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Iodine in PDB 3eri: 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: 3eri was solved by A.K.Singh, N.Singh, I.A.Sheikh, 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) 19.48 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.537, 80.592, 77.832, 90.00, 102.63, 90.00
R / Rfree (%) 18.1 / 20.1

Other elements in 3eri:

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

Iodine binding site 1 out of 7 in 3eri

Go back to Iodine Binding Sites List in 3eri
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:99.4
occ:1.00
 O A:HOH753 3.5 47.7 1.0
ND2 A:ASN80 3.5 25.9 1.0
CG A:PRO145 3.8 26.3 1.0
CB A:ASN80 3.9 26.4 1.0
CE A:LYS81 4.1 32.3 1.0
CB A:PRO145 4.2 28.7 1.0
CG A:ASN80 4.2 28.6 1.0
O A:LYS146 4.3 42.0 1.0
CG A:GLU77 4.5 33.3 1.0
OE2 A:GLU77 4.5 36.1 1.0
CG A:LYS81 4.6 28.9 1.0
NZ A:LYS81 4.7 34.7 1.0
CD A:GLU77 4.7 35.9 1.0
CA A:GLU77 4.8 26.6 1.0
CB A:GLU77 4.9 29.4 1.0
CD A:LYS81 5.0 31.0 1.0

Iodine binding site 2 out of 7 in 3eri

Go back to Iodine Binding Sites List in 3eri
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:59.3
occ:0.50
 NH2 A:ARG504 3.4 45.5 1.0
NE A:ARG504 3.6 46.2 1.0
NH1 A:ARG96 3.7 14.9 1.0
CZ A:ARG504 3.7 46.3 1.0
NH2 A:ARG96 4.0 13.6 1.0
NH1 A:ARG506 4.1 21.1 1.0
ND2 A:ASN95 4.1 51.9 1.0
NH2 A:ARG506 4.1 19.4 1.0
CZ A:ARG96 4.3 17.4 1.0
CA A:ARG504 4.3 32.3 1.0
O7 A:NAG617 4.4 56.6 1.0
O5 A:NAG617 4.5 61.6 1.0
CZ A:ARG506 4.6 19.3 1.0
CD A:ARG504 4.6 42.5 1.0
C2 A:NAG617 4.6 60.5 1.0
NH1 A:ARG504 4.6 46.9 1.0
O A:ARG504 4.7 30.9 1.0
C A:ARG504 4.7 30.9 1.0
C1 A:NAG617 4.7 58.0 1.0
O6 A:NAG617 4.8 64.4 1.0
CB A:ARG504 5.0 34.7 1.0

Iodine binding site 3 out of 7 in 3eri

Go back to Iodine Binding Sites List in 3eri
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:67.8
occ:1.00
 O A:HOH843 3.3 34.3 1.0
N A:PHE229 3.7 33.0 1.0
N A:GLN217 4.0 41.0 1.0
CG A:ASN216 4.0 34.6 1.0
ND2 A:ASN216 4.0 35.5 1.0
CA A:ASN216 4.0 37.2 1.0
CB A:PRO228 4.1 30.6 1.0
CA A:PRO228 4.1 30.2 1.0
OD1 A:ASN216 4.1 35.7 1.0
CD2 A:PHE229 4.2 36.4 1.0
C A:PRO228 4.4 31.0 1.0
CB A:PHE229 4.5 35.1 1.0
OE1 A:GLU218 4.5 51.6 1.0
C A:ASN216 4.5 38.6 1.0
CB A:ASN216 4.6 35.2 1.0
O A:VAL215 4.7 34.2 1.0
CA A:PHE229 4.7 35.6 1.0
O A:HOH879 4.7 44.2 1.0
CG A:PHE229 4.7 35.9 1.0
O A:HOH915 4.9 48.6 1.0
N A:GLU218 4.9 45.5 1.0
O A:PHE229 5.0 38.2 1.0

Iodine binding site 4 out of 7 in 3eri

Go back to Iodine Binding Sites List in 3eri
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:86.9
occ:1.00
 O A:HOH819 3.8 37.4 1.0
NE1 A:TRP530 3.8 29.2 1.0
CB A:PHE309 3.9 17.7 1.0
CZ2 A:TRP530 4.0 28.1 1.0
CE2 A:TRP530 4.3 28.6 1.0
OE1 A:GLU531 4.3 45.3 1.0
N A:ARG310 4.5 23.1 1.0
CZ2 A:TRP529 4.5 23.7 1.0
CB A:ARG310 4.6 23.5 1.0
C A:PHE309 4.6 21.4 1.0
CA A:ILE306 4.8 24.0 1.0
CD A:GLU531 4.8 46.0 1.0
CA A:PHE309 4.8 20.2 1.0
O A:GLN305 4.8 20.9 1.0
CA A:ARG310 4.9 23.6 1.0
O A:ILE306 4.9 23.7 1.0
CG A:PHE309 4.9 18.3 1.0
OE2 A:GLU531 5.0 46.8 1.0

