Magnesium in PDB 6za5: M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+
Enzymatic activity of M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+
All present enzymatic activity of M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+:
4.2.99.21;
5.4.4.2;
5.4.99.5;
Protein crystallography data
The structure of M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+, PDB code: 6za5
was solved by
M.Mori,
S.Villa,
F.Meneghetti,
M.Bellinzoni,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
154.83 /
2.11
|
Space group
|
I 4 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
193.973,
193.973,
257.034,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.5 /
21.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+
(pdb code 6za5). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+, PDB code: 6za5:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6za5
Go back to
Magnesium Binding Sites List in 6za5
Magnesium binding site 1 out
of 4 in the M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg518
b:44.0
occ:1.00
|
O
|
A:HOH730
|
2.0
|
38.8
|
1.0
|
O
|
A:HOH701
|
2.1
|
33.3
|
1.0
|
O1
|
A:SO4501
|
2.1
|
39.6
|
0.8
|
O
|
A:HOH799
|
2.2
|
48.2
|
1.0
|
O
|
A:HOH692
|
2.2
|
40.0
|
1.0
|
O
|
A:GLY421
|
2.3
|
36.2
|
1.0
|
C
|
A:GLY421
|
3.3
|
35.6
|
1.0
|
S
|
A:SO4501
|
3.3
|
39.1
|
0.8
|
O3
|
A:SO4501
|
3.5
|
39.5
|
0.8
|
CA
|
A:GLY421
|
3.7
|
34.8
|
1.0
|
O
|
A:HOH605
|
3.9
|
41.5
|
1.0
|
N
|
A:GLY421
|
3.9
|
33.9
|
1.0
|
O
|
A:HOH675
|
4.0
|
38.8
|
1.0
|
O
|
A:HOH892
|
4.1
|
52.6
|
1.0
|
O2
|
A:SO4501
|
4.2
|
37.8
|
0.8
|
O4
|
A:SO4501
|
4.3
|
39.1
|
0.8
|
OE1
|
A:GLU431
|
4.3
|
41.6
|
1.0
|
OE2
|
A:GLU431
|
4.4
|
42.0
|
1.0
|
N
|
A:ILE422
|
4.5
|
35.2
|
1.0
|
OE2
|
A:GLU434
|
4.6
|
49.5
|
1.0
|
OE2
|
A:GLU294
|
4.7
|
52.3
|
1.0
|
O
|
A:HOH621
|
4.7
|
45.9
|
1.0
|
OE1
|
A:GLU434
|
4.7
|
49.0
|
1.0
|
CD
|
A:GLU431
|
4.8
|
40.9
|
1.0
|
CA
|
A:ILE422
|
5.0
|
35.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6za5
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Magnesium Binding Sites List in 6za5
Magnesium binding site 2 out
of 4 in the M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg519
b:36.3
occ:1.00
|
OD1
|
A:ASP311
|
2.0
|
36.2
|
1.0
|
O
|
A:HOH620
|
2.0
|
33.4
|
1.0
|
O
|
C:HOH618
|
2.1
|
36.2
|
1.0
|
O
|
A:HOH636
|
2.2
|
34.6
|
1.0
|
O
|
C:HOH640
|
2.2
|
30.3
|
1.0
|
O
|
C:HOH631
|
2.2
|
35.7
|
1.0
|
CG
|
A:ASP311
|
3.0
|
36.8
|
1.0
|
OD2
|
A:ASP311
|
3.3
|
39.2
|
1.0
|
O
|
A:GLU307
|
3.9
|
33.6
|
1.0
|
OE1
|
C:GLU213
|
4.2
|
45.4
|
1.0
|
O
|
C:HOH609
|
4.2
|
34.5
|
1.0
|
O
|
C:GLY412
|
4.3
|
36.8
|
1.0
|
O
|
C:HOH673
|
4.4
|
37.0
|
1.0
|
O
|
A:HOH898
|
4.4
|
45.5
|
1.0
|
CB
|
A:ASP311
|
4.4
|
33.8
|
1.0
|
CB
|
C:GLU213
|
4.4
|
39.0
|
1.0
|
O
|
A:HOH877
|
4.5
|
47.9
|
1.0
|
O
|
C:VAL214
|
4.5
|
40.4
|
1.0
|
CA
|
C:ARG413
|
4.5
|
34.3
|
1.0
|
N
|
C:THR414
|
4.5
|
33.0
|
1.0
|
O
|
C:THR414
|
4.6
|
33.4
|
1.0
|
CG
|
C:ARG413
|
4.6
|
36.7
|
1.0
|
CA
|
A:ASP311
|
4.7
|
33.6
|
1.0
|
N
|
A:ASP311
|
4.7
|
33.4
|
1.0
|
CG
|
C:GLU213
|
4.8
|
42.1
|
1.0
|
C
|
A:GLU307
|
4.9
|
