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Iodine in PDB 3gck: 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: 3gck was solved by A.K.Singh, N.Singh, M.Sinha, A.Bhushan, 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) 19.95 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.515, 80.113, 68.571, 90.00, 93.99, 90.00
R / Rfree (%) 19.9 / 22.4

Other elements in 3gck:

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 3gck). 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: 3gck:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 3gck

Go back to Iodine Binding Sites List in 3gck
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:I608

b:32.4
occ:1.00
 N A:TRP46 3.3 17.1 1.0
O A:HOH717 3.5 35.4 1.0
N A:VAL342 3.5 10.2 1.0
CH2 A:TRP452 3.8 16.4 1.0
CA A:ARG45 3.8 17.9 1.0
CB A:VAL342 3.9 4.9 1.0
CB A:ASN341 3.9 13.7 1.0
N A:ASN341 4.0 13.0 1.0
CZ2 A:TRP452 4.0 15.9 1.0
O A:ALA44 4.0 17.8 1.0
C A:ARG45 4.1 17.9 1.0
CG1 A:VAL342 4.1 5.9 1.0
CE A:MET446 4.2 18.9 1.0
N A:LEU47 4.2 15.5 1.0
CA A:TRP46 4.3 16.9 1.0
CA A:ASN341 4.3 13.0 1.0
CA A:VAL342 4.3 8.7 1.0
CB A:TRP46 4.4 18.1 1.0
C A:ASN341 4.4 12.2 1.0
CD A:ARG45 4.4 17.4 1.0
O A:LEU47 4.4 15.4 1.0
CB A:SER340 4.6 14.5 1.0
CB A:ARG45 4.6 17.3 1.0
C A:TRP46 4.7 16.8 1.0
SD A:MET446 4.8 19.8 1.0
N A:ARG45 4.9 17.4 1.0
C A:ALA44 4.9 17.0 1.0
C A:SER340 4.9 13.0 1.0
CZ3 A:TRP452 5.0 15.9 1.0
CG A:TRP46 5.0 17.6 1.0

Iodine binding site 2 out of 8 in 3gck

Go back to Iodine Binding Sites List in 3gck
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:I609

b:96.1
occ:1.00
 O A:LYS146 3.7 41.4 1.0
CG A:PRO145 3.9 31.2 1.0
ND2 A:ASN80 4.0 18.7 1.0
CB A:ASN80 4.1 18.6 1.0
CG A:GLU77 4.2 18.3 1.0
O A:HOH734 4.3 46.3 1.0
O A:ASN147 4.3 40.3 1.0
OE1 A:GLU77 4.4 19.1 1.0
O A:HOH635 4.5 16.0 1.0
CB A:PRO145 4.5 31.5 1.0
CG A:ASN80 4.5 19.1 1.0
CE A:LYS81 4.5 23.6 1.0
CB A:ASN147 4.6 42.5 1.0
CG A:LYS81 4.7 21.3 1.0
C A:ASN147 4.7 39.4 1.0
CD A:GLU77 4.8 18.6 1.0
NZ A:LYS81 4.8 26.3 1.0
C A:LYS146 4.9 40.1 1.0

Iodine binding site 3 out of 8 in 3gck

Go back to Iodine Binding Sites List in 3gck
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:I610

b:76.6
occ:0.50
 NH2 A:ARG504 3.1 54.8 1.0
CZ A:ARG504 3.9 54.3 1.0
ND2 A:ASN95 4.0 57.0 1.0
NE A:ARG504 4.1 53.5 1.0
NH1 A:ARG96 4.1 35.7 1.0
O6 A:NAG596 4.1 69.5 1.0
NH2 A:ARG506 4.2 28.9 1.0
NH2 A:ARG96 4.2 34.4 1.0
O5 A:NAG596 4.3 65.6 1.0
NH1 A:ARG506 4.3 28.9 1.0
C1 A:NAG596 4.6 63.0 1.0
O A:ARG504 4.6 37.3 1.0
CZ A:ARG96 4.6 35.3 1.0
C2 A:NAG596 4.7 65.4 1.0
CZ A:ARG506 4.7 28.5 1.0
CA A:ARG504 4.7 38.6 1.0
O7 A:NAG596 4.8 66.8 1.0
C A:ARG504 5.0 36.9 1.0

Iodine binding site 4 out of 8 in 3gck

Go back to Iodine Binding Sites List in 3gck
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:I611

b:65.5
occ:1.00
 N A:PHE229 3.6 33.0 1.0
N A:GLN217 3.7 46.6 1.0
CB A:PHE229 4.1 34.0 1.0
OD1 A:ASN216 4.1 45.3 1.0
CD2 A:PHE229 4.1 33.2 1.0
CA A:ASN216 4.2 45.5 1.0
CG A:ASN216 4.3 45.4 1.0
O A:HOH658 4.3 28.5 1.0
CB A:GLN217 4.3 47.6 1.0
CA A:PRO228 4.3 29.5 1.0
CG A:GLN217 4.4 48.6 1.0
CA A:PHE229 4.4 34.9 1.0
CB A:PRO228 4.4 29.4 1.0
C A:PRO228 4.5 30.9 1.0
C A:ASN216 4.5 46.0 1.0
CA A:GLN217 4.6 47.5 1.0
CG A:PHE229 4.6 33.6 1.0
OE1 A:GLU218 4.6 52.1 1.0
ND2 A:ASN216 4.6 45.8 1.0
OE2 A:GLU218 4.6 52.1 1.0
O A:PHE229 4.7 36.6 1.0
N A:GLU218 4.7 47.3 1.0
CD A:GLU218 4.8 51.5 1.0
CB A:ASN216 4.8 45.6 1.0
O A:VAL215 4.8 42.6 1.0
C A:PHE229 5.0 36.7 1.0

