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Iodine in PDB 3gcl: Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid

Enzymatic activity of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid

All present enzymatic activity of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid:
1.11.1.7;

Protein crystallography data

The structure of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid, PDB code: 3gcl was solved by A.K.Singh, 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) 19.44 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.660, 80.520, 77.970, 90.00, 102.65, 90.00
R / Rfree (%) 20.1 / 22.3

Other elements in 3gcl:

The structure of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid 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 Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid (pdb code 3gcl). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid, PDB code: 3gcl:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 3gcl

Go back to Iodine Binding Sites List in 3gcl
Iodine binding site 1 out of 8 in the Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:24.9
occ:1.00
 N A:TRP46 3.4 20.1 1.0
N A:VAL342 3.4 14.4 1.0
O A:HOH629 3.5 17.2 1.0
CG1 A:VAL342 3.7 12.4 1.0
CH2 A:TRP452 3.7 20.0 1.0
CB A:VAL342 3.8 12.5 1.0
CB A:ASN341 3.8 16.1 1.0
CA A:ARG45 3.9 19.3 1.0
N A:ASN341 3.9 16.7 1.0
CZ2 A:TRP452 4.0 20.5 1.0
O A:ALA44 4.0 16.7 1.0
CE A:MET446 4.1 18.1 1.0
C A:ARG45 4.2 19.6 1.0
CA A:ASN341 4.2 16.3 1.0
CA A:VAL342 4.2 14.0 1.0
C A:ASN341 4.3 15.8 1.0
N A:LEU47 4.3 19.3 1.0
CB A:TRP46 4.3 19.8 1.0
CD A:ARG45 4.3 17.0 1.0
CA A:TRP46 4.3 19.8 1.0
O A:LEU47 4.5 19.9 1.0
CB A:SER340 4.6 16.5 1.0
NH1 A:ARG45 4.7 16.7 1.0
CB A:ARG45 4.7 18.8 1.0
SD A:MET446 4.8 20.6 1.0
C A:SER340 4.8 17.4 1.0
C A:TRP46 4.8 19.7 1.0
C A:ALA44 4.9 17.0 1.0
CG A:TRP46 4.9 20.9 1.0
N A:ARG45 4.9 18.3 1.0
CZ3 A:TRP452 5.0 18.8 1.0

Iodine binding site 2 out of 8 in 3gcl

Go back to Iodine Binding Sites List in 3gcl
Iodine binding site 2 out of 8 in the Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:87.3
occ:1.00
 O A:HOH802 3.4 44.0 1.0
CB A:PRO145 3.6 33.9 1.0
ND2 A:ASN80 3.7 20.8 1.0
O A:LYS146 3.9 40.6 1.0
CG A:PRO145 4.1 33.2 1.0
CB A:ASN80 4.1 22.0 1.0
CG A:ASN80 4.4 22.5 1.0
CE A:LYS81 4.4 30.2 1.0
CG A:GLU77 4.4 31.6 1.0
OD1 A:ASN147 4.8 44.8 1.0
CG A:LYS81 4.9 27.5 1.0
CD A:GLU77 4.9 33.6 1.0
CA A:GLU77 4.9 25.4 1.0
N A:ASP148 4.9 36.5 1.0

Iodine binding site 3 out of 8 in 3gcl

Go back to Iodine Binding Sites List in 3gcl
Iodine binding site 3 out of 8 in the Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:67.6
occ:0.50
 NH1 A:ARG504 3.6 43.6 1.0
NH2 A:ARG96 3.7 24.6 1.0
NH1 A:ARG96 3.7 25.4 1.0
CD A:ARG504 3.9 40.0 1.0
ND2 A:ASN95 4.1 51.9 1.0
CZ A:ARG96 4.2 26.1 1.0
CA A:ARG504 4.2 32.3 1.0
NH1 A:ARG506 4.3 22.9 1.0
O5 A:NAG596 4.3 60.5 1.0
NH2 A:ARG506 4.3 23.8 1.0
O6 A:NAG596 4.4 63.6 1.0
CZ A:ARG504 4.5 43.4 1.0
O A:ARG504 4.5 31.0 1.0
NE A:ARG504 4.6 42.5 1.0
O7 A:NAG596 4.6 60.5 1.0
C2 A:NAG596 4.6 60.6 1.0
C1 A:NAG596 4.6 58.0 1.0
C A:ARG504 4.6 30.9 1.0
CB A:ARG504 4.7 34.0 1.0
CZ A:ARG506 4.8 23.5 1.0
CG A:ARG504 4.9 37.2 1.0