33.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6za5
Go back to
Magnesium Binding Sites List in 6za5
Magnesium binding site 3 out
of 4 in the M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:55.6
occ:1.00
|
O
|
B:HOH608
|
2.0
|
40.1
|
1.0
|
O
|
B:HOH653
|
2.0
|
41.2
|
1.0
|
OE2
|
B:GLU297
|
2.1
|
50.2
|
1.0
|
O2'
|
B:SAL502
|
2.3
|
57.2
|
1.0
|
OE2
|
B:GLU434
|
2.4
|
45.0
|
1.0
|
O1'
|
B:SAL502
|
2.5
|
56.7
|
1.0
|
C1'
|
B:SAL502
|
2.7
|
57.7
|
1.0
|
CD
|
B:GLU297
|
3.0
|
50.5
|
1.0
|
CD
|
B:GLU434
|
3.1
|
46.2
|
1.0
|
OE1
|
B:GLU434
|
3.1
|
45.9
|
1.0
|
OE1
|
B:GLU297
|
3.2
|
52.7
|
1.0
|
OG1
|
B:THR271
|
4.0
|
38.6
|
1.0
|
N
|
B:GLY421
|
4.1
|
39.3
|
1.0
|
N
|
B:GLY270
|
4.2
|
37.9
|
1.0
|
NZ
|
B:LYS293
|
4.2
|
63.1
|
1.0
|
C1
|
B:SAL502
|
4.2
|
59.0
|
1.0
|
O
|
B:GLY421
|
4.2
|
41.7
|
1.0
|
OE1
|
B:GLU294
|
4.3
|
50.5
|
1.0
|
N
|
B:THR271
|
4.3
|
37.6
|
1.0
|
CB
|
B:THR271
|
4.3
|
37.7
|
1.0
|
CA
|
B:GLY270
|
4.3
|
38.0
|
1.0
|
O
|
B:HOH637
|
4.4
|
41.6
|
1.0
|
CG
|
B:GLU297
|
4.4
|
45.0
|
1.0
|
O
|
B:HOH647
|
4.4
|
60.3
|
1.0
|
CG
|
B:GLU434
|
4.5
|
42.9
|
1.0
|
OE1
|
B:GLU431
|
4.6
|
52.0
|
1.0
|
C
|
B:GLY270
|
4.6
|
38.5
|
1.0
|
CA
|
B:GLY421
|
4.7
|
39.5
|
1.0
|
NZ
|
B:LYS438
|
4.7
|
45.9
|
1.0
|
C
|
B:GLY421
|
4.9
|
40.6
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6za5
Go back to
Magnesium Binding Sites List in 6za5
Magnesium binding site 4 out
of 4 in the M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of M. Tuberculosis Salicylate Synthase Mbti in Complex with Salicylate and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg501
b:50.4
occ:1.00
|
O
|
D:HOH609
|
2.0
|
47.8
|
1.0
|
O
|
D:HOH610
|
2.1
|
45.7
|
1.0
|
OE1
|
D:GLU297
|
2.2
|
59.6
|
1.0
|
OE2
|
D:GLU434
|
2.3
|
56.4
|
1.0
|
O1'
|
D:SAL502
|
2.3
|
52.3
|
1.0
|
O2'
|
D:SAL502
|
2.5
|
52.4
|
1.0
|
C1'
|
D:SAL502
|
2.8
|
52.5
|
1.0
|
CD
|
D:GLU297
|
3.1
|
59.3
|
1.0
|
CD
|
D:GLU434
|
3.1
|
54.9
|
1.0
|
OE1
|
D:GLU434
|
3.1
|
56.0
|
1.0
|
OE2
|
D:GLU297
|
3.2
|
61.7
|
1.0
|
OG1
|
D:THR271
|
4.1
|
43.6
|
1.0
|
N
|
D:GLY421
|
4.1
|
51.1
|
1.0
|
N
|
D:GLY270
|
4.2
|
41.6
|
1.0
|
NZ
|
D:LYS293
|
4.2
|
63.9
|
1.0
|
O
|
D:GLY421
|
4.2
|
53.6
|
1.0
|
O
|
D:HOH618
|
4.2
|
42.0
|
1.0
|
N
|
D:THR271
|
4.3
|
40.7
|
1.0
|
C1
|
D:SAL502
|
4.3
|
52.8
|
1.0
|
OE1
|
D:GLU294
|
4.3
|
56.2
|
1.0
|
CA
|
D:GLY270
|
4.3
|
41.5
|
1.0
|
CB
|
D:THR271
|
4.4
|
42.4
|
1.0
|
CG
|
D:GLU297
|
4.5
|
53.3
|
1.0
|
OE2
|
D:GLU431
|
4.5
|
63.9
|
1.0
|
CG
|
D:GLU434
|
4.5
|
49.6
|
1.0
|
O
|
D:HOH675
|
4.5
|
55.5
|
1.0
|
C
|
D:GLY270
|
4.6
|
41.3
|
1.0
|
CA
|
D:GLY421
|
4.6
|
52.0
|
1.0
|
NZ
|
D:LYS438
|
4.7
|
51.6
|
1.0
|
C
|
D:GLY421
|
4.9
|
53.4
|
1.0
|
|
Reference:
M.Mori,
G.Stelitano,
A.Gelain,
E.Pini,
L.R.Chiarelli,
J.C.Sammartino,
G.Poli,
T.Tuccinardi,
G.Beretta,
A.Porta,
M.Bellinzoni,
S.Villa,
F.Meneghetti.
Shedding X-Ray Light on the Role of Magnesium in the Activity Ofmycobacterium Tuberculosissalicylate Synthase (Mbti) For Drug Design. J.Med.Chem. V. 63 7066 2020.
ISSN: ISSN 0022-2623
PubMed: 32530281
DOI: 10.1021/ACS.JMEDCHEM.0C00373
Page generated: Wed Oct 2 02:14:08 2024
|