Atomistry » Magnesium » PDB 6cu2-6d1v » 6czb
Atomistry »
  Magnesium »
    PDB 6cu2-6d1v »
      6czb »

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

Go back to Magnesium Binding Sites List in 6czb
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy