Iodine in PDB 3i6n: Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
Enzymatic activity of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
All present enzymatic activity of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution:
1.11.1.7;
Protein crystallography data
The structure of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution, PDB code: 3i6n
was solved by
A.K.Singh,
R.P.Kumar,
N.Pandey,
N.Singh,
M.Sinha,
A.Bhushan,
P.Kaur,
S.Sharma,
T.P.Singh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
75.81 /
2.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.490,
80.550,
77.780,
90.00,
102.66,
90.00
|
R / Rfree (%)
|
20.5 /
23.2
|
Other elements in 3i6n:
The structure of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
(pdb code 3i6n). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the
Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution, PDB code: 3i6n:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
Iodine binding site 1 out
of 7 in 3i6n
Go back to
Iodine Binding Sites List in 3i6n
Iodine binding site 1 out
of 7 in the Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I608
b:34.2
occ:1.00
|
N
|
A:TRP46
|
3.3
|
26.1
|
1.0
|
O
|
A:HOH645
|
3.5
|
41.7
|
1.0
|
N
|
A:VAL342
|
3.6
|
23.0
|
1.0
|
CA
|
A:ARG45
|
3.8
|
26.6
|
1.0
|
CH2
|
A:TRP452
|
3.9
|
19.4
|
1.0
|
CB
|
A:ASN341
|
3.9
|
24.9
|
1.0
|
N
|
A:ASN341
|
4.0
|
25.3
|
1.0
|
CB
|
A:VAL342
|
4.0
|
22.2
|
1.0
|
CZ2
|
A:TRP452
|
4.0
|
19.4
|
1.0
|
C
|
A:ARG45
|
4.0
|
26.5
|
1.0
|
O
|
A:ALA44
|
4.0
|
27.0
|
1.0
|
N
|
A:LEU47
|
4.0
|
27.1
|
1.0
|
CE
|
A:MET446
|
4.1
|
28.4
|
1.0
|
CB
|
A:TRP46
|
4.2
|
27.6
|
1.0
|
CA
|
A:TRP46
|
4.2
|
26.9
|
1.0
|
CA
|
A:ASN341
|
4.3
|
24.5
|
1.0
|
CG1
|
A:VAL342
|
4.3
|
22.3
|
1.0
|
O
|
A:LEU47
|
4.3
|
26.9
|
1.0
|
C
|
A:ASN341
|
4.3
|
23.8
|
1.0
|
CD
|
A:ARG45
|
4.4
|
28.0
|
1.0
|
CA
|
A:VAL342
|
4.4
|
22.3
|
1.0
|
CB
|
A:SER340
|
4.5
|
26.5
|
1.0
|
CB
|
A:ARG45
|
4.6
|
27.4
|
1.0
|
SD
|
A:MET446
|
4.6
|
29.3
|
1.0
|
C
|
A:TRP46
|
4.6
|
26.9
|
1.0
|
C
|
A:SER340
|
4.9
|
26.2
|
1.0
|
C
|
A:ALA44
|
4.9
|
26.7
|
1.0
|
N
|
A:ARG45
|
4.9
|
26.5
|
1.0
|
CG
|
A:TRP46
|
4.9
|
28.2
|
1.0
|
CG
|
A:ARG45
|
4.9
|
28.2
|
1.0
|
OG
|
A:SER340
|
5.0
|
26.9
|
1.0
|
CA
|
A:LEU47
|
5.0
|
26.8
|
1.0
|
|
Iodine binding site 2 out
of 7 in 3i6n
Go back to
Iodine Binding Sites List in 3i6n
Iodine binding site 2 out
of 7 in the Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I609
b:51.8
occ:0.50
|
ND2
|
A:ASN80
|
3.4
|
36.5
|
1.0
|
O
|
A:HOH842
|
3.5
|
66.4
|
1.0
|
CG
|
A:PRO145
|
3.7
|
42.7
|
1.0
|
CB
|
A:ASN80
|
3.9
|
35.7
|
1.0
|
O
|
A:LYS146
|
3.9
|
49.5
|
1.0
|
CG
|
A:ASN80
|
4.1
|
36.4
|
1.0
|
CB
|
A:PRO145
|
