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Magnesium in PDB 6czb: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Uridine Triphosphate (Utp) - Promiscuous Binding Mode with Disordered Nucleoside

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

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Uridine Triphosphate (Utp) - 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 Uridine Triphosphate (Utp) - Promiscuous Binding Mode with Disordered Nucleoside, PDB code: 6czb 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) 38.45 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.050, 105.290, 153.810, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 27.9

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 6czb

Go back to Magnesium Binding Sites List in 6czb
Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Uridine Triphosphate (Utp) - 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 Uridine Triphosphate (Utp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:29.3
occ:1.00
 O2B A:UTP302 1.9 32.6 1.0
O A:HOH429 1.9 33.5 1.0
OG1 A:THR16 2.1 29.3 1.0
OE1 A:GLU108 2.3 33.0 1.0
O2G A:UTP302 2.4 25.2 1.0
OD2 A:ASP49 2.6 31.6 1.0
PB A:UTP302 2.9 31.1 0.9
O3B A:UTP302 3.0 26.4 1.0
PG A:UTP302 3.1 36.6 0.9
CB A:THR16 3.2 30.7 1.0
CG A:ASP49 3.3 32.6 1.0
CD A:GLU108 3.4 30.9 1.0
O2A A:UTP302 3.4 43.6 0.9
N A:THR16 3.6 32.6 1.0
OD1 A:ASP49 3.7 35.5 1.0
O1G A:UTP302 3.9 32.9 1.0
OE2 A:GLU108 3.9 34.5 1.0
CA A:THR16 3.9 28.4 1.0
O1B A:UTP302 4.0 31.7 1.0
O3A A:UTP302 4.0 35.3 1.0
PA A:UTP302 4.2 40.6 0.3
O3G A:UTP302 4.2 39.5 0.9
NZ A:LYS37 4.3 23.0 1.0
CB A:ASP49 4.3 29.3 1.0
CG2 A:THR16 4.4 33.2 1.0
CB A:LYS15 4.4 30.7 1.0
O1A A:UTP302 4.5 30.6 1.0
CE A:LYS15 4.5 31.1 1.0
O A:HOH405 4.5 30.5 1.0
CG A:GLU108 4.6 29.1 1.0
C A:LYS15 4.7 31.6 1.0
NZ A:LYS15 4.8 28.3 1.0
CA A:LYS15 4.9 31.2 1.0
N A:LYS15 5.0 35.9 1.0

Magnesium binding site 2 out of 4 in 6czb

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Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Uridine Triphosphate (Utp) - 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 Uridine Triphosphate (Utp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:35.1
occ:1.00
 O3G B:UTP302 1.8 39.4 1.0
O B:HOH445 2.0 35.1 1.0
OG1 B:THR16 2.1 35.0 1.0
O1B B:UTP302 2.2 34.8 1.0
OE1 B:GLU108 2.3 32.5 1.0
OD2 B:ASP49 2.4 35.2 1.0
CG B:ASP49 2.9 36.3 1.0
PG B:UTP302 3.0 38.6 0.9
OD1 B:ASP49 3.2 35.2 1.0
PB B:UTP302 3.3 32.6 1.0
O B:HOH426 3.3 47.8 1.0
O3B B:UTP302 3.3 32.1 1.0
CD B:GLU108 3.4 31.8 1.0
CB B:THR16 3.5 34.9 1.0
NZ B:LYS37 3.8 32.7 1.0
O1G B:UTP302 3.8 33.0 1.0
OE2 B:GLU108 3.9 32.1 1.0
CB B:ASP49 4.1 35.1 1.0
N B:THR16 4.1 31.0 1.0
O2G B:UTP302 4.2 39.0 1.0
O1A B:UTP302 4.2 52.5 1.0
O3A B:UTP302 4.3 34.0 1.0
O B:HOH403 4.3 48.4 1.0
CA B:THR16 4.3 32.8 1.0
O2B B:UTP302 4.4 33.4 1.0
CG2 B:THR16 4.4 30.4 1.0
CG B:GLU108 4.7 28.7 1.0
PA B:UTP302 4.7 52.2 0.0
O B:HOH413 4.8 34.8 1.0
O2A B:UTP302 4.8 49.2 0.8
CE B:LYS37 5.0 31.6 1.0