Iodine binding site 5 out of 8 in 3gck

Go back to Iodine Binding Sites List in 3gck
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:I612

b:88.0
occ:1.00
 O A:HOH709 3.6 36.4 1.0
NE1 A:TRP530 3.8 46.1 1.0
CZ2 A:TRP530 3.9 46.1 1.0
CB A:PHE309 3.9 15.4 1.0
CE2 A:TRP530 4.2 46.2 1.0
OE1 A:GLU531 4.2 42.5 1.0
CA A:ILE306 4.4 24.3 1.0
CZ2 A:TRP529 4.4 44.6 1.0
O A:ILE306 4.5 24.1 1.0
CD A:GLU531 4.5 43.0 1.0
N A:ARG310 4.5 19.3 1.0
C A:PHE309 4.6 17.8 1.0
CB A:ARG310 4.7 20.4 1.0
CA A:PHE309 4.8 16.7 1.0
CG2 A:ILE306 4.9 25.1 1.0
CA A:ARG310 4.9 20.5 1.0
C A:ILE306 4.9 24.2 1.0
CG A:GLU531 5.0 42.7 1.0
OE2 A:GLU531 5.0 43.0 1.0
CG A:PHE309 5.0 16.3 1.0
O A:PHE309 5.0 18.3 1.0

Iodine binding site 6 out of 8 in 3gck

Go back to Iodine Binding Sites List in 3gck
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:I613

b:0.0
occ:1.00
 N A:THR560 3.2 41.1 1.0
CA A:ILE559 3.6 41.8 1.0
OG1 A:THR560 3.7 39.4 1.0
O A:GLU363 3.7 46.2 1.0
NE A:ARG397 3.8 31.1 1.0
C A:ILE559 3.9 41.5 1.0
CG2 A:ILE559 3.9 41.2 1.0
N A:LYS561 4.0 42.0 1.0
CA A:THR560 4.2 41.0 1.0
CB A:ILE559 4.2 41.7 1.0
CA A:GLU363 4.3 46.9 1.0
O A:HIS558 4.4 41.8 1.0
CB A:THR560 4.5 41.2 1.0
CD A:ARG397 4.5 29.8 1.0
C A:GLU363 4.5 46.4 1.0
CB A:GLU363 4.5 49.0 1.0
CE2 A:TYR365 4.5 40.8 1.0
CG1 A:ILE559 4.6 41.8 1.0
C A:THR560 4.6 41.2 1.0
NH2 A:ARG397 4.7 30.4 1.0
CZ A:ARG397 4.7 31.2 1.0
N A:ILE559 4.8 41.5 1.0
O A:LYS561 4.8 40.0 1.0
CG A:LYS561 4.8 43.9 1.0
CB A:LYS561 4.9 42.4 1.0
OH A:TYR365 4.9 40.2 1.0
CZ A:TYR365 5.0 40.6 1.0

Iodine binding site 7 out of 8 in 3gck

Go back to Iodine Binding Sites List in 3gck
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:I614

b:69.6
occ:1.00
 OG1 A:THR463 3.1 25.5 1.0
N A:LYS462 3.7 27.0 1.0
CA A:GLY466 4.0 28.6 1.0
N A:THR463 4.1 27.6 1.0
CB A:THR463 4.3 26.8 1.0
CB A:LYS462 4.3 27.1 1.0
CA A:PRO461 4.4 26.1 1.0
CA A:LYS462 4.4 27.7 1.0
N A:GLY466 4.5 28.0 1.0
C A:PRO461 4.5 25.8 1.0
CG2 A:THR463 4.5 25.6 1.0
C A:LYS462 4.6 27.7 1.0
CA A:THR463 4.8 27.2 1.0
O A:GLN460 4.9 28.4 1.0
CG A:LYS462 4.9 27.6 1.0

Iodine binding site 8 out of 8 in 3gck

Go back to Iodine Binding Sites List in 3gck
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:I615

b:64.8
occ:0.50
 CB A:HIS565 3.5 46.2 1.0
N A:PHE567 3.5 39.6 1.0
C A:HIS565 3.6 43.3 1.0
O A:HIS565 3.6 43.7 1.0
CA A:HIS565 3.6 44.5 1.0
CB A:PHE567 3.7 39.5 1.0
CD2 A:PHE567 4.0 39.8 1.0
CA A:PHE567 4.1 39.8 1.0
N A:ALA566 4.1 42.1 1.0
N A:GLN568 4.2 39.8 1.0
CG A:PHE567 4.4 39.8 1.0
CG A:HIS565 4.5 48.4 1.0
C A:ALA566 4.6 40.2 1.0
C A:PHE567 4.7 40.0 1.0
CB A:ASP311 4.7 22.7 1.0
ND1 A:HIS565 4.8 49.4 1.0
O A:ASP311 4.8 24.6 1.0
CA A:ALA566 4.9 40.7 1.0
OE1 A:GLN568 4.9 44.9 1.0

Reference:

A.K.Singh, N.Singh, M.Sinha, A.Bhushan, P.Kaur, A.Srinivasan, S.Sharma, T.P.Singh. 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 To Be Published.
Page generated: Sun Aug 11 15:14:41 2024

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