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Magnesium in PDB 6cze: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside, PDB code: 6cze 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) 49.69 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.410, 105.000, 153.980, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 26.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside (pdb code 6cze). 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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside, PDB code: 6cze:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6cze

Go back to Magnesium Binding Sites List in 6cze
Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside


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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:28.8
occ:1.00
 OG1 A:THR16 2.0 35.9 1.0
O1A A:ITT301 2.1 32.6 1.0
O A:HOH434 2.1 27.3 1.0
O1B A:ITT301 2.2 43.8 1.0
OE1 A:GLU108 2.2 40.4 1.0
OD2 A:ASP49 2.4 37.7 1.0
CG A:ASP49 3.1 36.5 1.0
PA A:ITT301 3.1 37.3 1.0
PB A:ITT301 3.2 43.7 1.0
O3A A:ITT301 3.2 33.9 1.0
CB A:THR16 3.2 35.0 1.0
CD A:GLU108 3.2 40.0 1.0
OD1 A:ASP49 3.6 39.8 1.0
OE2 A:GLU108 3.6 35.1 1.0
N A:THR16 3.7 32.0 1.0
CA A:THR16 4.0 28.8 1.0
O2A A:ITT301 4.1 33.3 1.0
CB A:ASP49 4.2 34.2 1.0
O3B A:ITT301 4.2 45.8 1.0
O A:HOH405 4.2 60.4 1.0
O2B A:ITT301 4.2 40.6 1.0
NZ A:LYS37 4.2 25.2 1.0
O A:HOH483 4.3 42.6 1.0
O5' A:ITT301 4.3 37.1 0.8
CG2 A:THR16 4.4 37.5 1.0
CB A:LYS15 4.4 27.6 1.0
C5' A:ITT301 4.4 44.5 0.9
C4' A:ITT301 4.4 51.8 0.5
CG A:GLU108 4.6 35.7 1.0
C A:LYS15 4.6 31.4 1.0
O3' A:ITT301 4.6 52.8 0.7
NZ A:LYS15 4.7 34.3 1.0
CE A:LYS15 4.8 34.6 1.0
CA A:LYS15 4.9 34.1 1.0
N A:LYS15 5.0 41.2 1.0

Magnesium binding site 2 out of 4 in 6cze

Go back to Magnesium Binding Sites List in 6cze
Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside


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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:36.9
occ:0.95
 O2B B:ITT301 1.9 41.7 1.0
O2A B:ITT301 1.9 35.8 1.0
O B:HOH423 2.0 33.4 1.0
OG1 B:THR16 2.1 29.7 1.0
OD2 B:ASP49 2.3 27.7 1.0
OE1 B:GLU108 2.4 37.4 1.0
CG B:ASP49 3.0 33.4 1.0
PB B:ITT301 3.1 45.3 0.9
PA B:ITT301 3.2 33.8 1.0
CB B:THR16 3.2 23.4 1.0
CD B:GLU108 3.3 35.6 1.0
OD1 B:ASP49 3.4 33.6 1.0
O3A B:ITT301 3.4 33.2 1.0
OE2 B:GLU108 3.5 35.6 1.0
N B:THR16 3.8 31.0 1.0
NZ B:LYS37 3.8 30.2 1.0
O1B B:ITT301 4.0 40.2 1.0
O B:HOH494 4.0 40.1 1.0
O5' B:ITT301 4.0 41.1 0.7
CA B:THR16 4.1 28.4 1.0
CB B:ASP49 4.2 33.7 1.0
O1A B:ITT301 4.3 30.4 1.0
CG2 B:THR16 4.3 31.9 1.0
O3B B:ITT301 4.3 44.1 1.0
O3' B:ITT301 4.6 54.0 0.7
O B:HOH501 4.6 39.7 1.0
O2G B:ITT301 4.7 60.1 0.9
CG B:GLU108 4.7 35.1 1.0
O B:HOH409 4.7 45.5 1.0
CB B:LYS15 4.8 26.4 1.0
C B:LYS15 4.8 31.5 1.0
CE B:LYS15 4.9 30.2 1.0
O B:HOH482 5.0 29.8 1.0

Magnesium binding site 3 out of 4 in 6cze

Go back to Magnesium Binding Sites List in 6cze
Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside


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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:34.7
occ:1.00
 O2B C:ITT301 2.0 42.6 1.0
OG1 C:THR16 2.1 36.0 1.0
O C:HOH417 2.2 38.0 1.0
OD2 C:ASP49 2.2 38.8 1.0
O3G C:ITT301 2.2 36.5 1.0
OE2 C:GLU108 2.4 36.7 1.0
PB C:ITT301 3.1 39.5 1.0
CG C:ASP49 3.1 42.7 1.0
PG C:ITT301 3.2 47.6 0.8
CB C:THR16 3.2 35.6 1.0
O3B C:ITT301 3.3 42.5 1.0
CD C:GLU108 3.4 38.8 1.0
OE1 C:GLU108 3.7 40.2 1.0
N C:THR16 3.7 41.4 1.0
OD1 C:ASP49 3.7 45.7 1.0
O2A C:ITT301 3.8 56.5 1.0
O2G C:ITT301 4.0 51.4 0.8
CA C:THR16 4.0 44.0 1.0
O3A C:ITT301 4.0 47.3 1.0
NZ C:LYS15 4.0 35.9 0.2
CB C:ASP49 4.1 33.1 1.0
O1B C:ITT301 4.3 38.2 1.0
PA C:ITT301 4.3 46.6 0.0
O C:HOH466 4.4 52.7 1.0
CG2 C:THR16 4.4 35.7 1.0
O1G C:ITT301 4.4 56.9 1.0
NZ C:LYS37 4.5 30.2 1.0
O1A C:ITT301 4.6 43.0 1.0
CB C:LYS15 4.6 40.1 0.8
CE C:LYS15 4.7 32.9 0.8
C C:LYS15 4.7 40.8 0.2
CG C:GLU108 4.7 36.2 1.0
C C:LYS15 4.7 40.5 0.8
CB C:LYS15 4.8 44.1 0.2
O C:HOH435 4.8 60.2 1.0
O C:HOH461 4.8 50.6 1.0
NZ C:LYS15 5.0 36.1 0.8

Magnesium binding site 4 out of 4 in 6cze

Go back to Magnesium Binding Sites List in 6cze
Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside


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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:38.7
occ:0.82
 OE1 D:GLU108 1.9 29.0 1.0
O1B D:ITT301 2.0 42.7 1.0
OG1 D:THR16 2.1 35.9 1.0
OD2 D:ASP49 2.2 38.3 1.0
O1A D:ITT301 2.2 42.1 1.0
O D:HOH426 2.3 38.4 1.0
CD D:GLU108 2.9 35.2 1.0
CG D:ASP49 3.0 36.9 1.0
OE2 D:GLU108 3.3 34.3 1.0
PB D:ITT301 3.4 42.9 1.0
CB D:THR16 3.4 39.7 1.0
PA D:ITT301 3.5 40.8 1.0
OD1 D:ASP49 3.6 38.0 1.0
NZ D:LYS37 3.7 30.4 1.0
O3A D:ITT301 3.8 49.9 1.0
N D:THR16 3.8 40.4 1.0
CB D:ASP49 4.1 38.1 1.0
CA D:THR16 4.1 39.1 1.0
O2B D:ITT301 4.2 49.0 0.8
CG D:GLU108 4.3 33.0 1.0
O D:HOH401 4.3 45.5 1.0
O3G D:ITT301 4.4 58.3 1.0
O2A D:ITT301 4.4 35.0 1.0
CG2 D:THR16 4.5 33.8 1.0
O3' D:ITT301 4.6 71.4 0.7
O5' D:ITT301 4.6 52.0 0.8
O3B D:ITT301 4.6 53.3 0.7
CB D:LYS15 4.6 34.6 1.0
NZ D:LYS15 4.7 32.9 1.0
C4' D:ITT301 4.8 68.1 0.6
C D:LYS15 4.8 39.5 1.0
CE D:LYS37 4.8 31.3 1.0
CE D:LYS15 4.8 32.1 1.0
O1G D:ITT301 4.9 56.7 0.7
C5' D:ITT301 4.9 59.8 0.7
O D:HOH446 4.9 37.9 1.0
PG D:ITT301 4.9 58.4 0.5

Reference:

A.P.Thompson, W.Salaemae, J.L.Pederick, A.D.Abell, G.W.Booker, J.B.Bruning, S.W.Polyak. Mycobacterium Tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity Through Alternate Binding Modes Acs Catalysis V.(11) 10774 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B03475
Page generated: Mon Sep 30 22:50:52 2024

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