Magnesium binding site 3 out of 4 in 6czb

Go back to Magnesium Binding Sites List in 6czb
Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Uridine Triphosphate (Utp) - 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 Uridine Triphosphate (Utp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:43.4
occ:1.00
 OG1 C:THR16 1.9 40.0 1.0
O1B C:UTP302 2.0 40.0 1.0
O C:HOH412 2.0 42.4 1.0
OD2 C:ASP49 2.3 39.2 1.0
OE2 C:GLU108 2.3 43.0 1.0
O1G C:UTP302 2.3 37.6 1.0
CG C:ASP49 2.9 38.6 1.0
CB C:THR16 3.1 38.3 1.0
PB C:UTP302 3.2 36.7 1.0
CD C:GLU108 3.2 42.4 1.0
O2A C:UTP302 3.3 44.7 0.7
OD1 C:ASP49 3.3 38.6 1.0
OE1 C:GLU108 3.4 40.6 1.0
PG C:UTP302 3.5 44.3 0.8
O3B C:UTP302 3.5 44.4 1.0
N C:THR16 3.6 44.8 1.0
O C:HOH402 3.8 42.9 1.0
CA C:THR16 3.8 41.3 1.0
CB C:ASP49 4.0 41.7 1.0
O3A C:UTP302 4.1 45.2 1.0
PA C:UTP302 4.2 47.1 0.2
O2B C:UTP302 4.2 37.6 1.0
CG2 C:THR16 4.2 40.4 1.0
NZ C:LYS37 4.3 34.8 1.0
O2G C:UTP302 4.5 45.3 0.6
O3G C:UTP302 4.5 47.7 1.0
O C:HOH426 4.5 48.5 1.0
O1A C:UTP302 4.6 40.2 1.0
CG C:GLU108 4.6 42.9 1.0
CB C:LYS15 4.6 39.0 1.0
C C:LYS15 4.6 42.8 1.0
CE C:LYS15 4.8 33.3 1.0
O C:HOH481 5.0 45.7 1.0

Magnesium binding site 4 out of 4 in 6czb

Go back to Magnesium Binding Sites List in 6czb
Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Uridine Triphosphate (Utp) - 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 Uridine Triphosphate (Utp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:31.1
occ:1.00
 O2G D:UTP302 2.1 37.5 1.0
OD2 D:ASP49 2.1 33.5 1.0
OE1 D:GLU108 2.1 34.2 1.0
O D:HOH413 2.2 33.2 1.0
O2B D:UTP302 2.2 39.1 1.0
OG1 D:THR16 2.2 29.5 1.0
CG D:ASP49 2.9 32.4 1.0
CD D:GLU108 3.2 35.0 1.0
PG D:UTP302 3.2 40.5 1.0
OD1 D:ASP49 3.3 34.5 1.0
PB D:UTP302 3.4 36.2 1.0
CB D:THR16 3.5 36.2 1.0
OE2 D:GLU108 3.6 34.5 1.0
O3B D:UTP302 3.6 32.5 1.0
O3G D:UTP302 3.7 40.7 1.0
NZ D:LYS37 3.8 30.9 1.0
N D:THR16 4.0 35.3 1.0
CB D:ASP49 4.2 30.1 1.0
O D:HOH488 4.2 37.9 1.0
O3A D:UTP302 4.3 40.6 0.9
CA D:THR16 4.3 36.7 1.0
O1A D:UTP302 4.4 67.7 0.8
O1G D:UTP302 4.4 44.1 1.0
O2A D:UTP302 4.5 48.2 1.0
CG D:GLU108 4.5 36.1 1.0
O1B D:UTP302 4.5 38.7 0.9
O D:HOH425 4.5 39.6 1.0
CG2 D:THR16 4.6 33.1 1.0
PA D:UTP302 4.6 56.2 0.0
O D:HOH432 4.7 42.7 1.0
CE D:LYS37 4.7 31.0 1.0
CE D:LYS15 4.8 31.2 1.0
CB D:LYS15 4.8 32.8 1.0
NZ D:LYS15 4.9 34.6 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 22:50:20 2024

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