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Iodine in PDB 3erh: First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species

Enzymatic activity of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species

All present enzymatic activity of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species:
1.11.1.7;

Protein crystallography data

The structure of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species, PDB code: 3erh was solved by I.A.Sheikh, N.Singh, A.K.Singh, M.Sinha, S.B.Singh, 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) 19.46 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.207, 80.541, 77.877, 90.00, 102.64, 90.00
R / Rfree (%) 18 / 19.5

Other elements in 3erh:

The structure of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species 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 First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species (pdb code 3erh). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species, PDB code: 3erh:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 3erh

Go back to Iodine Binding Sites List in 3erh
Iodine binding site 1 out of 7 in the First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:85.3
occ:1.00
 ND2 A:ASN80 3.5 20.7 1.0
CB A:ASN80 3.9 21.7 1.0
CG A:PRO145 3.9 33.1 1.0
O A:LYS146 4.2 48.8 1.0
CG A:ASN80 4.2 24.4 1.0
CB A:PRO145 4.3 35.1 1.0
OE2 A:GLU77 4.4 45.9 1.0
CE A:LYS81 4.5 39.5 1.0
CG A:GLU77 4.7 39.3 1.0
CG A:LYS81 4.7 31.9 1.0
CA A:GLU77 4.9 31.4 1.0
CD A:GLU77 4.9 43.4 1.0

Iodine binding site 2 out of 7 in 3erh

Go back to Iodine Binding Sites List in 3erh
Iodine binding site 2 out of 7 in the First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:0.0
occ:1.00
 NH2 A:ARG504 2.6 59.2 1.0
NE A:ARG504 3.0 59.1 1.0
CZ A:ARG504 3.2 60.3 1.0
NH1 A:ARG96 3.6 23.5 1.0
ND2 A:ASN95 3.9 49.7 1.0
NH2 A:ARG96 3.9 28.7 1.0
O5 A:NAG617 4.0 59.9 1.0
CD A:ARG504 4.2 54.7 1.0
NH2 A:ARG506 4.2 27.2 1.0
CZ A:ARG96 4.2 28.1 1.0
CA A:ARG504 4.4 37.5 1.0
O7 A:NAG617 4.4 52.3 1.0
NH1 A:ARG506 4.4 27.8 1.0
C2 A:NAG617 4.4 58.3 1.0
NH1 A:ARG504 4.4 61.5 1.0
C1 A:NAG617 4.5 54.8 1.0
O A:ARG504 4.6 35.1 1.0
CB A:ARG504 4.7 39.9 1.0
CZ A:ARG506 4.7 26.1 1.0
CG A:ARG504 4.7 48.0 1.0
C A:ARG504 4.8 35.5 1.0
O6 A:NAG617 4.8 71.8 1.0
CG A:ASN95 4.9 45.3 1.0
CB A:ASN95 5.0 38.3 1.0

Iodine binding site 3 out of 7 in 3erh

Go back to Iodine Binding Sites List in 3erh
Iodine binding site 3 out of 7 in the First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:75.8
occ:1.00
 N A:PHE229 3.7 37.3 1.0
N A:GLN217 3.8 42.8 1.0
O A:HOH919 3.9 49.6 1.0
ND2 A:ASN216 4.1 42.4 1.0
CG A:ASN216 4.1 40.1 1.0
CD2 A:PHE229 4.1 38.2 1.0
CA A:PRO228 4.1 33.8 1.0
CA A:ASN216 4.1 39.6 1.0
OD1 A:ASN216 4.2 42.2 1.0
OE1 A:GLU218 4.2 61.3 1.0
CB A:PRO228 4.3 33.4 1.0
C A:PRO228 4.4 36.2 1.0
CB A:PHE229 4.4 38.2 1.0
C A:ASN216 4.5 41.8 1.0
CA A:PHE229 4.6 38.9 1.0
CG A:PHE229 4.6 39.0 1.0
N A:GLU218 4.7 45.0 1.0
CB A:ASN216 4.7 38.8 1.0
CB A:GLN217 4.7 47.3 1.0
O A:VAL215 4.7 37.5 1.0
O A:PHE229 4.8 41.6 1.0
CA A:GLN217 4.8 45.0 1.0
CE2 A:PHE229 5.0 37.0 1.0

Iodine binding site 4 out of 7 in 3erh

Go back to Iodine Binding Sites List in 3erh
Iodine binding site 4 out of 7 in the First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:88.3
occ:1.00
 O A:HOH974 3.4 37.9 1.0
NE1 A:TRP530 3.6 37.9 1.0
CB A:PHE309 3.9 24.2 1.0
CZ2 A:TRP530 3.9 39.0 1.0
OE1 A:GLU531 4.0 47.5 1.0
CE2 A:TRP530 4.1 38.1 1.0
N A:ARG310 4.3 26.7 1.0
C A:PHE309 4.5 26.3 1.0
CB A:ARG310 4.5 29.3 1.0
CD A:GLU531 4.6 48.6 1.0
CZ2 A:TRP529 4.6 31.2 1.0
O A:HOH994 4.7 64.6 1.0
CA A:ARG310 4.7 28.6 1.0
CA A:PHE309 4.8 24.9 1.0
CA A:ILE306 4.8 28.0 1.0
O A:ILE306 4.8 27.1 1.0
CD1 A:TRP530 4.8 39.1 1.0
OE2 A:GLU531 4.9 48.1 1.0
O A:PHE309 4.9 27.8 1.0
O A:GLN305 4.9 26.0 1.0
CG A:PHE309 4.9 24.7 1.0

