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Magnesium in PDB 6nkb: Crystal Structure of Dethiobiotin Synthetase From Mycobacterium Tuberculosis in Complex with 2'-Deoxycytidine Diphosphate

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

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

Protein crystallography data

The structure of Crystal Structure of Dethiobiotin Synthetase From Mycobacterium Tuberculosis in Complex with 2'-Deoxycytidine Diphosphate, PDB code: 6nkb 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) 46.18 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.800, 105.200, 154.190, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26.5

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 3 in 6nkb

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Magnesium binding site 1 out of 3 in the Crystal Structure of Dethiobiotin Synthetase From Mycobacterium Tuberculosis in Complex with 2'-Deoxycytidine Diphosphate


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 Dethiobiotin Synthetase From Mycobacterium Tuberculosis in Complex with 2'-Deoxycytidine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:25.0
occ:0.68
O A:HOH448 2.1 24.1 1.0
O A:HOH529 2.1 18.6 1.0
O1B A:YYY301 2.1 18.7 1.0
OG1 A:THR16 2.2 21.4 1.0
OD2 A:ASP49 2.3 22.1 1.0
OE1 A:GLU108 2.3 16.7 1.0
CG A:ASP49 3.1 21.3 1.0
PB A:YYY301 3.3 17.8 1.0
OD1 A:ASP49 3.4 17.2 1.0
O2B A:YYY301 3.4 20.8 1.0
CD A:GLU108 3.5 19.3 1.0
CB A:THR16 3.6 17.0 1.0
NZ A:LYS37 3.8 11.8 1.0
O A:HOH554 3.9 24.6 1.0
N A:THR16 4.0 17.6 1.0
OE2 A:GLU108 4.0 19.6 1.0
O A:HOH559 4.1 25.0 1.0
O2A A:YYY301 4.2 30.9 1.0
CB A:ASP49 4.3 15.0 1.0
CA A:THR16 4.3 16.0 1.0
NZ A:LYS15 4.3 17.5 1.0
O3A A:YYY301 4.4 24.4 1.0
O3B A:YYY301 4.4 19.8 1.0
CG2 A:THR16 4.5 17.8 1.0
CB A:LYS15 4.6 11.1 1.0
PA A:YYY301 4.7 18.8 1.0
CG A:GLU108 4.7 16.3 1.0
O1A A:YYY301 4.7 18.5 1.0
CE A:LYS15 4.9 19.0 1.0
C A:LYS15 4.9 16.7 1.0
CE A:LYS37 5.0 6.7 1.0

Magnesium binding site 2 out of 3 in 6nkb

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


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 Dethiobiotin Synthetase From Mycobacterium Tuberculosis in Complex with 2'-Deoxycytidine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:25.0
occ:0.63
O C:HOH480 2.0 17.0 1.0
OG1 C:THR16 2.0 20.7 1.0
OD2 C:ASP49 2.0 23.9 1.0
OE2 C:GLU108 2.2 20.0 1.0
O2B C:YYY301 2.3 18.0 1.0
O C:HOH476 2.5 21.8 1.0
CG C:ASP49 2.9 20.2 1.0
CD C:GLU108 3.2 18.7 1.0
CB C:THR16 3.3 21.2 1.0
OE1 C:GLU108 3.6 15.3 1.0
OD1 C:ASP49 3.6 22.7 1.0
PB C:YYY301 3.6 22.4 1.0
N C:THR16 3.8 16.2 1.0
CB C:ASP49 3.8 19.5 1.0
NZ C:LYS37 3.9 12.7 1.0
O3B C:YYY301 3.9 22.3 1.0
CA C:THR16 4.0 16.3 1.0
O C:HOH581 4.1 20.1 1.0
O2A C:YYY301 4.1 18.0 1.0
O C:HOH565 4.3 25.1 1.0
CG2 C:THR16 4.4 16.9 1.0
CE C:LYS15 4.5 15.1 1.0
CG C:GLU108 4.5 17.1 1.0
CB C:LYS15 4.5 16.7 1.0
O3A C:YYY301 4.6 24.1 1.0
O1B C:YYY301 4.7 23.7 1.0
PA C:YYY301 4.7 20.4 1.0
O1A C:YYY301 4.8 19.1 1.0
C C:LYS15 4.8 16.0 1.0
NZ C:LYS15 4.9 19.3 1.0
CE C:LYS37 4.9 15.3 1.0
O C:HOH518 4.9 32.1 1.0

Magnesium binding site 3 out of 3 in 6nkb

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


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 Dethiobiotin Synthetase From Mycobacterium Tuberculosis in Complex with 2'-Deoxycytidine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:25.0
occ:0.85
O1B D:YYY301 2.0 26.2 1.0
O D:HOH506 2.1 28.6 1.0
OE1 D:GLU108 2.1 22.1 1.0
OD2 D:ASP49 2.2 19.1 1.0
OG1 D:THR16 2.3 19.4 1.0
O D:HOH405 2.6 25.4 1.0
CG D:ASP49 3.1 21.3 1.0
CD D:GLU108 3.3 19.7 1.0
PB D:YYY301 3.3 31.2 1.0
O3B D:YYY301 3.5 25.9 1.0
OD1 D:ASP49 3.6 26.7 1.0
CB D:THR16 3.6 21.8 1.0
NZ D:LYS37 3.8 16.6 1.0
OE2 D:GLU108 3.8 22.2 1.0
O D:HOH492 3.9 34.0 1.0
CB D:ASP49 4.1 21.5 1.0
N D:THR16 4.2 21.6 1.0
O2B D:YYY301 4.2 26.7 1.0
O1A D:YYY301 4.2 29.2 1.0
CA D:THR16 4.4 21.4 1.0
O D:HOH424 4.4 37.1 1.0
O3A D:YYY301 4.5 28.2 1.0
CG D:GLU108 4.5 18.4 1.0
CG2 D:THR16 4.6 18.6 1.0
O D:HOH531 4.6 36.9 1.0
CE D:LYS37 4.7 18.4 1.0
CB D:LYS15 4.7 20.9 1.0
PA D:YYY301 4.8 28.1 1.0
CE D:LYS15 4.8 28.1 1.0
NZ D:LYS15 4.8 33.0 1.0
O2A D:YYY301 5.0 20.4 1.0

Reference:

A.P.Thompson, S.W.Polyak, K.L.Wegener, J.B.Bruning. Crystal Structure of Dethiobiotin Synthetase From Mycobacterium Tuberculosis in Complex with 2'-Deoxycytidine Diphosphate To Be Published.
Page generated: Tue Oct 1 12:44:35 2024

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