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Magnesium in PDB 6nl5: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate, PDB code: 6nl5 was solved by A.P.Thompson, S.W.Polyak, K.L.Wegener, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.17 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.827, 103.835, 153.326, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 27.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate (pdb code 6nl5). 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 2'-Deoxycytidine Triphosphate, PDB code: 6nl5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6nl5

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Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate


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 2'-Deoxycytidine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:43.2
occ:0.74
 OE1 A:GLU108 2.1 57.7 1.0
OG1 A:THR16 2.1 44.4 1.0
O2B A:DCP301 2.2 43.0 1.0
O2G A:DCP301 2.2 40.4 1.0
O A:HOH411 2.3 45.5 1.0
OD2 A:ASP49 2.4 60.7 1.0
CG A:ASP49 2.8 55.0 1.0
OD1 A:ASP49 3.0 61.6 1.0
CD A:GLU108 3.3 54.5 1.0
PB A:DCP301 3.4 39.6 1.0
CB A:THR16 3.5 46.9 1.0
PG A:DCP301 3.5 45.1 1.0
O3B A:DCP301 3.6 46.3 1.0
OE2 A:GLU108 3.8 47.5 1.0
CB A:ASP49 3.9 47.8 1.0
N A:THR16 4.0 48.0 1.0
O2A A:DCP301 4.2 50.2 1.0
NZ A:LYS37 4.2 40.0 1.0
CA A:THR16 4.3 40.2 1.0
O1B A:DCP301 4.4 39.8 1.0
O3G A:DCP301 4.4 40.5 1.0
CG2 A:THR16 4.4 45.3 1.0
O1G A:DCP301 4.4 58.3 1.0
CG A:GLU108 4.5 48.9 1.0
O3A A:DCP301 4.6 49.1 1.0
O1A A:DCP301 4.6 43.7 1.0
CB A:LYS15 4.7 43.0 1.0
PA A:DCP301 4.7 54.9 1.0
O A:HOH431 4.8 39.5 1.0
CE A:LYS15 4.9 45.9 1.0

Magnesium binding site 2 out of 4 in 6nl5

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Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate


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 2'-Deoxycytidine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:46.7
occ:0.69
 OG1 B:THR16 2.0 58.3 1.0
OE1 B:GLU108 2.1 37.1 1.0
OD2 B:ASP49 2.3 65.8 1.0
O2B B:DCP301 2.3 29.2 1.0
O2G B:DCP301 2.4 39.0 1.0
CD B:GLU108 2.9 60.5 1.0
OE2 B:GLU108 3.3 45.2 1.0
CB B:THR16 3.3 37.2 1.0
CG B:ASP49 3.4 58.2 1.0
N B:THR16 3.5 41.5 1.0
NZ B:LYS37 3.7 36.3 1.0
PB B:DCP301 3.7 32.1 1.0
PG B:DCP301 3.7 36.5 1.0
CA B:THR16 3.8 47.3 1.0
O B:HOH433 3.8 54.2 1.0
CB B:LYS15 3.9 38.5 1.0
CE B:LYS15 4.1 41.6 1.0
CB B:ASP49 4.1 57.2 1.0
CG B:GLU108 4.1 54.7 1.0
O3B B:DCP301 4.2 45.0 1.0
OD1 B:ASP49 4.3 54.1 1.0
CG2 B:THR16 4.3 36.2 1.0
C B:LYS15 4.3 46.8 1.0
O3G B:DCP301 4.3 39.0 1.0
O1B B:DCP301 4.4 29.3 1.0
CE B:LYS37 4.6 38.7 1.0
CA B:LYS15 4.6 36.4 1.0
NZ B:LYS15 4.6 41.7 1.0
O2A B:DCP301 4.7 46.1 1.0
O1G B:DCP301 4.9 73.7 1.0
O3A B:DCP301 4.9 38.5 1.0
N B:LYS15 5.0 27.0 1.0

