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Magnesium in PDB 6cvf: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Diphosphate

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Diphosphate

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Diphosphate:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Diphosphate, PDB code: 6cvf was solved by A.P.Thompson, J.B.Bruning, K.L.Wegener, S.W.Polyak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.58 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.880, 104.750, 153.750, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Diphosphate (pdb code 6cvf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Diphosphate, PDB code: 6cvf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6cvf

Go back to Magnesium Binding Sites List in 6cvf
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Diphosphate


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 Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:18.5
occ:0.59
 O A:HOH547 1.9 20.9 1.0
O1B A:CDP301 2.2 21.4 1.0
OD2 A:ASP49 2.3 20.4 1.0
O A:HOH419 2.3 22.3 1.0
OG1 A:THR16 2.3 16.1 1.0
OE1 A:GLU108 2.6 21.0 1.0
CG A:ASP49 3.0 17.0 1.0
O A:HOH542 3.2 29.1 1.0
OD1 A:ASP49 3.3 17.8 1.0
PB A:CDP301 3.4 21.1 1.0
O3B A:CDP301 3.5 20.1 1.0
CB A:THR16 3.7 17.1 1.0
CD A:GLU108 3.8 14.8 1.0
O A:HOH522 3.8 24.3 1.0
O A:HOH534 3.9 32.0 1.0
O A:HOH528 3.9 21.3 1.0
NZ A:LYS37 4.0 14.2 1.0
O2A A:CDP301 4.1 20.0 1.0
N A:THR16 4.1 13.3 1.0
CB A:ASP49 4.3 13.6 1.0
OE2 A:GLU108 4.4 20.0 1.0
O2B A:CDP301 4.4 23.5 1.0
CE A:LYS15 4.4 20.6 1.0
CA A:THR16 4.4 18.2 1.0
O3A A:CDP301 4.5 22.0 1.0
O A:HOH596 4.5 29.1 1.0
CB A:LYS15 4.5 14.6 1.0
O1A A:CDP301 4.6 21.0 1.0
PA A:CDP301 4.6 18.5 1.0
CG2 A:THR16 4.7 13.0 1.0
O A:HOH480 4.7 27.9 1.0
NZ A:LYS15 5.0 19.3 1.0
CG A:GLU108 5.0 14.6 1.0

Magnesium binding site 2 out of 3 in 6cvf

Go back to Magnesium Binding Sites List in 6cvf
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Diphosphate


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 Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:21.7
occ:0.35
 O C:HOH519 1.8 19.9 1.0
OD2 C:ASP49 1.9 18.4 1.0
OE2 C:GLU108 2.0 19.8 1.0
OG1 C:THR16 2.5 20.8 1.0
O2B C:CDP301 2.7 21.8 1.0
CG C:ASP49 3.0 20.7 1.0
O C:HOH480 3.0 28.4 1.0
CD C:GLU108 3.2 18.7 1.0
NZ C:LYS37 3.3 15.8 1.0
OD1 C:ASP49 3.6 20.9 1.0
O C:HOH558 3.7 19.3 1.0
OE1 C:GLU108 3.8 21.9 1.0
CB C:THR16 3.9 18.5 1.0
PB C:CDP301 3.9 24.9 1.0
CB C:ASP49 3.9 16.8 1.0
O3B C:CDP301 4.0 22.5 1.0
CE C:LYS15 4.1 13.8 1.0
N C:THR16 4.1 18.9 1.0
CG C:GLU108 4.2 17.7 1.0
CE C:LYS37 4.4 16.4 1.0
CA C:THR16 4.4 20.5 1.0
CB C:LYS15 4.4 20.2 1.0
O C:HOH431 4.5 30.4 1.0
O C:HOH563 4.5 31.4 1.0
NZ C:LYS15 4.7 22.7 1.0
CG2 C:THR16 4.7 15.7 1.0
O2A C:CDP301 4.8 22.7 1.0
O1B C:CDP301 4.9 21.5 1.0
O C:GLY109 4.9 16.0 1.0

Magnesium binding site 3 out of 3 in 6cvf

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Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Diphosphate


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 Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:36.2
occ:1.00
 O1B D:CDP301 2.2 34.8 1.0
OD2 D:ASP49 2.4 26.1 1.0
O D:HOH415 2.7 46.8 1.0
OE1 D:GLU108 2.7 28.6 1.0
O D:HOH427 2.9 40.5 1.0
O3B D:CDP301 3.2 31.2 1.0
PB D:CDP301 3.2 37.0 1.0
OG1 D:THR16 3.2 24.9 1.0
O D:HOH533 3.4 35.8 1.0
CG D:ASP49 3.5 24.6 1.0
NZ D:LYS37 3.6 20.9 1.0
CD D:GLU108 3.9 22.5 1.0
OD1 D:ASP49 3.9 25.4 1.0
O2B D:CDP301 4.0 34.1 1.0
NZ D:LYS15 4.0 35.1 1.0
CE D:LYS15 4.2 27.3 1.0
O1A D:CDP301 4.5 32.7 1.0
O3A D:CDP301 4.5 35.3 1.0
CB D:THR16 4.5 24.5 1.0
OE2 D:GLU108 4.7 24.9 1.0
CE D:LYS37 4.8 19.9 1.0
CG D:GLU108 4.8 22.9 1.0
CB D:ASP49 4.8 22.9 1.0
N D:THR16 4.8 24.9 1.0
CB D:LYS15 4.9 21.2 1.0
O D:GLY109 4.9 24.6 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 22:46:30 2024

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