Magnesium in PDB 6cze: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside
Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside
All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - 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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside, PDB code: 6cze
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)
|
49.69 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.410,
105.000,
153.980,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
26.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside
(pdb code 6cze). 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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside, PDB code: 6cze:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6cze
Go back to
Magnesium Binding Sites List in 6cze
Magnesium binding site 1 out
of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - 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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:28.8
occ:1.00
|
OG1
|
A:THR16
|
2.0
|
35.9
|
1.0
|
O1A
|
A:ITT301
|
2.1
|
32.6
|
1.0
|
O
|
A:HOH434
|
2.1
|
27.3
|
1.0
|
O1B
|
A:ITT301
|
2.2
|
43.8
|
1.0
|
OE1
|
A:GLU108
|
2.2
|
40.4
|
1.0
|
OD2
|
A:ASP49
|
2.4
|
37.7
|
1.0
|
CG
|
A:ASP49
|
3.1
|
36.5
|
1.0
|
PA
|
A:ITT301
|
3.1
|
37.3
|
1.0
|
PB
|
A:ITT301
|
3.2
|
43.7
|
1.0
|
O3A
|
A:ITT301
|
3.2
|
33.9
|
1.0
|
CB
|
A:THR16
|
3.2
|
35.0
|
1.0
|
CD
|
A:GLU108
|
3.2
|
40.0
|
1.0
|
OD1
|
A:ASP49
|
3.6
|
39.8
|
1.0
|
OE2
|
A:GLU108
|
3.6
|
35.1
|
1.0
|
N
|
A:THR16
|
3.7
|
32.0
|
1.0
|
CA
|
A:THR16
|
4.0
|
28.8
|
1.0
|
O2A
|
A:ITT301
|
4.1
|
33.3
|
1.0
|
CB
|
A:ASP49
|
4.2
|
34.2
|
1.0
|
O3B
|
A:ITT301
|
4.2
|
45.8
|
1.0
|
O
|
A:HOH405
|
4.2
|
60.4
|
1.0
|
O2B
|
A:ITT301
|
4.2
|
40.6
|
1.0
|
NZ
|
A:LYS37
|
4.2
|
25.2
|
1.0
|
O
|
A:HOH483
|
4.3
|
42.6
|
1.0
|
O5'
|
A:ITT301
|
4.3
|
37.1
|
0.8
|
CG2
|
A:THR16
|
4.4
|
37.5
|
1.0
|
CB
|
A:LYS15
|
4.4
|
27.6
|
1.0
|
C5'
|
A:ITT301
|
4.4
|
44.5
|
0.9
|
C4'
|
A:ITT301
|
4.4
|
51.8
|
0.5
|
CG
|
A:GLU108
|
4.6
|
35.7
|
1.0
|
C
|
A:LYS15
|
4.6
|
31.4
|
1.0
|
O3'
|
A:ITT301
|
4.6
|
52.8
|
0.7
|
NZ
|
A:LYS15
|
4.7
|
34.3
|
1.0
|
CE
|
A:LYS15
|
4.8
|
34.6
|
1.0
|
CA
|
A:LYS15
|
4.9
|
34.1
|
1.0
|
N
|
A:LYS15
|
5.0
|
41.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6cze
Go back to
Magnesium Binding Sites List in 6cze
