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Magnesium in PDB 6e06: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant):
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant), PDB code: 6e06 was solved by A.P.Thompson, K.L.Wegener, J.B.Bruning, S.W.Polyak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.96 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.680, 105.700, 153.260, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 28.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) (pdb code 6e06). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant), PDB code: 6e06:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6e06

Go back to Magnesium Binding Sites List in 6e06
Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)


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 Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:22.1
occ:0.56
 O A:HOH401 1.9 33.9 1.0
O1B A:CTP301 2.0 17.1 0.8
OG1 A:THR16 2.1 50.1 1.0
O1G A:CTP301 2.1 17.1 0.8
OE1 A:GLU108 2.2 71.7 1.0
OD2 A:ASP49 2.4 65.3 1.0
CG A:ASP49 3.0 57.1 1.0
PG A:CTP301 3.0 18.0 0.8
PB A:CTP301 3.2 17.1 0.8
CD A:GLU108 3.2 71.8 1.0
OD1 A:ASP49 3.2 57.9 1.0
O2G A:CTP301 3.3 19.6 0.8
CB A:THR16 3.4 42.3 1.0
O3B A:CTP301 3.5 35.4 0.8
OE2 A:GLU108 3.6 70.5 1.0
N A:THR16 3.8 53.6 1.0
CA A:THR16 4.1 43.9 1.0
O2B A:CTP301 4.1 25.1 0.8
O2A A:CTP301 4.2 39.1 0.8
NZ A:LYS37 4.2 35.6 1.0
CB A:ASP49 4.3 50.9 1.0
CG2 A:THR16 4.4 39.2 1.0
O3G A:CTP301 4.4 41.3 0.8
O3A A:CTP301 4.4 34.3 0.8
CG A:GLU108 4.5 67.7 1.0
CB A:LYS15 4.5 43.1 1.0
O1A A:CTP301 4.6 17.1 0.8
NZ A:LYS15 4.6 50.6 1.0
CE A:LYS15 4.6 47.6 1.0
PA A:CTP301 4.6 31.9 0.8
C A:LYS15 4.8 59.8 1.0

Magnesium binding site 2 out of 4 in 6e06

Go back to Magnesium Binding Sites List in 6e06
Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)


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 Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:38.7
occ:0.69
 O3G B:CTP301 1.8 43.6 0.9
O B:HOH412 2.0 60.3 1.0
OG1 B:THR16 2.1 60.1 1.0
O2B B:CTP301 2.2 35.3 0.9
OE1 B:GLU108 2.3 52.1 1.0
OD2 B:ASP49 2.5 44.9 1.0
CG B:ASP49 3.0 44.9 1.0
PG B:CTP301 3.0 24.9 0.9
PB B:CTP301 3.3 17.1 0.9
CD B:GLU108 3.3 45.6 1.0
OD1 B:ASP49 3.4 44.3 1.0
CB B:THR16 3.5 46.3 1.0
NZ B:LYS37 3.5 47.0 1.0
O2G B:CTP301 3.6 30.3 0.9
O3B B:CTP301 3.6 36.3 0.9
OE2 B:GLU108 3.6 51.5 1.0
O3A B:CTP301 4.0 33.3 0.9
CB B:ASP49 4.0 44.3 1.0
N B:THR16 4.1 45.9 1.0
O1G B:CTP301 4.2 41.3 0.9
O2A B:CTP301 4.2 30.5 0.9
CA B:THR16 4.3 46.8 1.0
O1A B:CTP301 4.4 17.1 0.9
CG2 B:THR16 4.4 40.4 1.0
PA B:CTP301 4.5 38.6 0.9
NZ B:LYS15 4.5 56.6 1.0
O1B B:CTP301 4.6 33.0 0.9
CG B:GLU108 4.6 34.2 1.0
CE B:LYS15 4.8 50.6 1.0
CB B:LYS15 4.8 34.9 1.0
CE B:LYS37 4.8 46.6 1.0
O B:HOH425 5.0 45.2 1.0

Magnesium binding site 3 out of 4 in 6e06

Go back to Magnesium Binding Sites List in 6e06
Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)


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 Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:28.1
occ:0.65
 O3G C:CTP301 1.9 37.5 0.8
OD2 C:ASP49 2.0 55.3 1.0
OE1 C:GLU108 2.0 79.4 1.0
O2B C:CTP301 2.0 17.1 0.8
OG1 C:THR16 2.7 61.3 1.0
O C:HOH407 3.0 52.0 1.0
CD C:GLU108 3.0 83.0 1.0
PG C:CTP301 3.1 36.7 0.8
CG C:ASP49 3.2 57.1 1.0
NZ C:LYS37 3.2 49.9 1.0
PB C:CTP301 3.3 17.1 0.8
OE2 C:GLU108 3.5 82.8 1.0
O3B C:CTP301 3.6 38.8 0.8
O1G C:CTP301 3.6 38.6 0.8
O C:HOH414 3.6 51.4 1.0
OD1 C:ASP49 3.9 64.4 1.0
CG C:GLU108 4.1 82.5 1.0
CB C:THR16 4.1 61.1 1.0
CE C:LYS15 4.3 39.1 1.0
CB C:ASP49 4.3 58.2 1.0
O3A C:CTP301 4.3 35.0 0.8
O2G C:CTP301 4.4 37.4 0.8
O1B C:CTP301 4.4 34.9 0.8
CE C:LYS37 4.4 50.7 1.0
N C:THR16 4.4 79.9 1.0
NZ C:LYS15 4.5 39.0 1.0
CB C:LYS15 4.6 50.4 1.0
CA C:THR16 4.8 72.5 1.0
O2A C:CTP301 4.9 34.1 0.8
CG2 C:THR16 4.9 49.4 1.0
O C:GLY109 4.9 61.7 1.0
O1A C:CTP301 5.0 30.6 0.8
PA C:CTP301 5.0 36.1 0.8

Magnesium binding site 4 out of 4 in 6e06

Go back to Magnesium Binding Sites List in 6e06
Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)


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 Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:17.1
occ:0.73
 O1B D:CTP301 1.9 23.2 0.8
OG1 D:THR16 2.0 49.4 1.0
OD2 D:ASP49 2.0 43.3 1.0
OE1 D:GLU108 2.1 30.9 1.0
O D:HOH406 2.2 55.0 1.0
O1G D:CTP301 2.3 29.9 0.8
PB D:CTP301 3.0 17.1 0.8
CG D:ASP49 3.1 41.1 1.0
CD D:GLU108 3.1 27.9 1.0
O3B D:CTP301 3.2 23.7 0.8
CB D:THR16 3.3 37.2 1.0
PG D:CTP301 3.3 21.9 0.8
OE2 D:GLU108 3.4 32.8 1.0
OD1 D:ASP49 3.5 49.7 1.0
N D:THR16 3.8 37.3 1.0
O2A D:CTP301 3.9 29.1 0.8
CA D:THR16 4.0 38.3 1.0
NZ D:LYS15 4.1 62.3 1.0
NZ D:LYS37 4.1 40.1 1.0
O2B D:CTP301 4.1 17.1 0.8
O3A D:CTP301 4.2 24.8 0.8
CG2 D:THR16 4.2 35.6 1.0
O2G D:CTP301 4.2 41.7 0.8
CB D:ASP49 4.3 35.8 1.0
O3G D:CTP301 4.3 29.9 0.8
PA D:CTP301 4.4 35.6 0.8
CE D:LYS37 4.5 37.3 1.0
CG D:GLU108 4.6 22.1 1.0
O1A D:CTP301 4.6 29.6 0.8
CB D:LYS15 4.8 47.1 1.0
C D:LYS15 4.8 53.8 1.0

Reference:

A.P.Thompson, K.L.Wegener, G.W.Booker, S.W.Polyak, J.B.Bruning. Precipitant-Ligand Exchange Technique Reveals the Adp Binding Mode in Mycobacterium Tuberculosis Dethiobiotin Synthetase. Acta Crystallogr D Struct V. 74 965 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289406
DOI: 10.1107/S2059798318010136
Page generated: Wed Aug 13 05:34:50 2025

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