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Magnesium in PDB 6czc: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Thymidine Triphosphate (Ttp) - Promiscuous Binding Mode with Disordered Nucleoside

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

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Thymidine Triphosphate (Ttp) - 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 Thymidine Triphosphate (Ttp) - Promiscuous Binding Mode with Disordered Nucleoside, PDB code: 6czc 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) 36.36 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.580, 105.370, 154.970, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 27.3

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 6czc

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

b:15.6
occ:1.00
 O2G A:TTP302 1.9 20.2 0.9
OD2 A:ASP49 2.0 12.5 1.0
OE1 A:GLU108 2.1 14.1 1.0
OG1 A:THR16 2.1 13.5 1.0
O1A A:TTP302 2.1 16.4 1.0
O1B A:TTP302 2.2 23.9 1.0
CG A:ASP49 3.0 19.3 1.0
CD A:GLU108 3.1 13.1 1.0
PG A:TTP302 3.2 26.3 1.0
PB A:TTP302 3.2 26.1 0.8
CB A:THR16 3.3 13.8 1.0
PA A:TTP302 3.3 19.7 1.0
OE2 A:GLU108 3.5 9.9 1.0
O3A A:TTP302 3.5 18.5 1.0
O3B A:TTP302 3.6 22.9 0.9
OD1 A:ASP49 3.6 25.0 1.0
NZ A:LYS37 3.7 13.4 1.0
N A:THR16 3.8 11.0 1.0
O1G A:TTP302 3.8 21.8 0.9
CA A:THR16 4.0 12.5 1.0
CB A:ASP49 4.0 14.5 1.0
O A:HOH414 4.2 45.3 1.0
O2A A:TTP302 4.3 16.4 1.0
O3G A:TTP302 4.3 23.3 1.0
O5' A:TTP302 4.4 25.3 0.9
C5' A:TTP302 4.4 24.0 1.0
O A:HOH497 4.4 19.2 1.0
CG A:GLU108 4.4 13.0 1.0
CG2 A:THR16 4.4 14.1 1.0
CB A:LYS15 4.5 14.2 1.0
O2B A:TTP302 4.6 32.8 0.9
NZ A:LYS15 4.7 18.9 1.0
CE A:LYS15 4.7 12.0 1.0
C A:LYS15 4.7 14.7 1.0
CE A:LYS37 4.8 8.7 1.0

Magnesium binding site 2 out of 4 in 6czc

Go back to Magnesium Binding Sites List in 6czc
Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Thymidine Triphosphate (Ttp) - 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 Thymidine Triphosphate (Ttp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:17.9
occ:1.00
 O3G B:TTP302 2.0 16.7 1.0
O2A B:TTP302 2.1 19.9 1.0
O2B B:TTP302 2.1 30.8 1.0
OE1 B:GLU108 2.2 23.5 1.0
OD2 B:ASP49 2.2 13.6 1.0
OG1 B:THR16 2.3 16.9 1.0
O3B B:TTP302 2.9 31.9 1.0
PB B:TTP302 3.0 41.7 0.6
PG B:TTP302 3.0 38.8 1.0
CG B:ASP49 3.1 21.6 1.0
CD B:GLU108 3.3 21.5 1.0
PA B:TTP302 3.4 25.2 1.0
CB B:THR16 3.5 17.8 1.0
OD1 B:ASP49 3.6 17.7 1.0
NZ B:LYS37 3.6 12.4 1.0
OE2 B:GLU108 3.7 16.7 1.0
O3A B:TTP302 3.7 36.8 0.9
O B:HOH518 4.0 34.9 1.0
N B:THR16 4.0 11.6 1.0
O2G B:TTP302 4.0 32.8 1.0
O1G B:TTP302 4.1 26.8 1.0
O1B B:TTP302 4.2 35.6 1.0
O1A B:TTP302 4.3 19.8 1.0
CB B:ASP49 4.3 23.2 1.0
CA B:THR16 4.3 16.4 1.0
O B:HOH448 4.4 34.7 1.0
CE B:LYS15 4.4 12.1 1.0
O5' B:TTP302 4.5 25.0 0.3
CG B:GLU108 4.5 16.8 1.0
CG2 B:THR16 4.6 11.6 1.0
CB B:LYS15 4.6 12.2 1.0
C5' B:TTP302 4.6 24.2 1.0
NZ B:LYS15 4.8 15.8 1.0
CE B:LYS37 4.9 14.8 1.0
C B:LYS15 5.0 17.0 1.0