Magnesium binding site 2 out
of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - 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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg302
b:36.9
occ:0.95
|
O2B
|
B:ITT301
|
1.9
|
41.7
|
1.0
|
O2A
|
B:ITT301
|
1.9
|
35.8
|
1.0
|
O
|
B:HOH423
|
2.0
|
33.4
|
1.0
|
OG1
|
B:THR16
|
2.1
|
29.7
|
1.0
|
OD2
|
B:ASP49
|
2.3
|
27.7
|
1.0
|
OE1
|
B:GLU108
|
2.4
|
37.4
|
1.0
|
CG
|
B:ASP49
|
3.0
|
33.4
|
1.0
|
PB
|
B:ITT301
|
3.1
|
45.3
|
0.9
|
PA
|
B:ITT301
|
3.2
|
33.8
|
1.0
|
CB
|
B:THR16
|
3.2
|
23.4
|
1.0
|
CD
|
B:GLU108
|
3.3
|
35.6
|
1.0
|
OD1
|
B:ASP49
|
3.4
|
33.6
|
1.0
|
O3A
|
B:ITT301
|
3.4
|
33.2
|
1.0
|
OE2
|
B:GLU108
|
3.5
|
35.6
|
1.0
|
N
|
B:THR16
|
3.8
|
31.0
|
1.0
|
NZ
|
B:LYS37
|
3.8
|
30.2
|
1.0
|
O1B
|
B:ITT301
|
4.0
|
40.2
|
1.0
|
O
|
B:HOH494
|
4.0
|
40.1
|
1.0
|
O5'
|
B:ITT301
|
4.0
|
41.1
|
0.7
|
CA
|
B:THR16
|
4.1
|
28.4
|
1.0
|
CB
|
B:ASP49
|
4.2
|
33.7
|
1.0
|
O1A
|
B:ITT301
|
4.3
|
30.4
|
1.0
|
CG2
|
B:THR16
|
4.3
|
31.9
|
1.0
|
O3B
|
B:ITT301
|
4.3
|
44.1
|
1.0
|
O3'
|
B:ITT301
|
4.6
|
54.0
|
0.7
|
O
|
B:HOH501
|
4.6
|
39.7
|
1.0
|
O2G
|
B:ITT301
|
4.7
|
60.1
|
0.9
|
CG
|
B:GLU108
|
4.7
|
35.1
|
1.0
|
O
|
B:HOH409
|
4.7
|
45.5
|
1.0
|
CB
|
B:LYS15
|
4.8
|
26.4
|
1.0
|
C
|
B:LYS15
|
4.8
|
31.5
|
1.0
|
CE
|
B:LYS15
|
4.9
|
30.2
|
1.0
|
O
|
B:HOH482
|
5.0
|
29.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6cze
Go back to
Magnesium Binding Sites List in 6cze
Magnesium binding site 3 out
of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - 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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg302
b:34.7
occ:1.00
|
O2B
|
C:ITT301
|
2.0
|
42.6
|
1.0
|
OG1
|
C:THR16
|
2.1
|
36.0
|
1.0
|
O
|
C:HOH417
|
2.2
|
38.0
|
1.0
|
OD2
|
C:ASP49
|
2.2
|
38.8
|
1.0
|
O3G
|
C:ITT301
|
2.2
|
36.5
|
1.0
|
OE2
|
C:GLU108
|
2.4
|
36.7
|
1.0
|
PB
|
C:ITT301
|
3.1
|
39.5
|
1.0
|
CG
|
C:ASP49
|
3.1
|
42.7
|
1.0
|
PG
|
C:ITT301
|
3.2
|
47.6
|
0.8
|
CB
|
C:THR16
|
3.2
|
35.6
|
1.0
|
O3B
|
C:ITT301
|
3.3
|
42.5
|
1.0
|
CD
|
C:GLU108
|
3.4
|
38.8
|
1.0
|
OE1
|
C:GLU108
|
3.7
|
40.2
|
1.0
|
N
|
C:THR16
|
3.7
|
41.4
|
1.0
|
OD1
|
C:ASP49
|
3.7
|
45.7
|
1.0
|
O2A
|
C:ITT301
|
3.8
|
56.5
|
1.0
|
O2G
|
C:ITT301
|
4.0
|
51.4
|
0.8
|
CA
|
C:THR16
|
4.0
|
44.0
|
1.0
|
O3A
|
C:ITT301
|
4.0
|
47.3
|
1.0
|
NZ
|
C:LYS15
|
4.0
|
