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Magnesium in PDB 9imr: Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp

Enzymatic activity of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp

All present enzymatic activity of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp:
2.5.1.10; 2.5.1.29; 2.5.1.85;

Protein crystallography data

The structure of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp, PDB code: 9imr 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) 32.78 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.796, 115.643, 119.27, 90, 90, 90
R / Rfree (%) 14.2 / 19.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp (pdb code 9imr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp, PDB code: 9imr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 9imr

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Magnesium binding site 1 out of 6 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp


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 Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:7.8
occ:1.00
 O A:HOH540 2.1 6.9 1.0
OD1 A:ASP97 2.1 7.8 1.0
O2A A:IPE401 2.1 6.4 1.0
OD2 A:ASP101 2.2 8.0 1.0
O A:HOH601 2.2 8.2 1.0
O A:HOH648 2.2 9.5 1.0
CG A:ASP97 3.0 7.9 1.0
CG A:ASP101 3.0 8.9 1.0
MG A:MG404 3.2 7.5 1.0
OD1 A:ASP101 3.3 9.2 1.0
OD2 A:ASP97 3.3 8.3 1.0
PA A:IPE401 3.4 7.2 1.0
O1 A:IPE401 3.7 8.1 1.0
OE1 A:GLU161 3.7 12.2 1.0
C2 A:IPE401 4.0 9.0 1.0
O A:HOH730 4.1 6.8 1.0
NE2 A:GLN158 4.2 7.9 1.0
O A:HOH720 4.2 7.0 1.0
O1A A:IPE401 4.3 7.1 1.0
O A:HOH600 4.3 6.6 1.0
OE1 A:GLN158 4.3 12.1 1.0
CB A:ASP97 4.4 7.5 1.0
CB A:ASP101 4.4 8.7 1.0
O A:HOH778 4.4 19.9 1.0
C1 A:IPE401 4.5 8.9 1.0
O3A A:IPE401 4.5 7.4 1.0
CD A:GLN158 4.7 10.1 1.0
O3B A:IPE401 4.7 7.9 1.0
NZ A:LYS182 4.7 8.6 1.0
CD A:GLU161 4.7 11.2 1.0
O A:ASP97 4.8 6.6 1.0
O A:HOH750 5.0 32.1 1.0
CA A:ASP97 5.0 7.2 1.0
OE2 A:GLU161 5.0 12.0 1.0

Magnesium binding site 2 out of 6 in 9imr

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Magnesium binding site 2 out of 6 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp


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 Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:7.5
occ:1.00
 OD2 A:ASP97 1.9 8.3 1.0
O3B A:IPE401 2.0 7.9 1.0
O A:HOH711 2.1 3.9 1.0
O A:HOH730 2.1 6.8 1.0
OD2 A:ASP101 2.1 8.0 1.0
O2A A:IPE401 2.2 6.4 1.0
CG A:ASP97 3.0 7.9 1.0
CG A:ASP101 3.2 8.9 1.0
MG A:MG403 3.2 7.8 1.0
PB A:IPE401 3.3 7.6 1.0
PA A:IPE401 3.4 7.2 1.0
OD1 A:ASP97 3.4 7.8 1.0
CB A:ASP101 3.5 8.7 1.0
O3A A:IPE401 3.5 7.4 1.0
O A:HOH833 3.9 13.5 1.0
O2B A:IPE401 4.0 6.8 1.0
NH2 A:ARG106 4.1 8.8 1.0
O1A A:IPE401 4.2 7.1 1.0
O A:ASP97 4.2 6.6 1.0
O A:HOH720 4.2 7.0 1.0
OD1 A:ASP101 4.3 9.2 1.0
CB A:ASP97 4.3 7.5 1.0
O A:HOH648 4.3 9.5 1.0
O A:HOH594 4.4 4.8 1.0
O1B A:IPE401 4.5 7.5 1.0
OD1 A:ASP98 4.5 7.2 1.0
C A:ASP97 4.5 7.1 1.0
O A:HOH707 4.6 20.0 1.0
O1 A:IPE401 4.7 8.1 1.0
O A:HOH601 4.9 8.2 1.0
CA A:ASP97 4.9 7.2 1.0