Iodine binding site 4 out of 8 in 3gcl

Go back to Iodine Binding Sites List in 3gcl
Iodine binding site 4 out of 8 in the Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:75.7
occ:1.00
 N A:PHE229 3.5 38.3 1.0
N A:GLN217 3.9 41.6 1.0
OD1 A:ASN216 4.1 39.4 1.0
CB A:PHE229 4.1 40.0 1.0
CG A:ASN216 4.1 39.6 1.0
CA A:ASN216 4.1 39.5 1.0
ND2 A:ASN216 4.2 39.6 1.0
CA A:PRO228 4.2 35.5 1.0
CB A:PRO228 4.3 35.2 1.0
CA A:PHE229 4.4 40.5 1.0
CD2 A:PHE229 4.4 39.7 1.0
C A:PRO228 4.4 36.7 1.0
CG A:GLU218 4.6 49.4 1.0
C A:ASN216 4.6 40.5 1.0
CG A:PHE229 4.6 39.7 1.0
O A:PHE229 4.7 41.9 1.0
CB A:ASN216 4.7 39.4 1.0
O A:VAL215 4.9 36.4 1.0
O A:HOH754 4.9 46.9 1.0
N A:GLU218 4.9 45.0 1.0
CB A:GLN217 5.0 43.7 1.0
CA A:GLN217 5.0 43.4 1.0

Iodine binding site 5 out of 8 in 3gcl

Go back to Iodine Binding Sites List in 3gcl
Iodine binding site 5 out of 8 in the Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:49.1
occ:0.50
 NE1 A:TRP530 3.6 29.1 1.0
CB A:PHE309 3.8 21.0 1.0
CZ2 A:TRP530 3.9 28.0 1.0
CE2 A:TRP530 4.1 29.1 1.0
OE1 A:GLU531 4.3 38.3 1.0
N A:ARG310 4.5 21.8 1.0
CD A:GLU531 4.5 37.5 1.0
CZ2 A:TRP529 4.5 30.9 1.0
C A:PHE309 4.6 21.8 1.0
CB A:ARG310 4.7 22.9 1.0
OE2 A:GLU531 4.7 38.2 1.0
CA A:ILE306 4.7 24.4 1.0
CA A:PHE309 4.8 21.8 1.0
O A:ILE306 4.8 24.7 1.0
CD1 A:TRP530 4.9 30.1 1.0
CG A:PHE309 4.9 20.6 1.0
CA A:ARG310 4.9 22.2 1.0
O A:GLN305 4.9 23.3 1.0

Iodine binding site 6 out of 8 in 3gcl

Go back to Iodine Binding Sites List in 3gcl
Iodine binding site 6 out of 8 in the Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:69.2
occ:1.00
 NE A:ARG397 3.4 30.0 1.0
O A:GLU363 3.4 48.7 1.0
NH2 A:ARG397 3.7 31.4 1.0
CZ A:ARG397 4.0 29.8 1.0
N A:THR560 4.0 33.8 1.0
CA A:GLU363 4.1 49.2 1.0
CE2 A:TYR365 4.1 43.4 1.0
CG2 A:ILE559 4.2 32.7 1.0
C A:GLU363 4.2 49.0 1.0
CA A:ILE559 4.2 33.3 1.0
OG1 A:THR560 4.3 35.8 1.0
O A:HOH895 4.3 41.1 1.0
N A:LYS561 4.3 34.7 1.0
CB A:GLU363 4.4 50.2 1.0
CD A:ARG397 4.4 29.6 1.0
CB A:LYS561 4.5 36.0 1.0
CG A:LYS561 4.5 37.4 1.0
C A:ILE559 4.7 33.6 1.0
CB A:ILE559 4.7 33.0 1.0
CD2 A:TYR365 4.7 44.0 1.0
O A:HIS558 4.8 34.5 1.0
CZ A:TYR365 5.0 43.2 1.0
OH A:TYR365 5.0 42.8 1.0