4.2
|
43.2
|
1.0
|
CG
|
A:GLU77
|
4.4
|
39.2
|
1.0
|
CD
|
A:LYS81
|
4.7
|
41.9
|
1.0
|
CE
|
A:LYS81
|
4.8
|
43.2
|
1.0
|
CA
|
A:GLU77
|
4.8
|
34.2
|
1.0
|
O
|
A:ASN147
|
4.9
|
48.7
|
1.0
|
O
|
A:GLU77
|
4.9
|
33.8
|
1.0
|
C
|
A:ASN147
|
5.0
|
48.5
|
1.0
|
|
Iodine binding site 3 out
of 7 in 3i6n
Go back to
Iodine Binding Sites List in 3i6n
Iodine binding site 3 out
of 7 in the Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I610
b:58.0
occ:0.50
|
NH1
|
A:ARG96
|
3.9
|
39.2
|
1.0
|
CD
|
A:ARG504
|
3.9
|
48.6
|
1.0
|
NH2
|
A:ARG96
|
4.2
|
38.9
|
1.0
|
CA
|
A:ARG504
|
4.2
|
41.5
|
1.0
|
NH1
|
A:ARG504
|
4.2
|
53.2
|
1.0
|
ND2
|
A:ASN95
|
4.2
|
60.3
|
1.0
|
O6
|
A:NAG596
|
4.3
|
72.3
|
1.0
|
O
|
A:ARG504
|
4.3
|
40.0
|
1.0
|
O5
|
A:NAG596
|
4.5
|
69.5
|
1.0
|
CZ
|
A:ARG96
|
4.5
|
39.1
|
1.0
|
C
|
A:ARG504
|
4.5
|
40.2
|
1.0
|
NH1
|
A:ARG506
|
4.5
|
38.1
|
1.0
|
NH2
|
A:ARG506
|
4.6
|
37.3
|
1.0
|
O7
|
A:NAG596
|
4.6
|
70.1
|
1.0
|
CB
|
A:ARG504
|
4.6
|
43.3
|
1.0
|
C2
|
A:NAG596
|
4.7
|
69.3
|
1.0
|
C1
|
A:NAG596
|
4.8
|
66.5
|
1.0
|
CG
|
A:ARG504
|
4.9
|
45.9
|
1.0
|
CZ
|
A:ARG506
|
4.9
|
37.4
|
1.0
|
NE
|
A:ARG504
|
4.9
|
51.3
|
1.0
|
|
Iodine binding site 4 out
of 7 in 3i6n
Go back to
Iodine Binding Sites List in 3i6n
Iodine binding site 4 out
of 7 in the Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I611
b:44.9
occ:0.50
|
N
|
A:PHE229
|
3.7
|
48.8
|
1.0
|
N
|
A:GLN217
|
3.9
|
51.3
|
1.0
|
CG
|
A:ASN216
|
4.1
|
47.1
|
1.0
|
OD1
|
A:ASN216
|
4.1
|
47.1
|
1.0
|
CD2
|
A:PHE229
|
4.1
|
52.0
|
1.0
|
CA
|
A:ASN216
|
4.1
|
48.1
|
1.0
|
ND2
|
A:ASN216
|
4.2
|
46.8
|
1.0
|
CA
|
A:PRO228
|
4.2
|
45.9
|
1.0
|
CB
|
A:PHE229
|
4.3
|
50.9
|
1.0
|
CB
|
A:PRO228
|
4.4
|
45.5
|
1.0
|
C
|
A:PRO228
|
4.5
|
47.2
|
1.0
|
CA
|
A:PHE229
|
4.6
|
50.5
|
1.0
|
C
|
A:ASN216
|
4.6
|
49.5
|
1.0
|
CG
|
A:PHE229
|
4.6
|
51.8
|
1.0
|
CB
|
A:ASN216
|
4.7
|
47.3
|
1.0
|
CG
|
A:GLU218
|
4.7
|
60.4
|
1.0
|
O
|
A:PHE229
|
4.7
|
52.0
|
1.0
|
O
|
A:VAL215
|
4.9
|
45.2
|
1.0
|
N
|
A:GLU218
|
4.9
|
54.2
|
1.0
|
CB
|
A:GLN217
|
4.9
|
53.5
|
1.0
|
CA
|
A:GLN217
|
5.0
|
52.9
|
1.0
|
|
Iodine binding site 5 out
of 7 in 3i6n
Go back to
Iodine Binding Sites List in 3i6n
Iodine binding site 5 out
of 7 in the Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I612
b:54.6
occ:0.50
|
O
|
A:HOH732
|
3.6
|
39.7
|
1.0
|
NE1
|
A:TRP530
|
3.7
|
40.4
|
1.0
|
CB
|
A:PHE309
|
3.9
|
25.4
|
1.0
|
CZ2
|
A:TRP530
|
4.0
|
40.0
|
1.0
|
OE1
|
A:GLU531
|
4.2
|
52.5
|
1.0
|
CE2
|
A:TRP530
|
4.2
|
40.5
|
1.0
|
CZ2
|
A:TRP529
|
4.3
|
36.0
|
1.0
|
N
|
A:ARG310
|
4.3
|
28.1
|
1.0
|
O
|
A:HOH895
|
4.3
|
54.2
|
1.0
|
CA
|
A:ILE306
|
4.5
|
31.7
|
1.0
|
CB
|
A:ARG310
|
4.5
|
29.2
|
1.0
|
C
|
