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Iodine in PDB 3gc1: Crystal Structure of Bovine Lactoperoxidase

Enzymatic activity of Crystal Structure of Bovine Lactoperoxidase

All present enzymatic activity of Crystal Structure of Bovine Lactoperoxidase:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Bovine Lactoperoxidase, PDB code: 3gc1 was solved by A.K.Singh, N.Singh, M.Sinha, P.Kaur, A.Srinivasan, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.97 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.650, 80.710, 75.680, 90.00, 101.75, 90.00
R / Rfree (%) 24.7 / 26.8

Other elements in 3gc1:

The structure of Crystal Structure of Bovine Lactoperoxidase 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 Crystal Structure of Bovine Lactoperoxidase (pdb code 3gc1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of Bovine Lactoperoxidase, PDB code: 3gc1:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 3gc1

Go back to Iodine Binding Sites List in 3gc1
Iodine binding site 1 out of 7 in the Crystal Structure of Bovine Lactoperoxidase


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 Bovine Lactoperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:43.2
occ:1.00
 N A:TRP46 3.4 35.7 1.0
CG1 A:VAL342 3.5 29.6 1.0
CH2 A:TRP452 3.5 32.7 1.0
N A:VAL342 3.6 31.1 1.0
CA A:ARG45 3.8 36.0 1.0
CZ2 A:TRP452 3.9 31.1 1.0
O A:ALA44 3.9 32.8 1.0
CB A:ASN341 3.9 31.0 1.0
CB A:VAL342 4.0 29.5 1.0
N A:ASN341 4.1 32.9 1.0
C A:ARG45 4.1 35.4 1.0
N A:LEU47 4.2 29.7 1.0
CB A:TRP46 4.3 34.1 1.0
CA A:TRP46 4.3 32.9 1.0
CA A:ASN341 4.3 32.2 1.0
CE A:MET446 4.4 33.2 1.0
CD A:ARG45 4.4 40.4 1.0
C A:ASN341 4.4 32.3 1.0
CA A:VAL342 4.4 29.8 1.0
O A:LEU47 4.5 29.5 1.0
OG A:SER340 4.7 36.0 1.0
CB A:ARG45 4.7 37.1 1.0
CZ3 A:TRP452 4.7 32.5 1.0
C A:ALA44 4.7 34.4 1.0
CB A:SER340 4.7 35.2 1.0
CG A:TRP46 4.8 34.5 1.0
C A:TRP46 4.8 31.0 1.0
N A:ARG45 4.8 35.2 1.0
NH1 A:ARG45 4.8 44.1 1.0
SD A:MET446 5.0 35.9 1.0
C A:SER340 5.0 32.9 1.0
CG A:ARG45 5.0 38.3 1.0

Iodine binding site 2 out of 7 in 3gc1

Go back to Iodine Binding Sites List in 3gc1
Iodine binding site 2 out of 7 in the Crystal Structure of Bovine Lactoperoxidase


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 Bovine Lactoperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:60.1
occ:1.00
 ND2 A:ASN80 3.6 43.6 1.0
CB A:PRO145 3.7 47.5 1.0
CG A:PRO145 3.8 45.9 1.0
CB A:ASN80 3.9 43.2 1.0
O A:LYS146 4.1 47.8 1.0
CG A:GLU77 4.1 48.2 1.0
CG A:ASN80 4.3 43.2 1.0
CE A:LYS81 4.5 44.8 1.0
O A:HOH809 4.5 55.2 1.0
CB A:ASN147 4.6 46.1 1.0
CG A:LYS81 4.6 43.5 1.0
CA A:GLU77 4.7 44.1 1.0
CD A:LYS81 4.8 46.0 1.0
N A:ASP148 4.9 48.5 1.0
CB A:GLU77 4.9 46.3 1.0
C A:ASN147 4.9 47.7 1.0
CD A:GLU77 4.9 50.8 1.0

Iodine binding site 3 out of 7 in 3gc1

Go back to Iodine Binding Sites List in 3gc1
Iodine binding site 3 out of 7 in the Crystal Structure of Bovine Lactoperoxidase


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 Bovine Lactoperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:56.9
occ:1.00
 O A:PRO424 2.6 50.3 1.0
O A:HOH717 2.9 60.6 1.0
O A:HOH782 3.5 52.4 1.0
C A:PRO424 3.8 48.6 1.0
CA A:PRO236 3.9 45.6 1.0
CB A:PRO236 4.0 44.6 1.0
N A:PRO236 4.0 47.8 1.0
CG A:PRO236 4.1 45.3 1.0
CB A:PHE239 4.3 43.1 1.0
CD1 A:PHE239 4.4 41.7 1.0
CG A:PHE239 4.4 42.8 1.0
CA A:THR425 4.4 50.0 1.0
C A:SER235 4.5 50.2 1.0
CB A:PRO234 4.5 56.0 1.0
CA A:PRO424 4.6 47.8 1.0
CD A:PRO236 4.7 45.6 1.0
OG1 A:THR425 4.7 49.1 1.0
N A:THR425 4.7 49.3 1.0
O A:SER235 4.8 51.4 1.0
CZ A:PHE422 4.8 41.7 1.0
C A:PRO234 4.9 54.5 1.0