Magnesium binding site 3 out of 6 in 9imr

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Magnesium binding site 3 out of 6 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp


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 Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:8.5
occ:1.00
 OD2 A:ASP223 2.0 6.7 1.0
O2B A:IPE401 2.0 6.8 1.0
O A:HOH565 2.1 5.2 1.0
O1A A:IPE401 2.1 7.1 1.0
O A:HOH572 2.2 5.3 1.0
O A:HOH594 2.3 4.8 1.0
CG A:ASP223 3.1 6.9 1.0
PA A:IPE401 3.2 7.2 1.0
PB A:IPE401 3.2 7.6 1.0
O3A A:IPE401 3.3 7.4 1.0
OD1 A:ASP223 3.6 7.3 1.0
OD1 A:ASP227 3.8 10.1 1.0
O A:HOH707 3.9 20.0 1.0
NZ A:LYS237 3.9 10.2 1.0
O A:HOH600 4.0 6.6 1.0
O A:ASP223 4.1 7.5 1.0
O A:HOH730 4.1 6.8 1.0
OE1 A:GLN220 4.2 8.4 1.0
O2A A:IPE401 4.2 6.4 1.0
O3B A:IPE401 4.2 7.9 1.0
OD1 A:ASP242 4.2 9.3 1.0
OD2 A:ASP242 4.3 8.3 1.0
O1B A:IPE401 4.3 7.5 1.0
CB A:ASP223 4.3 6.8 1.0
OD1 A:ASP224 4.3 8.5 1.0
O1 A:IPE401 4.4 8.1 1.0
C A:ASP223 4.4 7.3 1.0
CG A:ASP227 4.5 9.9 1.0
CG A:ASP242 4.7 8.3 1.0
CB A:ASP227 4.7 8.9 1.0
CE A:LYS237 4.8 10.6 1.0
CA A:ASP223 5.0 7.2 1.0
N A:ASP224 5.0 7.2 1.0

Magnesium binding site 4 out of 6 in 9imr

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Magnesium binding site 4 out of 6 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:8.9
occ:1.00
 OD2 B:ASP97 2.0 7.7 1.0
O2B B:IPE401 2.0 7.8 1.0
O B:HOH663 2.1 5.6 1.0
OD2 B:ASP101 2.1 7.6 1.0
O B:HOH705 2.2 9.1 1.0
O1A B:IPE401 2.3 8.9 1.0
CG B:ASP97 3.0 7.7 1.0
CG B:ASP101 3.1 7.8 1.0
MG B:MG405 3.2 10.4 1.0
PB B:IPE401 3.3 8.5 1.0
OD1 B:ASP97 3.4 7.4 1.0
PA B:IPE401 3.4 8.2 1.0
O3A B:IPE401 3.5 7.8 1.0
CB B:ASP101 3.5 7.9 1.0
O1B B:IPE401 3.9 7.9 1.0
O B:HOH820 4.0 11.0 1.0
NH2 B:ARG106 4.1 8.5 1.0
O B:ASP97 4.1 8.6 1.0
O2A B:IPE401 4.2 8.7 1.0
O B:HOH691 4.2 6.3 1.0
O B:HOH704 4.3 6.5 1.0
OD1 B:ASP101 4.3 8.4 1.0
CB B:ASP97 4.3 7.1 1.0
OD1 B:ASP98 4.4 9.4 1.0
O3B B:IPE401 4.5 8.4 1.0
C B:ASP97 4.5 7.5 1.0
O B:HOH709 4.5 7.1 1.0
O B:HOH575 4.5 8.1 1.0
O1 B:IPE401 4.7 9.2 1.0
O B:HOH582 4.9 9.7 1.0
CA B:ASP97 5.0 7.7 1.0
N B:ASP98 5.0 8.1 1.0