A:PHE309
|
4.6
|
27.3
|
1.0
|
CD
|
A:GLU531
|
4.6
|
52.0
|
1.0
|
O
|
A:GLN305
|
4.7
|
32.7
|
1.0
|
O
|
A:ILE306
|
4.7
|
31.3
|
1.0
|
CA
|
A:ARG310
|
4.8
|
29.2
|
1.0
|
CA
|
A:PHE309
|
4.8
|
26.8
|
1.0
|
CG1
|
A:ILE306
|
4.9
|
31.8
|
1.0
|
CD1
|
A:TRP530
|
4.9
|
40.6
|
1.0
|
OE2
|
A:GLU531
|
4.9
|
52.9
|
1.0
|
|
Iodine binding site 6 out
of 7 in 3i6n
Go back to
Iodine Binding Sites List in 3i6n
Iodine binding site 6 out
of 7 in the Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I613
b:45.8
occ:0.50
|
O
|
A:GLU363
|
3.3
|
57.8
|
1.0
|
N
|
A:THR560
|
3.6
|
47.5
|
1.0
|
NE
|
A:ARG397
|
3.8
|
37.1
|
1.0
|
OG1
|
A:THR560
|
3.9
|
48.0
|
1.0
|
CA
|
A:ILE559
|
4.0
|
46.8
|
1.0
|
O
|
A:HOH870
|
4.0
|
74.2
|
1.0
|
CA
|
A:GLU363
|
4.1
|
57.9
|
1.0
|
C
|
A:GLU363
|
4.1
|
57.9
|
1.0
|
CG2
|
A:ILE559
|
4.3
|
46.1
|
1.0
|
C
|
A:ILE559
|
4.3
|
47.1
|
1.0
|
CE2
|
A:TYR365
|
4.3
|
52.8
|
1.0
|
N
|
A:LYS561
|
4.3
|
48.2
|
1.0
|
NH2
|
A:ARG397
|
4.5
|
39.3
|
1.0
|
CD
|
A:ARG397
|
4.5
|
35.8
|
1.0
|
CZ
|
A:ARG397
|
4.6
|
38.6
|
1.0
|
CB
|
A:GLU363
|
4.6
|
59.6
|
1.0
|
CA
|
A:THR560
|
4.6
|
47.8
|
1.0
|
O
|
A:HIS558
|
4.7
|
47.2
|
1.0
|
CG
|
A:LYS561
|
4.8
|
51.5
|
1.0
|
OE1
|
A:GLU363
|
4.8
|
63.9
|
1.0
|
CB
|
A:ILE559
|
4.8
|
46.5
|
1.0
|
CB
|
A:THR560
|
4.8
|
47.9
|
1.0
|
CD2
|
A:TYR365
|
4.9
|
53.6
|
1.0
|
OH
|
A:TYR365
|
4.9
|
52.3
|
1.0
|
CZ
|
A:TYR365
|
5.0
|
52.4
|
1.0
|
|
Iodine binding site 7 out
of 7 in 3i6n
Go back to
Iodine Binding Sites List in 3i6n
Iodine binding site 7 out
of 7 in the Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Mode of Binding of the Tuberculosis Prodrug Isoniazid to Peroxidases: Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I614
b:32.6
occ:0.50
|
OG1
|
A:THR463
|
3.4
|
39.6
|
1.0
|
N
|
A:LYS462
|
3.6
|
37.1
|
1.0
|
CA
|
A:GLY466
|
3.9
|
39.8
|
1.0
|
N
|
A:THR463
|
3.9
|
38.9
|
1.0
|
CA
|
A:PRO461
|
4.2
|
35.8
|
1.0
|
CG2
|
A:THR463
|
4.4
|
39.3
|
1.0
|
CB
|
A:THR463
|
4.4
|
39.2
|
1.0
|
CA
|
A:LYS462
|
4.4
|
37.9
|
1.0
|
CB
|
A:LYS462
|
4.4
|
37.8
|
1.0
|
C
|
A:PRO461
|
4.4
|
36.3
|
1.0
|
N
|
A:GLY466
|
4.6
|
40.6
|
1.0
|
C
|
A:LYS462
|
4.7
|
38.4
|
1.0
|
CA
|
A:THR463
|
4.8
|
39.2
|
1.0
|
CB
|
A:PRO461
|
4.8
|
35.7
|
1.0
|
CG
|
A:LYS462
|
4.9
|
37.4
|
1.0
|
O
|
A:GLN460
|
5.0
|
34.7
|
1.0
|
|
Reference:
A.K.Singh,
R.P.Kumar,
N.Pandey,
N.Singh,
M.Sinha,
A.Bhushan,
P.Kaur,
S.Sharma,
T.P.Singh.
Mode of Binding of the Tuberculosis Prodrug Isoniazid to Heme Peroxidases: Binding Studies and Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 A Resolution. J.Biol.Chem. V. 285 1569 2010.
ISSN: ISSN 0021-9258
PubMed: 19907057
DOI: 10.1074/JBC.M109.060327
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