Atomistry » Magnesium » PDB 6dw7-6e8s » 6e06
Atomistry »
  Magnesium »
    PDB 6dw7-6e8s »
      6e06 »

Magnesium in PDB 6e06: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant):
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant), PDB code: 6e06 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) 49.96 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.680, 105.700, 153.260, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 28.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) (pdb code 6e06). 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 Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant), PDB code: 6e06:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6e06

Go back to Magnesium Binding Sites List in 6e06
Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)


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 Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:22.1
occ:0.56
O A:HOH401 1.9 33.9 1.0
O1B A:CTP301 2.0 17.1 0.8
OG1 A:THR16 2.1 50.1 1.0
O1G A:CTP301 2.1 17.1 0.8
OE1 A:GLU108 2.2 71.7 1.0
OD2 A:ASP49 2.4 65.3 1.0
CG A:ASP49 3.0 57.1 1.0
PG A:CTP301 3.0 18.0 0.8
PB A:CTP301 3.2 17.1 0.8
CD A:GLU108 3.2 71.8 1.0
OD1 A:ASP49 3.2 57.9 1.0
O2G A:CTP301 3.3 19.6 0.8
CB A:THR16 3.4 42.3 1.0
O3B A:CTP301 3.5 35.4 0.8
OE2 A:GLU108 3.6 70.5 1.0
N A:THR16 3.8 53.6 1.0
CA A:THR16 4.1 43.9 1.0
O2B A:CTP301 4.1 25.1 0.8
O2A A:CTP301 4.2 39.1 0.8
NZ A:LYS37 4.2 35.6 1.0
CB A:ASP49 4.3 50.9 1.0
CG2 A:THR16 4.4 39.2 1.0
O3G A:CTP301 4.4 41.3 0.8
O3A A:CTP301 4.4 34.3 0.8
CG A:GLU108 4.5 67.7 1.0
CB A:LYS15 4.5 43.1 1.0
O1A A:CTP301 4.6 17.1 0.8
NZ A:LYS15 4.6 50.6 1.0
CE A:LYS15 4.6 47.6 1.0
PA A:CTP301 4.6 31.9 0.8
C A:LYS15 4.8 59.8 1.0

Magnesium binding site 2 out of 4 in 6e06

Go back to Magnesium Binding Sites List in 6e06
Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)


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 Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:38.7
occ:0.69
O3G B:CTP301 1.8 43.6 0.9
O B:HOH412 2.0 60.3 1.0
OG1 B:THR16 2.1 60.1 1.0
O2B B:CTP301 2.2 35.3 0.9
OE1 B:GLU108 2.3 52.1 1.0
OD2 B:ASP49 2.5 44.9 1.0
CG B:ASP49 3.0 44.9 1.0
PG B:CTP301 3.0 24.9 0.9
PB B:CTP301 3.3 17.1 0.9
CD B:GLU108 3.3 45.6 1.0
OD1 B:ASP49 3.4 44.3 1.0
CB B:THR16 3.5 46.3 1.0
NZ B:LYS37 3.5 47.0 1.0
O2G B:CTP301 3.6 30.3 0.9
O3B B:CTP301 3.6 36.3 0.9
OE2 B:GLU108 3.6 51.5 1.0
O3A B:CTP301 4.0 33.3 0.9
CB B:ASP49 4.0 44.3 1.0
N B:THR16 4.1 45.9 1.0
O1G B:CTP301 4.2 41.3 0.9
O2A B:CTP301 4.2 30.5 0.9
CA B:THR16 4.3 46.8 1.0
O1A B:CTP301 4.4 17.1 0.9
CG2 B:THR16 4.4 40.4 1.0
PA B:CTP301 4.5 38.6 0.9
NZ B:LYS15 4.5 56.6 1.0
O1B B:CTP301 4.6 33.0 0.9
CG B:GLU108 4.6 34.2 1.0
CE B:LYS15 4.8 50.6 1.0
CB B:LYS15 4.8 34.9 1.0
CE B:LYS37 4.8 46.6 1.0
O B:HOH425 5.0 45.2 1.0

Magnesium binding site 3 out of 4 in 6e06

Go back to Magnesium Binding Sites List in 6e06
Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)