Magnesium binding site 5 out of 6 in 9imr

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Magnesium binding site 5 out of 6 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:9.7
occ:1.00
 O1B B:IPE401 2.0 7.9 1.0
O B:HOH573 2.1 5.8 1.0
OD2 B:ASP223 2.1 8.4 1.0
O2A B:IPE401 2.1 8.7 1.0
O B:HOH687 2.2 6.6 1.0
O B:HOH575 2.2 8.1 1.0
CG B:ASP223 3.1 7.7 1.0
PA B:IPE401 3.2 8.2 1.0
PB B:IPE401 3.3 8.5 1.0
O3A B:IPE401 3.4 7.8 1.0
OD1 B:ASP223 3.6 7.7 1.0
O B:HOH709 3.9 7.1 1.0
OD1 B:ASP227 3.9 9.7 1.0
O B:HOH593 4.0 8.8 1.0
O1A B:IPE401 4.1 8.9 1.0
O B:ASP223 4.2 7.5 1.0
NZ B:LYS237 4.2 9.4 1.0
OD2 B:ASP242 4.2 8.4 1.0
OE1 B:GLN220 4.2 10.4 1.0
O B:HOH705 4.2 9.1 1.0
OD1 B:ASP242 4.2 9.4 1.0
OD1 B:ASP224 4.2 10.5 1.0
O3B B:IPE401 4.3 8.4 1.0
O2B B:IPE401 4.3 7.8 1.0
O1 B:IPE401 4.4 9.2 1.0
CB B:ASP223 4.4 8.4 1.0
C B:ASP223 4.5 8.5 1.0
CG B:ASP227 4.6 9.4 1.0
CG B:ASP242 4.6 9.2 1.0
CE B:LYS237 4.7 10.3 1.0
CB B:ASP227 4.9 9.3 1.0
N B:ASP224 4.9 8.6 1.0

Magnesium binding site 6 out of 6 in 9imr

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Magnesium binding site 6 out of 6 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase RV0562 From Mycobacterium Tuberculosis in Complex with Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:10.4
occ:1.00
 OD1 B:ASP97 2.1 7.4 1.0
O B:HOH704 2.2 6.5 1.0
OD2 B:ASP101 2.2 7.6 1.0
O B:HOH549 2.2 7.7 1.0
O B:HOH582 2.2 9.7 1.0
O1A B:IPE401 2.2 8.9 1.0
CG B:ASP97 3.0 7.7 1.0
CG B:ASP101 3.0 7.8 1.0
MG B:MG403 3.2 8.9 1.0
OD1 B:ASP101 3.3 8.4 1.0
OD2 B:ASP97 3.3 7.7 1.0
PA B:IPE401 3.5 8.2 1.0
OE1 B:GLU161 3.7 13.1 1.0
O1 B:IPE401 3.8 9.2 1.0
C2 B:IPE401 4.1 11.3 1.0
O B:HOH705 4.1 9.1 1.0
O B:HOH691 4.2 6.3 1.0
O2A B:IPE401 4.2 8.7 1.0
O B:HOH593 4.3 8.8 1.0
NE2 B:GLN158 4.3 11.2 1.0
CB B:ASP97 4.4 7.1 1.0
OE1 B:GLN158 4.4 15.2 1.0
CB B:ASP101 4.5 7.9 1.0
C1 B:IPE401 4.6 10.8 1.0
O B:HOH620 4.6 21.3 1.0
O3A B:IPE401 4.6 7.8 1.0
O B:ASP97 4.7 8.6 1.0
O2B B:IPE401 4.7 7.8 1.0
NZ B:LYS182 4.7 9.9 1.0
CD B:GLU161 4.7 12.2 1.0
CD B:GLN158 4.8 12.8 1.0
CA B:ASP97 5.0 7.7 1.0
O B:HOH663 5.0 5.6 1.0

Reference:

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
Page generated: Sat Aug 16 04:15:10 2025

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