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Magnesium in PDB 6cvv: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Triphosphate (Atp) - Promiscuous Binding Mode with Disordered Nucleoside

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

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Triphosphate (Atp) - 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 Adenosine Triphosphate (Atp) - Promiscuous Binding Mode with Disordered Nucleoside, PDB code: 6cvv 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) 49.25 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.480, 106.920, 152.780, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 27.8

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 6cvv

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Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Triphosphate (Atp) - 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 Adenosine Triphosphate (Atp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:41.4
occ:0.58
 O1G A:ATP301 1.8 52.1 0.8
OG1 A:THR16 1.9 37.3 1.0
OE1 A:GLU108 2.1 44.3 1.0
O1B A:ATP301 2.2 48.6 0.7
OD2 A:ASP49 2.5 43.1 1.0
O1A A:ATP301 2.8 65.2 0.8
PG A:ATP301 2.9 56.9 0.5
CG A:ASP49 3.0 44.0 1.0
CD A:GLU108 3.1 45.2 1.0
CB A:THR16 3.2 36.9 1.0
O2G A:ATP301 3.2 51.6 0.9
PB A:ATP301 3.3 46.9 0.6
N A:THR16 3.4 26.6 1.0
OD1 A:ASP49 3.4 45.0 1.0
O3B A:ATP301 3.5 53.0 0.7
OE2 A:GLU108 3.5 44.9 1.0
CA A:THR16 3.7 38.6 1.0
CB A:ASP49 3.9 40.2 1.0
PA A:ATP301 4.0 73.3 0.0
NZ A:LYS37 4.1 22.7 1.0
CB A:LYS15 4.2 41.5 1.0
O3A A:ATP301 4.2 51.3 0.8
O3G A:ATP301 4.2 60.9 0.9
CG2 A:THR16 4.3 30.3 1.0
C A:LYS15 4.4 45.0 1.0
CG A:GLU108 4.4 42.9 1.0
NZ A:LYS15 4.4 48.5 1.0
O A:HOH453 4.4 45.2 1.0
O2B A:ATP301 4.6 43.1 1.0
CA A:LYS15 4.7 36.8 1.0
O2A A:ATP301 4.7 41.7 1.0
O3' A:ATP301 4.8 60.2 0.7
O A:HOH401 4.8 54.5 1.0
N A:LYS15 4.9 46.2 1.0

Magnesium binding site 2 out of 4 in 6cvv

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Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Triphosphate (Atp) - 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 Adenosine Triphosphate (Atp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:57.6
occ:0.48
 OD2 B:ASP49 1.8 56.1 1.0
OE1 B:GLU108 1.8 52.8 1.0
CG B:ASP49 2.3 49.7 1.0
OG1 B:THR16 2.5 46.9 1.0
CD B:GLU108 2.5 51.4 1.0
NZ B:LYS37 2.7 48.6 1.0
O2G B:ATP301 2.8 84.0 1.0
CB B:ASP49 2.8 49.0 1.0
OE2 B:GLU108 3.0 53.3 1.0
OD1 B:ASP49 3.2 60.9 1.0
O3B B:ATP301 3.5 81.1 0.5
PG B:ATP301 3.6 87.3 0.3
CG B:GLU108 3.7 35.3 1.0
CB B:THR16 3.8 43.9 1.0
O1G B:ATP301 3.8 83.9 1.0
CE B:LYS37 3.9 54.4 1.0
O B:HOH427 4.1 57.3 1.0
CG2 B:THR16 4.2 40.1 1.0
CA B:ASP49 4.3 37.0 1.0
CA B:THR16 4.4 49.2 1.0
CD B:LYS37 4.5 49.2 1.0
N B:THR16 4.5 35.9 1.0
CG B:LYS37 4.6 44.1 1.0
CG B:LYS15 4.7 45.3 1.0
CB B:GLU108 4.9 41.6 1.0
NZ B:LYS15 4.9 47.8 1.0
O B:GLY109 4.9 38.1 1.0
O2B B:ATP301 5.0 58.5 0.9
N B:ASP49 5.0 40.6 1.0
CE B:LYS15 5.0 41.9 1.0
PB B:ATP301 5.0 67.1 0.5

Magnesium binding site 3 out of 4 in 6cvv

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Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Triphosphate (Atp) - 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 Adenosine Triphosphate (Atp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:72.7
occ:0.49
 OD2 C:ASP49 1.8 91.9 1.0
OG1 C:THR16 1.9 72.1 1.0
OE2 C:GLU108 2.2 74.7 1.0
O3G C:ATP301 2.4 62.7 0.9
CD C:GLU108 2.6 74.0 1.0
OE1 C:GLU108 2.6 66.5 1.0
CG C:ASP49 2.7 79.7 1.0
CB C:THR16 3.1 65.8 1.0
CB C:ASP49 3.1 74.6 1.0
O3B C:ATP301 3.2 57.4 0.6
NZ C:LYS37 3.2 64.0 1.0
PG C:ATP301 3.2 60.1 0.1
CG2 C:THR16 3.4 70.2 1.0
O2G C:ATP301 3.5 64.6 0.9
OD1 C:ASP49 3.7 82.5 1.0
CA C:THR16 3.7 64.5 1.0
N C:THR16 3.8 72.3 1.0
CG C:GLU108 4.0 70.4 1.0
CE C:LYS37 4.4 67.0 1.0
CA C:ASP49 4.5 77.8 1.0
O2A C:ATP301 4.5 64.8 0.8
CB C:LYS15 4.5 62.8 1.0
C C:LYS15 4.5 68.9 1.0
O1G C:ATP301 4.6 64.4 1.0
PB C:ATP301 4.7 66.6 0.4
CE C:LYS15 4.8 63.8 1.0
CD C:LYS37 4.8 69.3 1.0

Magnesium binding site 4 out of 4 in 6cvv

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Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Adenosine Triphosphate (Atp) - 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 Adenosine Triphosphate (Atp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:67.1
occ:1.00
 OG1 D:THR16 2.1 45.6 1.0
O1B D:ATP301 2.2 58.0 1.0
OD2 D:ASP49 2.4 50.5 1.0
O1A D:ATP301 2.4 95.3 0.8
O1G D:ATP301 2.6 63.1 1.0
CG D:ASP49 2.9 56.4 1.0
CB D:THR16 2.9 53.4 1.0
OE1 D:GLU108 3.1 60.0 1.0
OD1 D:ASP49 3.2 60.8 1.0
PB D:ATP301 3.4 65.8 0.7
PA D:ATP301 3.7 91.6 0.7
PG D:ATP301 3.7 72.7 0.7
N D:THR16 3.8 56.6 1.0
O3A D:ATP301 3.9 74.1 0.9
O3B D:ATP301 3.9 61.0 1.0
CA D:THR16 3.9 59.2 1.0
CB D:ASP49 3.9 48.9 1.0
CG2 D:THR16 4.0 49.4 1.0
O D:HOH432 4.1 56.7 1.0
O3G D:ATP301 4.1 77.1 1.0
CD D:GLU108 4.2 56.2 1.0
OE2 D:GLU108 4.5 53.8 1.0
O2A D:ATP301 4.5 86.8 1.0
O2B D:ATP301 4.7 63.3 1.0
O D:HOH401 4.8 74.5 1.0
O5' D:ATP301 4.8 98.9 0.6
NZ D:LYS37 4.9 47.3 1.0
C D:LYS15 5.0 53.8 1.0
CA D:ASP49 5.0 52.8 1.0

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 22:46:59 2024

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