1 29.8 1.0 CA A:GLY56 4.3 43.0 1.0 CB A:LYS57 4.4 39.5 1.0 CG A:ARG107 4.5 40.0 1.0 CE A:LYS57 4.5 38.3 1.0 CD A:ARG107 4.5 43.5 1.0 CE1 A:HIS90 4.6 27.2 1.0 C A:GLY56 4.6 48.1 1.0 CA A:LYS57 4.8 37.8 1.0 NH1 A:ARG106 4.9 35.2 1.0 CD2 A:HIS90 4.9 35.7 1.0

Q.Wang, Y.Yang, B.He, J.W.Huang, C.J.Kuo, C.C.Chen, R.T.Guo. Structural Insight of A Bi-Functional Isoprenyl Diphosphate Synthase RV0562 From Mycobacterium Tuberculosis. Int.J.Biol.Macromol. 45171 2025.
ISSN: ISSN 0141-8130
PubMed: 40513738
DOI: 10.1016/J.IJBIOMAC.2025.145171