Magnesium in PDB 6czd: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Diphosphate

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Diphosphate

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Diphosphate:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Diphosphate, PDB code: 6czd 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) 43.70 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.770, 105.750, 155.200, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 25.9

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 6czd

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Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine 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 Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:16.3
occ:1.00
 O1B A:ADP302 1.9 11.9 0.9
O1A A:ADP302 2.0 16.8 0.9
O A:HOH456 2.0 18.4 1.0
OG1 A:THR16 2.1 18.8 1.0
OE1 A:GLU108 2.1 17.7 1.0
OD2 A:ASP49 2.3 17.3 1.0
PA A:ADP302 3.2 23.5 0.9
CG A:ASP49 3.2 18.5 1.0
CD A:GLU108 3.2 20.2 1.0
PB A:ADP302 3.2 16.8 0.9
CB A:THR16 3.3 15.2 1.0
O3A A:ADP302 3.3 17.7 0.9
OE2 A:GLU108 3.6 19.9 1.0
OD1 A:ASP49 3.7 18.8 1.0
N A:THR16 3.8 13.4 1.0
NZ A:LYS37 3.8 17.6 1.0
O3B A:ADP302 4.1 23.2 0.9
CA A:THR16 4.1 14.6 1.0
O2A A:ADP302 4.2 17.9 0.9
CB A:ASP49 4.2 11.8 1.0
O2B A:ADP302 4.2 16.8 0.9
O5' A:ADP302 4.3 24.5 0.9
C5' A:ADP302 4.3 27.5 0.9
CG2 A:THR16 4.4 19.7 1.0
O A:HOH416 4.4 18.5 1.0
O A:HOH531 4.5 27.9 1.0
CG A:GLU108 4.5 18.5 1.0
O A:HOH473 4.5 33.9 1.0
O A:HOH485 4.6 32.8 1.0
CB A:LYS15 4.7 15.9 1.0
NZ A:LYS15 4.8 15.0 1.0
C A:LYS15 4.8 18.8 1.0
CE A:LYS37 4.8 21.6 1.0
CE A:LYS15 4.8 12.4 1.0

Magnesium binding site 2 out of 4 in 6czd

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Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine 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 Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:18.2
occ:0.94
 O3B B:ADP302 1.8 17.8 1.0
O2A B:ADP302 1.9 15.0 1.0
OE1 B:GLU108 2.0 21.9 1.0
O B:HOH427 2.1 19.8 1.0
OG1 B:THR16 2.1 21.1 1.0
OD2 B:ASP49 2.4 17.1 1.0
PB B:ADP302 3.1 19.7 1.0
PA B:ADP302 3.1 20.7 1.0
CD B:GLU108 3.1 19.1 1.0
CG B:ASP49 3.1 19.8 1.0
O3A B:ADP302 3.3 18.4 1.0
CB B:THR16 3.4 21.2 1.0
OE2 B:GLU108 3.6 23.2 1.0
OD1 B:ASP49 3.6 16.8 1.0
NZ B:LYS37 3.7 11.5 1.0
N B:THR16 3.8 15.4 1.0
O B:HOH425 4.0 22.0 1.0
CA B:THR16 4.1 20.6 1.0
O1B B:ADP302 4.1 22.2 1.0
O1A B:ADP302 4.1 18.4 1.0
O2B B:ADP302 4.1 21.3 1.0
CB B:ASP49 4.1 19.4 1.0
O5' B:ADP302 4.3 19.2 1.0
C5' B:ADP302 4.4 20.0 1.0
CG B:GLU108 4.4 16.9 1.0
CB B:LYS15 4.5 16.8 1.0
CG2 B:THR16 4.5 13.0 1.0
O B:HOH504 4.6 25.1 1.0
CE B:LYS15 4.6 15.9 1.0
C B:LYS15 4.7 17.6 1.0
CE B:LYS37 4.8 15.9 1.0
NZ B:LYS15 4.9 13.0 1.0
O B:HOH480 4.9 24.9 1.0
CA B:LYS15 5.0 18.2 1.0

Magnesium binding site 3 out of 4 in 6czd

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Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine 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 Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:39.8
occ:0.91
 O2A C:ADP302 1.8 47.5 1.0
O2B C:ADP302 2.1 55.2 1.0
OE2 C:GLU108 2.1 34.3 1.0
OG1 C:THR16 2.1 34.1 1.0
O C:HOH440 2.2 32.3 1.0
OD2 C:ASP49 2.4 37.6 1.0
CG C:ASP49 2.9 31.6 1.0
PA C:ADP302 3.1 43.4 1.0
CD C:GLU108 3.1 35.9 1.0
OD1 C:ASP49 3.3 30.8 1.0
PB C:ADP302 3.3 52.6 1.0
CB C:THR16 3.4 34.0 1.0
NZ C:LYS37 3.5 35.4 1.0
OE1 C:GLU108 3.5 35.9 1.0
O3A C:ADP302 3.6 34.3 1.0
O5' C:ADP302 3.7 51.3 1.0
CB C:ASP49 3.9 31.8 1.0
O C:HOH483 4.0 38.0 1.0
N C:THR16 4.0 37.1 1.0
O3B C:ADP302 4.1 57.9 1.0
O C:HOH464 4.2 35.9 1.0
CA C:THR16 4.2 37.5 1.0
O1A C:ADP302 4.4 38.7 1.0
CG C:GLU108 4.4 35.0 1.0
CG2 C:THR16 4.4 39.2 1.0
O1B C:ADP302 4.5 60.3 1.0
CE C:LYS37 4.8 34.6 1.0
O C:HOH438 4.8 42.3 1.0
CB C:LYS15 5.0 35.0 1.0
O C:HOH461 5.0 27.8 1.0

Magnesium binding site 4 out of 4 in 6czd

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Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Diphosphate


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 Adenosine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:21.9
occ:0.77
 O1B D:ADP302 2.0 20.0 0.9
O D:HOH419 2.0 18.3 1.0
O1A D:ADP302 2.0 26.9 0.9
OG1 D:THR16 2.1 23.9 1.0
OE1 D:GLU108 2.1 24.9 1.0
OD2 D:ASP49 2.2 18.7 1.0
CG D:ASP49 3.0 22.1 1.0
PA D:ADP302 3.2 21.5 0.9
CD D:GLU108 3.2 22.3 1.0
PB D:ADP302 3.2 22.7 0.9
CB D:THR16 3.3 22.8 1.0
O3A D:ADP302 3.4 16.9 0.9
OD1 D:ASP49 3.4 21.9 1.0
OE2 D:GLU108 3.6 21.3 1.0
NZ D:LYS37 3.8 14.9 1.0
N D:THR16 3.9 24.5 1.0
O3B D:ADP302 4.0 21.4 0.9
CA D:THR16 4.1 24.7 1.0
CB D:ASP49 4.2 20.1 1.0
O2A D:ADP302 4.2 24.6 0.9
O5' D:ADP302 4.3 24.0 0.9
C5' D:ADP302 4.4 26.9 0.9
O2B D:ADP302 4.4 26.1 0.9
CG2 D:THR16 4.4 20.1 1.0
CG D:GLU108 4.5 23.6 1.0
O D:HOH436 4.6 24.1 1.0
CB D:LYS15 4.8 27.4 1.0
O D:HOH444 4.8 23.6 1.0
O D:HOH478 4.8 30.6 1.0
CE D:LYS37 4.9 17.7 1.0
CE D:LYS15 4.9 25.5 1.0
C D:LYS15 4.9 30.2 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 22:33:07 2020

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