Magnesium in PDB 6e05: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Sulfate Precipitant)

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Sulfate 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 Sulfate 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 Sulfate Precipitant), PDB code: 6e05 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) 48.98 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.330, 105.290, 153.760, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 28.5

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 Sulfate Precipitant) (pdb code 6e05). 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 Sulfate Precipitant), PDB code: 6e05:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6e05

Go back to Magnesium Binding Sites List in 6e05
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 Sulfate 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 Sulfate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:27.9
occ:0.66
 O A:HOH443 2.0 44.9 1.0
O1G A:CTP302 2.1 28.1 0.9
O1B A:CTP302 2.2 26.0 0.9
OG1 A:THR16 2.2 18.4 1.0
OE1 A:GLU108 2.8 52.4 1.0
O3B A:CTP302 2.9 22.7 0.9
OD2 A:ASP49 2.9 44.1 1.0
PG A:CTP302 3.0 33.1 0.9
PB A:CTP302 3.1 34.2 0.9
CG A:ASP49 3.3 44.3 1.0
CB A:THR16 3.4 24.2 1.0
O2A A:CTP302 3.4 37.2 0.9
OD1 A:ASP49 3.4 41.3 1.0
O2G A:CTP302 3.7 46.5 0.9
N A:THR16 3.9 28.3 1.0
O1A A:CTP302 4.0 36.0 0.9
CD A:GLU108 4.0 48.5 1.0
PA A:CTP302 4.0 33.0 0.9
O3A A:CTP302 4.1 27.6 0.9
O2B A:CTP302 4.2 27.3 0.9
CA A:THR16 4.2 22.6 1.0
O3G A:CTP302 4.3 17.9 0.9
CG2 A:THR16 4.5 19.0 1.0
CB A:ASP49 4.6 35.5 1.0
NZ A:LYS15 4.6 41.9 1.0
OE2 A:GLU108 4.6 44.7 1.0
NZ A:LYS37 4.7 23.4 1.0
CB A:LYS15 4.7 20.4 1.0
CE A:LYS15 4.8 44.0 1.0
C A:LYS15 5.0 25.3 1.0

Magnesium binding site 2 out of 4 in 6e05

Go back to Magnesium Binding Sites List in 6e05
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 Sulfate 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 Sulfate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:19.9
occ:0.67
 O2B B:CTP302 1.8 30.5 0.9
O B:HOH433 2.2 20.7 1.0
OE1 B:GLU108 2.5 39.3 1.0
OG1 B:THR16 2.6 26.6 1.0
OD2 B:ASP49 2.8 25.6 1.0
O2G B:CTP302 3.0 39.2 0.9
O3G B:CTP302 3.0 40.4 0.9
PB B:CTP302 3.1 27.4 0.9
O B:HOH426 3.1 34.6 1.0
PG B:CTP302 3.2 44.0 0.9
O3B B:CTP302 3.3 31.4 0.9
NZ B:LYS37 3.4 29.9 1.0
CD B:GLU108 3.6 33.4 1.0
CG B:ASP49 3.6 26.5 1.0
CB B:THR16 3.9 29.4 1.0
O3A B:CTP302 4.0 33.4 0.9
OE2 B:GLU108 4.1 39.4 1.0
NZ B:LYS15 4.1 51.3 1.0
OD1 B:ASP49 4.1 31.8 1.0
O1B B:CTP302 4.2 28.7 0.9
N B:THR16 4.3 37.0 1.0
CE B:LYS15 4.3 50.6 1.0
O2A B:CTP302 4.5 41.3 0.9
CB B:ASP49 4.6 25.6 1.0
CA B:THR16 4.6 25.3 1.0
CB B:LYS15 4.6 30.7 1.0
O1G B:CTP302 4.7 60.0 0.9
CE B:LYS37 4.8 35.1 1.0
CG B:GLU108 4.8 26.6 1.0
PA B:CTP302 4.8 40.4 0.9
CG2 B:THR16 4.9 25.1 1.0

Magnesium binding site 3 out of 4 in 6e05

Go back to Magnesium Binding Sites List in 6e05
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 Sulfate 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 Sulfate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:22.0
occ:0.59
 O3G C:CTP302 1.9 38.1 0.9
OE1 C:GLU108 2.1 51.5 1.0
OG1 C:THR16 2.2 41.8 1.0
O2B C:CTP302 2.2 28.8 0.9
OD2 C:ASP49 2.4 37.9 1.0
O C:HOH420 2.8 30.6 1.0
CG C:ASP49 3.1 29.2 1.0
O C:HOH408 3.1 42.1 1.0
CD C:GLU108 3.2 44.2 1.0
PG C:CTP302 3.3 47.1 0.9
PB C:CTP302 3.4 30.7 0.9
CB C:THR16 3.5 34.5 1.0
OD1 C:ASP49 3.6 30.6 1.0
O3B C:CTP302 3.7 34.6 0.9
OE2 C:GLU108 3.7 50.3 1.0
NZ C:LYS37 3.8 28.1 1.0
O2A C:CTP302 3.9 45.4 0.9
N C:THR16 3.9 40.7 1.0
CB C:ASP49 4.1 31.0 1.0
O2G C:CTP302 4.2 47.1 0.9
O1G C:CTP302 4.2 42.9 0.9
CA C:THR16 4.2 36.7 1.0
CG C:GLU108 4.4 42.5 1.0
O1B C:CTP302 4.4 25.4 0.9
CG2 C:THR16 4.5 33.8 1.0
O3A C:CTP302 4.5 42.8 0.9
PA C:CTP302 4.6 50.6 0.9
CB C:LYS15 4.6 30.5 1.0
CE C:LYS15 4.7 36.2 1.0
NZ C:LYS15 4.7 54.1 1.0
O1A C:CTP302 4.8 52.2 0.9
CE C:LYS37 4.8 29.4 1.0
C C:LYS15 4.9 47.6 1.0

Magnesium binding site 4 out of 4 in 6e05

Go back to Magnesium Binding Sites List in 6e05
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 Sulfate 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 Sulfate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:27.1
occ:0.58
 OD2 D:ASP49 2.0 57.5 1.0
O1B D:CTP302 2.1 34.7 0.8
OE1 D:GLU108 2.2 43.0 1.0
OG1 D:THR16 2.3 27.0 1.0
O D:HOH405 2.4 30.7 1.0
O1G D:CTP302 2.4 47.9 0.8
PB D:CTP302 3.2 36.0 0.8
O3B D:CTP302 3.2 23.3 0.8
CG D:ASP49 3.2 43.5 1.0
PG D:CTP302 3.3 44.4 0.8
CD D:GLU108 3.3 28.8 1.0
CB D:THR16 3.5 29.2 1.0
OE2 D:GLU108 3.8 36.6 1.0
OD1 D:ASP49 3.8 48.9 1.0
N D:THR16 4.0 39.8 1.0
NZ D:LYS15 4.0 46.5 1.0
NZ D:LYS37 4.0 38.2 1.0
O2A D:CTP302 4.1 35.5 0.8
O3A D:CTP302 4.2 40.8 0.8
O3G D:CTP302 4.2 42.5 0.8
O2B D:CTP302 4.3 31.0 0.8
CA D:THR16 4.3 31.4 1.0
CB D:ASP49 4.4 31.6 1.0
O2G D:CTP302 4.5 52.0 0.8
PA D:CTP302 4.5 38.0 0.8
CE D:LYS37 4.5 42.6 1.0
CG2 D:THR16 4.5 26.2 1.0
CG D:GLU108 4.6 21.1 1.0
O1A D:CTP302 4.6 26.4 0.8
CB D:LYS15 4.9 32.0 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: Mon Dec 14 22:37:38 2020

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