Iodine binding site 5 out of 7 in 3erh

Go back to Iodine Binding Sites List in 3erh
Iodine binding site 5 out of 7 in the First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:69.8
occ:1.00
 O A:GLU363 3.2 46.4 1.0
O A:HOH813 3.4 50.7 1.0
NE A:ARG397 3.6 33.0 1.0
O A:HOH795 3.8 54.3 1.0
N A:THR560 3.8 34.3 1.0
CG2 A:ILE559 4.0 29.3 1.0
CA A:GLU363 4.0 47.1 1.0
NH2 A:ARG397 4.0 37.2 1.0
C A:GLU363 4.0 47.5 1.0
CA A:ILE559 4.0 32.6 1.0
CE2 A:TYR365 4.1 42.1 1.0
OG1 A:THR560 4.2 41.5 1.0
CZ A:ARG397 4.3 35.7 1.0
N A:LYS561 4.4 37.0 1.0
C A:ILE559 4.4 32.8 1.0
CB A:GLU363 4.5 49.3 1.0
CD A:ARG397 4.5 33.5 1.0
CB A:ILE559 4.7 32.8 1.0
CD2 A:TYR365 4.7 41.3 1.0
CB A:LYS561 4.8 38.5 1.0
CG A:LYS561 4.8 41.6 1.0
O A:HIS558 4.8 38.7 1.0
CA A:THR560 4.8 36.9 1.0
CZ A:TYR365 5.0 40.9 1.0

Iodine binding site 6 out of 7 in 3erh

Go back to Iodine Binding Sites List in 3erh
Iodine binding site 6 out of 7 in the First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:28.9
occ:1.00
 N A:TRP46 3.4 23.6 1.0
O A:HOH656 3.5 33.5 1.0
N A:VAL342 3.5 21.6 1.0
CH2 A:TRP452 3.8 24.6 1.0
CB A:ASN341 3.8 23.2 1.0
CB A:VAL342 3.9 21.3 1.0
CA A:ARG45 3.9 23.8 1.0
CG1 A:VAL342 4.0 20.8 1.0
N A:ASN341 4.0 22.7 1.0
O A:ALA44 4.0 23.1 1.0
CZ2 A:TRP452 4.0 25.1 1.0
CE A:MET446 4.1 21.5 1.0
C A:ARG45 4.2 24.0 1.0
CA A:ASN341 4.2 22.6 1.0
N A:LEU47 4.2 24.9 1.0
C A:ASN341 4.3 23.8 1.0
CA A:VAL342 4.3 21.3 1.0
CB A:TRP46 4.3 22.6 1.0
CA A:TRP46 4.4 23.2 1.0
O A:LEU47 4.4 31.3 1.0
CD A:ARG45 4.4 22.1 1.0
CB A:SER340 4.5 19.5 1.0
CB A:ARG45 4.8 24.9 1.0
C A:TRP46 4.8 25.2 1.0
C A:SER340 4.8 21.6 1.0
C A:ALA44 4.9 22.5 1.0
SD A:MET446 4.9 26.5 1.0
NH1 A:ARG45 4.9 24.5 1.0
N A:ARG45 4.9 23.1 1.0
CG A:TRP46 4.9 21.8 1.0
CZ3 A:TRP452 4.9 24.6 1.0
OG A:SER340 5.0 20.9 1.0

Iodine binding site 7 out of 7 in 3erh

Go back to Iodine Binding Sites List in 3erh
Iodine binding site 7 out of 7 in the First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of First Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Crystal Structures of Substrate Complexes with Lactoperoxidases From Two Different Species within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:55.0
occ:1.00
 OG1 A:THR463 3.3 38.4 1.0
N A:LYS462 3.6 34.0 1.0
N A:THR463 3.8 34.1 1.0
CA A:GLY466 4.0 30.6 1.0
CG2 A:THR463 4.1 34.5 1.0
CB A:THR463 4.2 34.6 1.0
O A:HOH790 4.3 64.1 1.0
CA A:PRO461 4.3 33.4 1.0
CA A:LYS462 4.4 35.8 1.0
CB A:LYS462 4.4 37.1 1.0
C A:PRO461 4.5 33.2 1.0
N A:GLY466 4.5 33.3 1.0
C A:LYS462 4.6 35.0 1.0
CA A:THR463 4.6 34.7 1.0
CG A:LYS462 4.8 43.1 1.0
O A:GLN460 5.0 33.2 1.0

Reference:

I.A.Sheikh, A.K.Singh, N.Singh, M.Sinha, S.B.Singh, A.Bhushan, P.Kaur, A.Srinivasan, S.Sharma, T.P.Singh. Structural Evidence of Substrate Specificity in Mammalian Peroxidases: Structure of the Thiocyanate Complex with Lactoperoxidase and Its Interactions at 2.4 A Resolution J.Biol.Chem. V. 284 14849 2009.
ISSN: ISSN 0021-9258
PubMed: 19339248
DOI: 10.1074/JBC.M807644200
Page generated: Sun Aug 11 15:06:44 2024

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