Iodine in PDB 7nnw: Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.
Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.
All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.:
2.1.3.3;
Protein crystallography data
The structure of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate., PDB code: 7nnw
was solved by
V.Mendes,
P.Gupta,
A.Burgess,
V.Sebastian-Perez,
E.Cattermole,
C.Meghir,
T.L.Blundell,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
53.80 /
1.78
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.802,
143.512,
97.524,
90,
117.69,
90
|
R / Rfree (%)
|
18.1 /
20.6
|
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.
(pdb code 7nnw). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the
Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate., PDB code: 7nnw:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
Iodine binding site 1 out
of 6 in 7nnw
Go back to
Iodine Binding Sites List in 7nnw
Iodine binding site 1 out
of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I402
b:106.0
occ:1.00
|
I11
|
B:98T402
|
0.0
|
106.0
|
1.0
|
C10
|
B:98T402
|
2.1
|
75.4
|
1.0
|
C08
|
B:98T402
|
3.1
|
71.4
|
1.0
|
C12
|
B:98T402
|
3.2
|
66.3
|
1.0
|
O09
|
B:98T402
|
3.2
|
75.9
|
1.0
|
CD1
|
B:ILE45
|
3.8
|
36.7
|
1.0
|
CG
|
B:LEU78
|
3.9
|
63.8
|
1.0
|
CG2
|
A:THR51
|
4.1
|
46.4
|
1.0
|
CD1
|
B:LEU78
|
4.2
|
54.0
|
1.0
|
CG2
|
B:THR87
|
4.3
|
48.3
|
1.0
|
CG1
|
B:ILE45
|
4.4
|
32.2
|
1.0
|
C07
|
B:98T402
|
4.4
|
68.9
|
1.0
|
CG2
|
B:ILE45
|
4.5
|
33.9
|
1.0
|
C05
|
B:98T402
|
4.5
|
55.7
|
1.0
|
CE1
|
A:PHE55
|
4.6
|
33.0
|
1.0
|
CD2
|
B:LEU78
|
4.7
|
68.6
|
1.0
|
CG1
|
B:VAL71
|
4.8
|
41.4
|
1.0
|
CG2
|
B:VAL71
|
4.9
|
43.1
|
1.0
|
CB
|
B:LEU78
|
4.9
|
67.7
|
1.0
|
CD1
|
B:LEU91
|
4.9
|
40.3
|
1.0
|
CD2
|
B:LEU91
|
5.0
|
40.3
|
1.0
|
C06
|
B:98T402
|
5.0
|
65.6
|
1.0
|
|
Iodine binding site 2 out
of 6 in 7nnw
Go back to
Iodine Binding Sites List in 7nnw
Iodine binding site 2 out
of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:I703
b:76.1
occ:1.00
|
I11
|
C:98T703
|
0.0
|
76.1
|
1.0
|
C10
|
C:98T703
|
2.1
|
43.6
|
1.0
|
O
|
C:HOH991
|
2.9
|
53.3
|
1.0
|
C08
|
C:98T703
|
3.0
|
52.8
|
1.0
|
O09
|
C:98T703
|
3.1
|
60.0
|
1.0
|
C12
|
C:98T703
|
3.1
|
41.2
|
1.0
|
CD2
|
A:LEU78
|
3.8
|
60.2
|
1.0
|
CD1
|
A:ILE45
|
3.8
|
32.0
|
1.0
|
CG1
|
A:ILE45
|
3.9
|
32.2
|
1.0
|
C07
|
C:98T703
|
4.3
|
51.4
|
1.0
|
CG2
|
A:VAL71
|
4.3
|
32.5
|
1.0
|
CG1
|
A:VAL71
|
4.4
|
40.8
|
1.0
|
CG2
|
A:ILE45
|
4.4
|
29.6
|
1.0
|
CE1
|
C:PHE55
|
4.4
|
41.0
|
1.0
|
C05
|
C:98T703
|
4.4
|
39.4
|
1.0
|
CD1
