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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:

Iron (Fe) 1 atom
Calcium (Ca) 1 atom

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
Page generated: Fri Aug 8 14:23:02 2025

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