Iodine binding site 7 out of 8 in 3gcl

Go back to Iodine Binding Sites List in 3gcl
Iodine binding site 7 out of 8 in the Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:74.5
occ:1.00
 OG1 A:THR463 3.5 31.1 1.0
N A:LYS462 3.7 32.4 1.0
CA A:GLY466 3.9 31.7 1.0
N A:THR463 4.0 32.8 1.0
CA A:PRO461 4.2 30.8 1.0
CG2 A:THR463 4.4 31.3 1.0
CB A:THR463 4.4 31.9 1.0
C A:PRO461 4.4 31.6 1.0
N A:GLY466 4.5 33.1 1.0
CA A:LYS462 4.6 33.5 1.0
CB A:LYS462 4.7 34.3 1.0
CA A:THR463 4.8 32.4 1.0
CB A:PRO461 4.8 30.8 1.0
C A:LYS462 4.8 33.6 1.0
O A:GLN460 4.9 29.6 1.0

Iodine binding site 8 out of 8 in 3gcl

Go back to Iodine Binding Sites List in 3gcl
Iodine binding site 8 out of 8 in the Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Mode of Ligand Binding and Assignment of Subsites in Mammalian Peroxidases: Crystal Structure of Lactoperoxidase Complexes with Acetyl Salycylic Acid, Salicylhydroxamic Acid and Benzylhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I617

b:93.3
occ:0.50
 CB A:HIS565 3.4 34.7 1.0
CA A:HIS565 3.5 33.6 1.0
C A:HIS565 3.7 32.8 1.0
N A:PHE567 3.8 30.6 1.0
CB A:PHE567 3.9 30.1 1.0
CD2 A:PHE567 3.9 29.2 1.0
O A:HOH904 3.9 60.3 1.0
N A:ALA566 4.1 31.3 1.0
O A:HIS565 4.1 33.2 1.0
ND1 A:HIS565 4.2 37.3 1.0
CG A:HIS565 4.3 36.2 1.0
CG A:PHE567 4.3 29.4 1.0
CA A:PHE567 4.3 30.6 1.0
CB A:ASP311 4.4 26.1 1.0
N A:GLN568 4.6 31.9 1.0
CG A:ASP311 4.7 27.4 1.0
C A:ALA566 4.8 31.3 1.0
OD1 A:ASP311 4.8 28.5 1.0
O A:ASP311 4.9 25.7 1.0
CE2 A:PHE567 4.9 29.2 1.0
C8 A:NAG597 4.9 79.2 1.0
C A:PHE567 5.0 30.8 1.0
N A:HIS565 5.0 33.2 1.0
CA A:ALA566 5.0 31.2 1.0

Reference:

A.K.Singh, N.Singh, M.Sinha, A.Bhushan, P.Kaur, A.Srinivasan, S.Sharma, T.P.Singh. Binding Modes of Aromatic Ligands to Mammalian Heme Peroxidases with Associated Functional Implications: Crystal Structures of Lactoperoxidase Complexes with Acetylsalicylic Acid, Salicylhydroxamic Acid, and Benzylhydroxamic Acid J.Biol.Chem. V. 284 20311 2009.
ISSN: ISSN 0021-9258
PubMed: 19465478
DOI: 10.1074/JBC.M109.010280
Page generated: Sun Aug 11 15:15:30 2024

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