35.9
|
0.2
|
CB
|
C:ASP49
|
4.1
|
33.1
|
1.0
|
O1B
|
C:ITT301
|
4.3
|
38.2
|
1.0
|
PA
|
C:ITT301
|
4.3
|
46.6
|
0.0
|
O
|
C:HOH466
|
4.4
|
52.7
|
1.0
|
CG2
|
C:THR16
|
4.4
|
35.7
|
1.0
|
O1G
|
C:ITT301
|
4.4
|
56.9
|
1.0
|
NZ
|
C:LYS37
|
4.5
|
30.2
|
1.0
|
O1A
|
C:ITT301
|
4.6
|
43.0
|
1.0
|
CB
|
C:LYS15
|
4.6
|
40.1
|
0.8
|
CE
|
C:LYS15
|
4.7
|
32.9
|
0.8
|
C
|
C:LYS15
|
4.7
|
40.8
|
0.2
|
CG
|
C:GLU108
|
4.7
|
36.2
|
1.0
|
C
|
C:LYS15
|
4.7
|
40.5
|
0.8
|
CB
|
C:LYS15
|
4.8
|
44.1
|
0.2
|
O
|
C:HOH435
|
4.8
|
60.2
|
1.0
|
O
|
C:HOH461
|
4.8
|
50.6
|
1.0
|
NZ
|
C:LYS15
|
5.0
|
36.1
|
0.8
|
|
Magnesium binding site 4 out
of 4 in 6cze
Go back to
Magnesium Binding Sites List in 6cze
Magnesium binding site 4 out
of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Inosine Triphosphate (Itp) - 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 Inosine Triphosphate (Itp) - Promiscuous Binding Mode with Disordered Nucleoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:38.7
occ:0.82
|
OE1
|
D:GLU108
|
1.9
|
29.0
|
1.0
|
O1B
|
D:ITT301
|
2.0
|
42.7
|
1.0
|
OG1
|
D:THR16
|
2.1
|
35.9
|
1.0
|
OD2
|
D:ASP49
|
2.2
|
38.3
|
1.0
|
O1A
|
D:ITT301
|
2.2
|
42.1
|
1.0
|
O
|
D:HOH426
|
2.3
|
38.4
|
1.0
|
CD
|
D:GLU108
|
2.9
|
35.2
|
1.0
|
CG
|
D:ASP49
|
3.0
|
36.9
|
1.0
|
OE2
|
D:GLU108
|
3.3
|
34.3
|
1.0
|
PB
|
D:ITT301
|
3.4
|
42.9
|
1.0
|
CB
|
D:THR16
|
3.4
|
39.7
|
1.0
|
PA
|
D:ITT301
|
3.5
|
40.8
|
1.0
|
OD1
|
D:ASP49
|
3.6
|
38.0
|
1.0
|
NZ
|
D:LYS37
|
3.7
|
30.4
|
1.0
|
O3A
|
D:ITT301
|
3.8
|
49.9
|
1.0
|
N
|
D:THR16
|
3.8
|
40.4
|
1.0
|
CB
|
D:ASP49
|
4.1
|
38.1
|
1.0
|
CA
|
D:THR16
|
4.1
|
39.1
|
1.0
|
O2B
|
D:ITT301
|
4.2
|
49.0
|
0.8
|
CG
|
D:GLU108
|
4.3
|
33.0
|
1.0
|
O
|
D:HOH401
|
4.3
|
45.5
|
1.0
|
O3G
|
D:ITT301
|
4.4
|
58.3
|
1.0
|
O2A
|
D:ITT301
|
4.4
|
35.0
|
1.0
|
CG2
|
D:THR16
|
4.5
|
33.8
|
1.0
|
O3'
|
D:ITT301
|
4.6
|
71.4
|
0.7
|
O5'
|
D:ITT301
|
4.6
|
52.0
|
0.8
|
O3B
|
D:ITT301
|
4.6
|
53.3
|
0.7
|
CB
|
D:LYS15
|
4.6
|
34.6
|
1.0
|
NZ
|
D:LYS15
|
4.7
|
32.9
|
1.0
|
C4'
|
D:ITT301
|
4.8
|
68.1
|
0.6
|
C
|
D:LYS15
|
4.8
|
39.5
|
1.0
|
CE
|
D:LYS37
|
4.8
|
31.3
|
1.0
|
CE
|
D:LYS15
|
4.8
|
32.1
|
1.0
|
O1G
|
D:ITT301
|
4.9
|
56.7
|
0.7
|
C5'
|
D:ITT301
|
4.9
|
59.8
|
0.7
|
O
|
D:HOH446
|
4.9
|
37.9
|
1.0
|
PG
|
D:ITT301
|
4.9
|
58.4
|
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 22:50:52 2024
|