Magnesium binding site 3 out of 4 in 6nl5

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Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate


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 2'-Deoxycytidine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:56.1
occ:0.58
 OD2 C:ASP49 1.8 54.1 1.0
OG1 C:THR16 2.0 52.9 1.0
O2G C:DCP301 2.0 52.3 1.0
OE1 C:GLU108 2.0 57.7 1.0
O C:HOH408 2.3 45.2 1.0
O2B C:DCP301 2.6 42.7 1.0
CG C:ASP49 2.8 52.8 1.0
CD C:GLU108 3.1 58.9 1.0
CB C:THR16 3.4 40.9 1.0
PG C:DCP301 3.4 69.2 1.0
OE2 C:GLU108 3.5 64.5 1.0
CB C:ASP49 3.5 51.0 1.0
OD1 C:ASP49 3.6 48.2 1.0
O1A C:DCP301 3.7 48.5 1.0
NZ C:LYS37 3.8 39.6 1.0
PB C:DCP301 3.8 41.7 1.0
O3B C:DCP301 3.9 45.8 1.0
N C:THR16 4.0 52.6 1.0
CA C:THR16 4.1 48.6 1.0
O1G C:DCP301 4.3 74.1 1.0
CG2 C:THR16 4.3 31.0 1.0
O3G C:DCP301 4.3 65.4 1.0
CG C:GLU108 4.4 61.9 1.0
CE C:LYS37 4.4 36.3 1.0
CB C:LYS15 4.7 52.9 1.0
CA C:ASP49 4.8 49.0 1.0
PA C:DCP301 4.8 52.2 1.0
O3A C:DCP301 4.8 42.9 1.0
CE C:LYS15 4.8 53.7 1.0
O1B C:DCP301 4.9 41.4 1.0
C C:LYS15 4.9 50.5 1.0

Magnesium binding site 4 out of 4 in 6nl5

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Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate


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 2'-Deoxycytidine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:53.4
occ:0.67
 OE1 D:GLU108 1.9 52.8 1.0
OD2 D:ASP49 2.0 59.6 1.0
O3G D:DCP301 2.1 43.0 1.0
OG1 D:THR16 2.2 58.0 1.0
O2B D:DCP301 2.3 41.6 1.0
O D:HOH406 2.7 89.4 1.0
CD D:GLU108 3.0 50.1 1.0
CG D:ASP49 3.1 53.9 1.0
NZ D:LYS37 3.4 46.4 1.0
OE2 D:GLU108 3.4 54.1 1.0
PG D:DCP301 3.5 53.7 1.0
CB D:THR16 3.6 47.2 1.0
PB D:DCP301 3.6 45.0 1.0
OD1 D:ASP49 3.7 61.0 1.0
NZ D:LYS15 3.8 56.1 1.0
O3B D:DCP301 4.0 62.2 1.0
N D:THR16 4.1 57.7 1.0
CB D:ASP49 4.2 48.7 1.0
CG D:GLU108 4.2 47.1 1.0
CE D:LYS37 4.2 45.3 1.0
O2G D:DCP301 4.3 69.9 1.0
CA D:THR16 4.3 55.5 1.0
O1A D:DCP301 4.3 57.2 1.0
CG2 D:THR16 4.4 46.3 1.0
O1B D:DCP301 4.5 45.5 1.0
O1G D:DCP301 4.5 69.4 1.0
CB D:LYS15 4.7 51.6 1.0
O3A D:DCP301 4.7 59.2 1.0
CD D:LYS37 4.8 40.0 1.0
O D:GLY109 4.9 58.2 1.0
CE D:LYS15 5.0 49.5 1.0

Reference:

A.P.Thompson, J.B.Bruning, K.L.Wegener, S.W.Polyak. Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with 2'-Deoxycytidine Triphosphate To Be Published.
Page generated: Tue Oct 1 12:45:50 2024

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