Iodine binding site 5 out of 7 in 3eri

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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:65.1
occ:1.00
 O A:GLU363 3.4 43.3 1.0
NE A:ARG397 3.5 31.0 1.0
O A:HOH847 3.8 48.2 1.0
N A:THR560 3.9 36.9 1.0
CG2 A:ILE559 4.0 29.7 1.0
C A:GLU363 4.1 45.1 1.0
CA A:ILE559 4.1 35.4 1.0
CG A:GLU363 4.2 48.3 1.0
OG1 A:THR560 4.2 37.4 1.0
CE2 A:TYR365 4.2 42.2 1.0
CD A:ARG397 4.2 29.1 1.0
CA A:GLU363 4.2 45.0 1.0
CZ A:ARG397 4.4 30.7 1.0
NH2 A:ARG397 4.4 31.4 1.0
N A:LYS561 4.4 38.7 1.0
CB A:ILE559 4.5 33.8 1.0
C A:ILE559 4.6 35.2 1.0
CG A:LYS561 4.7 42.5 1.0
CD2 A:TYR365 4.8 43.1 1.0
CB A:GLU363 4.8 46.5 1.0
CG1 A:ILE559 4.8 33.5 1.0
CB A:LYS561 4.8 39.6 1.0
O A:HIS558 4.9 39.3 1.0
CA A:THR560 4.9 37.2 1.0
O A:LYS561 5.0 36.3 1.0

Iodine binding site 6 out of 7 in 3eri

Go back to Iodine Binding Sites List in 3eri
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:26.1
occ:1.00
 O A:HOH649 3.3 19.3 1.0
N A:VAL342 3.5 17.9 1.0
N A:TRP46 3.5 21.6 1.0
CH2 A:TRP452 3.7 16.3 1.0
CB A:ASN341 3.7 25.1 1.0
O A:ALA44 3.8 19.1 1.0
CB A:VAL342 3.9 18.4 1.0
N A:ASN341 3.9 22.0 1.0
CZ2 A:TRP452 3.9 15.0 1.0
CA A:ARG45 4.0 20.1 1.0
CG1 A:VAL342 4.0 17.8 1.0
CE A:MET446 4.1 18.9 1.0
CA A:ASN341 4.2 21.0 1.0
N A:LEU47 4.2 21.3 1.0
C A:ARG45 4.2 22.1 1.0
CA A:VAL342 4.3 18.2 1.0
C A:ASN341 4.3 20.3 1.0
CB A:TRP46 4.4 21.2 1.0
CD A:ARG45 4.4 16.0 1.0
CB A:SER340 4.4 16.4 1.0
CA A:TRP46 4.4 20.6 1.0
O A:LEU47 4.5 22.9 1.0
NH1 A:ARG45 4.7 15.9 1.0
SD A:MET446 4.8 23.9 1.0
C A:ALA44 4.8 17.5 1.0
C A:SER340 4.8 21.4 1.0
OG A:SER340 4.8 15.9 1.0
C A:TRP46 4.8 21.2 1.0
CB A:ARG45 4.8 18.2 1.0
N A:ARG45 4.9 18.8 1.0
CG A:TRP46 4.9 20.2 1.0
CZ3 A:TRP452 4.9 14.5 1.0

Iodine binding site 7 out of 7 in 3eri

Go back to Iodine Binding Sites List in 3eri
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:60.9
occ:1.00
 OG1 A:THR463 3.3 28.2 1.0
N A:LYS462 3.5 27.5 1.0
N A:THR463 3.9 30.9 1.0
CA A:GLY466 4.0 29.7 1.0
CA A:PRO461 4.2 26.3 1.0
CB A:THR463 4.3 30.4 1.0
CA A:LYS462 4.3 29.8 1.0
CG2 A:THR463 4.3 27.5 1.0
CB A:LYS462 4.3 30.7 1.0
C A:PRO461 4.4 26.7 1.0
O A:HOH936 4.5 50.6 1.0
C A:LYS462 4.5 30.4 1.0
N A:GLY466 4.5 31.4 1.0
CA A:THR463 4.7 29.2 1.0
CB A:PRO461 4.9 25.1 1.0
CG A:LYS462 5.0 31.9 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 15:06:45 2024

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