|
A:LEU78
|
4.5
|
50.3
|
1.0
|
CB
|
A:VAL71
|
4.5
|
34.2
|
1.0
|
CG
|
A:LEU78
|
4.5
|
61.9
|
1.0
|
CG2
|
C:THR51
|
4.5
|
37.4
|
1.0
|
CD1
|
A:LEU91
|
4.6
|
29.6
|
1.0
|
CG2
|
A:THR87
|
4.6
|
35.4
|
1.0
|
CD2
|
A:LEU91
|
4.7
|
33.3
|
1.0
|
CB
|
A:ILE45
|
4.8
|
28.1
|
1.0
|
C06
|
C:98T703
|
4.9
|
52.8
|
1.0
|
CZ
|
C:PHE55
|
4.9
|
36.5
|
1.0
|
CG
|
A:LEU91
|
5.0
|
33.8
|
1.0
|
|
Iodine binding site 3 out
of 6 in 7nnw
Go back to
Iodine Binding Sites List in 7nnw
Iodine binding site 3 out
of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:I704
b:94.6
occ:1.00
|
I11
|
C:98T704
|
0.0
|
94.6
|
1.0
|
C10
|
C:98T704
|
2.1
|
55.9
|
1.0
|
C08
|
C:98T704
|
3.0
|
60.2
|
1.0
|
C12
|
C:98T704
|
3.1
|
50.5
|
1.0
|
O09
|
C:98T704
|
3.2
|
59.4
|
1.0
|
CD1
|
C:LEU78
|
3.6
|
60.3
|
1.0
|
CD1
|
C:ILE45
|
3.8
|
35.2
|
1.0
|
CG1
|
C:ILE45
|
4.1
|
29.7
|
1.0
|
CG2
|
B:THR51
|
4.2
|
49.7
|
1.0
|
CE1
|
B:PHE55
|
4.3
|
48.8
|
1.0
|
CG2
|
C:ILE45
|
4.3
|
33.4
|
1.0
|
CD2
|
C:LEU78
|
4.3
|
50.5
|
1.0
|
CG2
|
C:VAL71
|
4.3
|
38.8
|
1.0
|
C07
|
C:98T704
|
4.3
|
54.8
|
1.0
|
CG
|
C:LEU78
|
4.4
|
52.2
|
1.0
|
C05
|
C:98T704
|
4.4
|
49.4
|
1.0
|
CD2
|
C:LEU91
|
4.5
|
41.9
|
1.0
|
CD1
|
C:LEU91
|
4.5
|
37.3
|
1.0
|
CG2
|
C:THR87
|
4.6
|
43.4
|
1.0
|
CZ
|
B:PHE55
|
4.7
|
41.6
|
1.0
|
CG1
|
C:VAL71
|
4.8
|
41.9
|
1.0
|
CB
|
C:VAL71
|
4.8
|
36.4
|
1.0
|
CG
|
C:LEU91
|
4.8
|
37.0
|
1.0
|
CB
|
C:ILE45
|
4.9
|
31.6
|
1.0
|
C06
|
C:98T704
|
4.9
|
56.9
|
1.0
|
|
Iodine binding site 4 out
of 6 in 7nnw
Go back to
Iodine Binding Sites List in 7nnw
Iodine binding site 4 out
of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I502
b:72.5
occ:1.00
|
I11
|
D:98T502
|
0.0
|
72.5
|
1.0
|
C10
|
D:98T502
|
2.1
|
47.5
|
1.0
|
C08
|
D:98T502
|
3.0
|
53.0
|
1.0
|
O09
|
D:98T502
|
3.1
|
52.9
|
1.0
|
C12
|
D:98T502
|
3.2
|
45.7
|
1.0
|
CD1
|
E:ILE45
|
3.6
|
31.8
|
1.0
|
CD2
|
E:LEU78
|
3.9
|
61.4
|
1.0
|
CG1
|
E:ILE45
|
3.9
|
30.9
|
1.0
|
C07
|
D:98T502
|
4.3
|
51.7
|
1.0
|
CG2
|
E:VAL71
|
4.3
|
36.7
|
1.0
|
CD1
|
E:LEU78
|
4.4
|
54.9
|
1.0
|
CG1
|
E:VAL71
|
4.4
|
39.8
|
1.0
|
CG
|
E:LEU78
|
4.4
|
59.2
|
1.0
|
CG2
|
D:THR51
|
4.5
|
42.3
|
1.0
|
CE1
|
D:PHE55
|
4.5
|
36.5
|
1.0
|
C05
|
D:98T502
|
4.5
|
43.8
|
1.0
|
CG2
|
E:ILE45
|
4.5
|
27.5
|
1.0
|
CD1
|
E:LEU91
|
4.5
|
35.4
|
1.0
|
CB
|
E:VAL71
|
4.6
|
36.6
|
1.0
|
CG2
|
E:THR87
|
4.7
|
42.4
|
1.0
|
CD2
|
E:LEU91
|
4.8
|
36.3
|
1.0
|
CB
|
E:ILE45
|
4.9
|
28.3
|
1.0
|
C06
|
D:98T502
|
4.9
|
47.5
|
1.0
|
CZ
|
D:PHE55
|
4.9
|
31.2
|
1.0
|
CG
|
E:LEU91
|
5.0
|
32.7
|
1.0
|
|
Iodine binding site 5 out
of 6 in 7nnw