Magnesium binding site 3 out of 4 in 6czc

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

b:29.7
occ:1.00
 O2A C:TTP302 1.9 24.5 1.0
O3G C:TTP302 2.0 34.6 0.6
OE2 C:GLU108 2.0 25.6 1.0
OG1 C:THR16 2.1 19.1 1.0
O2B C:TTP302 2.1 45.7 1.0
OD2 C:ASP49 2.2 28.6 1.0
PB C:TTP302 3.0 39.8 0.7
PA C:TTP302 3.1 27.2 1.0
CG C:ASP49 3.1 27.5 1.0
CD C:GLU108 3.2 24.6 1.0
PG C:TTP302 3.3 40.6 0.9
CB C:THR16 3.3 26.4 1.0
O3A C:TTP302 3.3 31.1 1.0
O3B C:TTP302 3.5 42.0 0.9
OD1 C:ASP49 3.6 29.7 1.0
OE1 C:GLU108 3.6 31.1 1.0
NZ C:LYS37 3.7 21.2 1.0
N C:THR16 3.8 28.2 1.0
CA C:THR16 4.0 30.6 1.0
O2G C:TTP302 4.1 32.8 1.0
O1A C:TTP302 4.1 30.9 1.0
O5' C:TTP302 4.2 37.2 1.0
CB C:ASP49 4.2 22.7 1.0
O1G C:TTP302 4.3 37.0 1.0
O C:HOH499 4.4 28.9 1.0
CG2 C:THR16 4.4 36.7 1.0
CG C:GLU108 4.4 23.0 1.0
O1B C:TTP302 4.4 42.5 1.0
CE C:LYS15 4.6 22.2 1.0
CB C:LYS15 4.7 25.8 1.0
NZ C:LYS15 4.7 24.7 1.0
C5' C:TTP302 4.7 49.0 0.7
C C:LYS15 4.8 29.4 1.0
C4' C:TTP302 4.9 54.6 0.7
CE C:LYS37 4.9 24.6 1.0

Magnesium binding site 4 out of 4 in 6czc

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

b:21.7
occ:1.00
 OG1 D:THR16 1.9 14.9 1.0
O1A D:TTP302 2.0 22.3 1.0
OE1 D:GLU108 2.1 23.6 1.0
O1B D:TTP302 2.1 27.4 0.8
O D:HOH408 2.2 25.6 1.0
OD2 D:ASP49 2.3 14.3 1.0
CG D:ASP49 3.0 21.1 1.0
CD D:GLU108 3.1 20.6 1.0
PA D:TTP302 3.2 20.6 1.0
CB D:THR16 3.2 16.4 1.0
PB D:TTP302 3.3 30.8 1.0
OE2 D:GLU108 3.4 14.9 1.0
OD1 D:ASP49 3.5 24.0 1.0
O3A D:TTP302 3.5 26.9 1.0
N D:THR16 3.7 16.8 1.0
NZ D:LYS37 3.8 12.0 1.0
O3G D:TTP302 3.9 32.8 1.0
CA D:THR16 4.0 12.8 1.0
O5' D:TTP302 4.0 28.3 0.9
CB D:ASP49 4.0 15.7 1.0
O D:HOH402 4.1 27.7 1.0
CG2 D:THR16 4.2 14.2 1.0
O2B D:TTP302 4.3 32.7 1.0
O2A D:TTP302 4.3 24.9 1.0
O3B D:TTP302 4.4 32.9 0.9
CG D:GLU108 4.4 19.1 1.0
NZ D:LYS15 4.7 23.0 1.0
PG D:TTP302 4.7 35.6 0.5
CB D:LYS15 4.7 14.8 1.0
O D:HOH524 4.8 15.8 1.0
C D:LYS15 4.8 19.7 1.0
O1G D:TTP302 4.9 31.3 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 22:50:19 2024

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