Iodine binding site 4 out of 7 in 3gc1

Go back to Iodine Binding Sites List in 3gc1
Iodine binding site 4 out of 7 in the Crystal Structure of Bovine Lactoperoxidase


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 Bovine Lactoperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:57.5
occ:1.00
 CZ2 A:TRP530 3.8 56.7 1.0
NE1 A:TRP530 3.8 56.1 1.0
O A:HOH818 3.9 50.2 1.0
CB A:PHE309 4.0 43.9 1.0
CE2 A:TRP530 4.2 57.2 1.0
CZ2 A:TRP529 4.2 62.6 1.0
CG1 A:ILE306 4.2 42.5 1.0
CA A:ILE306 4.3 42.6 1.0
CB A:ARG310 4.4 47.6 1.0
N A:ARG310 4.5 46.6 1.0
C A:PHE309 4.6 46.2 1.0
O A:GLN305 4.7 45.1 1.0
CB A:ILE306 4.7 42.9 1.0
CG2 A:ILE306 4.7 41.8 1.0
CA A:ARG310 4.8 47.8 1.0
OE1 A:GLU531 4.8 59.8 1.0
O A:ILE306 4.8 42.6 1.0
CH2 A:TRP529 4.8 63.0 1.0
CA A:PHE309 4.9 45.2 1.0
O A:PHE309 5.0 47.9 1.0
CG A:ARG310 5.0 46.9 1.0
N A:ILE306 5.0 43.7 1.0

Iodine binding site 5 out of 7 in 3gc1

Go back to Iodine Binding Sites List in 3gc1
Iodine binding site 5 out of 7 in the Crystal Structure of Bovine Lactoperoxidase


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 Bovine Lactoperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:75.4
occ:1.00
 N A:THR560 3.5 60.9 1.0
N A:LYS561 4.0 62.2 1.0
CA A:ILE559 4.0 60.8 1.0
CG2 A:ILE559 4.0 62.3 1.0
OE1 A:GLU363 4.1 52.5 1.0
C A:ILE559 4.1 60.8 1.0
CB A:LYS561 4.2 64.8 1.0
O A:GLU363 4.2 52.8 1.0
CG A:LYS561 4.3 65.8 1.0
NE A:ARG397 4.4 40.5 1.0
CA A:GLU363 4.4 53.7 1.0
CE2 A:TYR365 4.4 49.9 1.0
CA A:THR560 4.5 60.8 1.0
O A:HIS558 4.5 60.6 1.0
C A:THR560 4.5 61.5 1.0
CB A:ILE559 4.6 61.6 1.0
CA A:LYS561 4.7 63.2 1.0
CB A:GLU363 4.7 53.8 1.0
OG1 A:THR560 4.7 60.8 1.0
NH2 A:ARG397 4.8 41.2 1.0
C A:GLU363 4.9 52.6 1.0
CZ A:ARG397 4.9 41.0 1.0
OH A:TYR365 5.0 50.8 1.0

Iodine binding site 6 out of 7 in 3gc1

Go back to Iodine Binding Sites List in 3gc1
Iodine binding site 6 out of 7 in the Crystal Structure of Bovine Lactoperoxidase


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 Bovine Lactoperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:85.5
occ:1.00
 CD2 A:PHE229 3.4 61.5 1.0
N A:PHE229 3.5 55.9 1.0
CB A:PHE229 3.7 59.2 1.0
OD1 A:ASN216 3.8 60.5 1.0
CG A:PHE229 3.9 60.5 1.0
CG A:ASN216 3.9 59.3 1.0
ND2 A:ASN216 4.0 59.1 1.0
N A:GLN217 4.1 59.0 1.0
CA A:PHE229 4.2 58.1 1.0
OE2 A:GLU218 4.3 63.5 1.0
CE2 A:PHE229 4.4 60.8 1.0
CA A:ASN216 4.4 59.7 1.0
C A:PRO228 4.4 54.1 1.0
CA A:PRO228 4.5 52.8 1.0
N A:GLU218 4.6 60.5 1.0
C A:ASN216 4.8 59.6 1.0
CB A:ASN216 4.8 59.0 1.0
CB A:GLU218 4.9 61.6 1.0
CD A:GLU218 5.0 64.3 1.0

Iodine binding site 7 out of 7 in 3gc1

Go back to Iodine Binding Sites List in 3gc1
Iodine binding site 7 out of 7 in the Crystal Structure of Bovine Lactoperoxidase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Bovine Lactoperoxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:54.5
occ:1.00
 NE2 A:HIS377 3.5 50.8 1.0
CD2 A:HIS377 3.5 49.2 1.0
ND1 A:HIS429 3.9 38.3 1.0
CG A:HIS429 4.0 36.4 1.0
CE1 A:HIS429 4.2 35.9 1.0
CG2 A:THR378 4.2 43.2 1.0
CD2 A:HIS429 4.3 36.4 1.0
O A:HIS377 4.4 46.7 1.0
NE2 A:HIS429 4.4 36.6 1.0
CB A:HIS429 4.5 37.3 1.0
CE1 A:HIS377 4.8 48.6 1.0
CG A:HIS377 4.8 48.4 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: Sun Aug 11 15:13:29 2024

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