Go back to
Iodine Binding Sites List in 7nnw
Iodine binding site 5 out
of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I503
b:101.5
occ:1.00
|
I11
|
D:98T503
|
0.0
|
101.5
|
1.0
|
C10
|
D:98T503
|
2.1
|
57.3
|
1.0
|
O
|
D:HOH805
|
2.8
|
52.2
|
1.0
|
C08
|
D:98T503
|
3.0
|
60.0
|
1.0
|
C12
|
D:98T503
|
3.0
|
48.2
|
1.0
|
O09
|
D:98T503
|
3.1
|
52.2
|
1.0
|
CD1
|
D:ILE45
|
3.7
|
40.3
|
1.0
|
CD1
|
D:LEU78
|
3.8
|
61.5
|
1.0
|
CG1
|
D:ILE45
|
4.0
|
40.3
|
1.0
|
CG2
|
D:THR87
|
4.3
|
47.3
|
1.0
|
CD2
|
D:LEU91
|
4.3
|
38.0
|
1.0
|
C07
|
D:98T503
|
4.3
|
54.2
|
1.0
|
C05
|
D:98T503
|
4.4
|
40.0
|
1.0
|
CG2
|
D:VAL71
|
4.4
|
40.1
|
1.0
|
CD1
|
D:LEU91
|
4.4
|
33.8
|
1.0
|
CG2
|
F:THR51
|
4.5
|
44.1
|
1.0
|
CE1
|
F:PHE55
|
4.5
|
41.8
|
1.0
|
CG2
|
D:ILE45
|
4.5
|
36.9
|
1.0
|
CG
|
D:LEU91
|
4.7
|
36.5
|
1.0
|
CG
|
D:LEU78
|
4.8
|
56.2
|
1.0
|
CB
|
D:VAL71
|
4.8
|
44.0
|
1.0
|
C06
|
D:98T503
|
4.8
|
54.9
|
1.0
|
CG1
|
D:VAL71
|
4.9
|
46.7
|
1.0
|
CB
|
D:ILE45
|
4.9
|
34.6
|
1.0
|
CD2
|
D:LEU78
|
4.9
|
59.9
|
1.0
|
|
Iodine binding site 6 out
of 6 in 7nnw
Go back to
Iodine Binding Sites List in 7nnw
Iodine binding site 6 out
of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:I402
b:86.4
occ:1.00
|
I11
|
E:98T402
|
0.0
|
86.4
|
1.0
|
C10
|
E:98T402
|
2.1
|
45.0
|
1.0
|
C08
|
E:98T402
|
3.0
|
50.9
|
1.0
|
C12
|
E:98T402
|
3.1
|
39.2
|
1.0
|
O09
|
E:98T402
|
3.2
|
59.4
|
1.0
|
CD1
|
F:LEU78
|
3.5
|
61.7
|
1.0
|
CD1
|
F:ILE45
|
3.8
|
31.3
|
1.0
|
CG1
|
F:ILE45
|
4.0
|
31.0
|
1.0
|
CG2
|
F:VAL71
|
4.2
|
37.1
|
1.0
|
CG
|
F:LEU78
|
4.4
|
53.8
|
1.0
|
C07
|
E:98T402
|
4.4
|
53.9
|
1.0
|
CD2
|
F:LEU78
|
4.4
|
45.9
|
1.0
|
C05
|
E:98T402
|
4.5
|
36.7
|
1.0
|
CG2
|
F:ILE45
|
4.5
|
30.8
|
1.0
|
CG2
|
E:THR51
|
4.5
|
37.3
|
1.0
|
CG1
|
F:VAL71
|
4.5
|
39.6
|
1.0
|
CE2
|
E:PHE55
|
4.6
|
40.5
|
1.0
|
CB
|
F:VAL71
|
4.6
|
35.5
|
1.0
|
CD2
|
F:LEU91
|
4.6
|
31.2
|
1.0
|
CD1
|
F:LEU91
|
4.6
|
28.3
|
1.0
|
CG2
|
F:THR87
|
4.7
|
39.2
|
1.0
|
CB
|
F:ILE45
|
4.9
|
28.4
|
1.0
|
C06
|
E:98T402
|
4.9
|
50.9
|
1.0
|
CG
|
F:LEU91
|
5.0
|
28.9
|
1.0
|
|
Reference:
P.Gupta,
S.E.Thomas,
S.A.Zaidan,
M.A.Pasillas,
J.Cory-Wright,
V.Sebastian-Perez,
A.Burgess,
E.Cattermole,
C.Meghir,
C.Abell,
A.G.Coyne,
W.R.Jacobs,
T.L.Blundell,
S.Tiwari,
V.Mendes.
A Fragment-Based Approach to Assess the Ligandability of Argb, Argc, Argd and Argf in the L-Arginine Biosynthetic Pathway of Mycobacterium Tuberculosis Comput Struct Biotechnol J V. 19 3491 2021.
ISSN: ESSN 2001-0370
DOI: 10.1016/J.CSBJ.2021.06.006
Page generated: Mon Aug 12 01:49:32 2024
|