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 Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:28.1
occ:0.65
O3G C:CTP301 1.9 37.5 0.8
OD2 C:ASP49 2.0 55.3 1.0
OE1 C:GLU108 2.0 79.4 1.0
O2B C:CTP301 2.0 17.1 0.8
OG1 C:THR16 2.7 61.3 1.0
O C:HOH407 3.0 52.0 1.0
CD C:GLU108 3.0 83.0 1.0
PG C:CTP301 3.1 36.7 0.8
CG C:ASP49 3.2 57.1 1.0
NZ C:LYS37 3.2 49.9 1.0
PB C:CTP301 3.3 17.1 0.8
OE2 C:GLU108 3.5 82.8 1.0
O3B C:CTP301 3.6 38.8 0.8
O1G C:CTP301 3.6 38.6 0.8
O C:HOH414 3.6 51.4 1.0
OD1 C:ASP49 3.9 64.4 1.0
CG C:GLU108 4.1 82.5 1.0
CB C:THR16 4.1 61.1 1.0
CE C:LYS15 4.3 39.1 1.0
CB C:ASP49 4.3 58.2 1.0
O3A C:CTP301 4.3 35.0 0.8
O2G C:CTP301 4.4 37.4 0.8
O1B C:CTP301 4.4 34.9 0.8
CE C:LYS37 4.4 50.7 1.0
N C:THR16 4.4 79.9 1.0
NZ C:LYS15 4.5 39.0 1.0
CB C:LYS15 4.6 50.4 1.0
CA C:THR16 4.8 72.5 1.0
O2A C:CTP301 4.9 34.1 0.8
CG2 C:THR16 4.9 49.4 1.0
O C:GLY109 4.9 61.7 1.0
O1A C:CTP301 5.0 30.6 0.8
PA C:CTP301 5.0 36.1 0.8

Magnesium binding site 4 out of 4 in 6e06

Go back to Magnesium Binding Sites List in 6e06
Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant)


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 Cytidine Triphosphate Solved By Precipitant-Ligand Exchange (Crystals Grown in Citrate Precipitant) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:17.1
occ:0.73
O1B D:CTP301 1.9 23.2 0.8
OG1 D:THR16 2.0 49.4 1.0
OD2 D:ASP49 2.0 43.3 1.0
OE1 D:GLU108 2.1 30.9 1.0
O D:HOH406 2.2 55.0 1.0
O1G D:CTP301 2.3 29.9 0.8
PB D:CTP301 3.0 17.1 0.8
CG D:ASP49 3.1 41.1 1.0
CD D:GLU108 3.1 27.9 1.0
O3B D:CTP301 3.2 23.7 0.8
CB D:THR16 3.3 37.2 1.0
PG D:CTP301 3.3 21.9 0.8
OE2 D:GLU108 3.4 32.8 1.0
OD1 D:ASP49 3.5 49.7 1.0
N D:THR16 3.8 37.3 1.0
O2A D:CTP301 3.9 29.1 0.8
CA D:THR16 4.0 38.3 1.0
NZ D:LYS15 4.1 62.3 1.0
NZ D:LYS37 4.1 40.1 1.0
O2B D:CTP301 4.1 17.1 0.8
O3A D:CTP301 4.2 24.8 0.8
CG2 D:THR16 4.2 35.6 1.0
O2G D:CTP301 4.2 41.7 0.8
CB D:ASP49 4.3 35.8 1.0
O3G D:CTP301 4.3 29.9 0.8
PA D:CTP301 4.4 35.6 0.8
CE D:LYS37 4.5 37.3 1.0
CG D:GLU108 4.6 22.1 1.0
O1A D:CTP301 4.6 29.6 0.8
CB D:LYS15 4.8 47.1 1.0
C D:LYS15 4.8 53.8 1.0

Reference:

A.P.Thompson, K.L.Wegener, G.W.Booker, S.W.Polyak, J.B.Bruning. Precipitant-Ligand Exchange Technique Reveals the Adp Binding Mode in Mycobacterium Tuberculosis Dethiobiotin Synthetase. Acta Crystallogr D Struct V. 74 965 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289406
DOI: 10.1107/S2059798318010136
Page generated: Mon Sep 30 23:45:01 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy