Iodine in PDB 3faq: Crystal Structure of Lactoperoxidase Complex with Cyanide

The structure of Crystal Structure of Lactoperoxidase Complex with Cyanide, PDB code: 3faq was solved by I.A.Sheikh, N.Singh, S.Sharma, P.Kaur, A.Srinivasan, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.94 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.453, 80.665, 77.796, 90.00, 102.87, 90.00
R / Rfree (%)	20.8 / 23.5

The structure of Crystal Structure of Lactoperoxidase Complex with Cyanide also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Iodine atom in the Crystal Structure of Lactoperoxidase Complex with Cyanide (pdb code 3faq). 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 Lactoperoxidase Complex with Cyanide, PDB code: 3faq:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Crystal Structure of Lactoperoxidase Complex with Cyanide


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 Lactoperoxidase Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:I597 b:52.8 occ:0.50 ND2 A:ASN80 3.6 20.8 1.0 CB A:ASN80 3.7 22.7 1.0 CG A:GLU77 3.8 30.9 1.0 CG A:PRO145 3.9 36.6 1.0 O A:HOH771 4.0 50.1 1.0 O A:LYS146 4.1 44.9 1.0 CG A:ASN80 4.2 21.9 1.0 CE A:LYS81 4.3 31.2 1.0 CB A:PRO145 4.4 38.4 1.0 CD A:LYS81 4.7 29.3 1.0 CD A:GLU77 4.7 33.6 1.0 CG A:LYS81 4.8 27.4 1.0 O A:ASN147 4.8 42.2 1.0 CA A:GLU77 4.8 23.5 1.0 CB A:GLU77 4.9 26.0 1.0 C A:ASN147 5.0 42.1 1.0

Iodine binding site 2 out of 7 in the Crystal Structure of Lactoperoxidase Complex with Cyanide


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 Lactoperoxidase Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:I598 b:56.2 occ:0.50 O A:HOH779 2.9 45.2 1.0 NE A:ARG504 3.7 43.1 1.0 O7 A:NAG604 3.9 62.8 1.0 NH1 A:ARG96 3.9 17.9 1.0 NH2 A:ARG504 4.0 42.3 1.0 NH1 A:ARG506 4.0 18.1 1.0 CA A:ARG504 4.2 30.4 1.0 ND2 A:ASN95 4.2 51.1 1.0 NH2 A:ARG96 4.3 17.4 1.0 NH2 A:ARG506 4.3 19.6 1.0 CZ A:ARG504 4.3 43.0 1.0 O A:ARG504 4.4 30.7 1.0 CZ A:ARG96 4.6 20.3 1.0 C A:ARG504 4.6 29.9 1.0 CZ A:ARG506 4.6 18.7 1.0 C2 A:NAG604 4.6 60.9 1.0 O5 A:NAG604 4.7 61.3 1.0 CD A:ARG504 4.7 40.6 1.0 C1 A:NAG604 4.8 57.7 1.0 CB A:ARG504 4.8 32.8 1.0 C7 A:NAG604 4.8 63.3 1.0 O A:HOH745 5.0 33.8 1.0

Iodine binding site 3 out of 7 in the Crystal Structure of Lactoperoxidase Complex with Cyanide


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 Lactoperoxidase Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:I599 b:79.1 occ:1.00 N A:PHE229 3.3 40.8 1.0 CB A:ASN216 3.7 36.3 1.0 CG A:ASN216 3.8 36.3 1.0 CA A:ASN216 3.9 36.8 1.0 CB A:PHE229 3.9 40.7 1.0 N A:GLN217 4.0 40.4 1.0 CD2 A:PHE229 4.0 39.3 1.0 O A:HOH851 4.0 34.1 1.0 OD1 A:ASN216 4.1 37.6 1.0 CA A:PRO228 4.1 37.9 1.0 C A:PRO228 4.2 39.7 1.0 CA A:PHE229 4.2 41.6 1.0 O A:HOH753 4.2 47.5 1.0 ND2 A:ASN216 4.3 36.0 1.0 CG A:PHE229 4.3 40.2 1.0 OE1 A:GLU218 4.4 50.9 1.0 CB A:PRO228 4.5 37.3 1.0 C A:ASN216 4.5 39.0 1.0 O A:HOH876 4.7 47.2 1.0 N A:GLU218 4.8 43.8 1.0 O A:PHE229 4.8 44.8 1.0 O A:VAL215 4.9 32.9 1.0 CE2 A:PHE229 5.0 39.2 1.0

Iodine binding site 4 out of 7 in the Crystal Structure of Lactoperoxidase Complex with Cyanide


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 Lactoperoxidase Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:I600 b:90.2 occ:1.00 O A:HOH670 3.5 25.0 1.0 NE1 A:TRP530 3.7 31.1 1.0 CZ2 A:TRP530 4.0 30.3 1.0 CB A:PHE309 4.0 19.3 1.0 CE2 A:TRP530 4.2 31.3 1.0 OE1 A:GLU531 4.2 33.1 1.0 N A:ARG310 4.4 21.3 1.0 CB A:ARG310 4.4 20.5 1.0 CA A:ILE306 4.5 22.5 1.0 O A:ILE306 4.6 23.3 1.0 C A:PHE309 4.6 21.0 1.0 CG2 A:ILE306 4.7 21.6 1.0 CA A:ARG310 4.8 21.8 1.0 CD A:GLU531 4.8 35.9 1.0 O A:GLN305 4.8 23.3 1.0 CA A:PHE309 4.9 20.5 1.0 CD1 A:TRP530 4.9 31.1 1.0 CZ2 A:TRP529 5.0 23.7 1.0

Iodine binding site 5 out of 7 in the Crystal Structure of Lactoperoxidase Complex with Cyanide


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 Lactoperoxidase Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:I601 b:66.1 occ:1.00 O A:GLU363 3.4 45.2 1.0 NE A:ARG397 3.4 29.7 1.0 N A:THR560 3.8 35.0 1.0 CG2 A:ILE559 3.8 33.8 1.0 OG1 A:THR560 4.0 39.1 1.0 NH2 A:ARG397 4.0 30.2 1.0 CA A:ILE559 4.1 34.8 1.0 CA A:GLU363 4.1 43.8 1.0 CZ A:ARG397 4.2 29.8 1.0 C A:GLU363 4.2 44.5 1.0 CD A:ARG397 4.3 29.7 1.0 CE2 A:TYR365 4.3 34.9 1.0 N A:LYS561 4.4 35.5 1.0 C A:ILE559 4.5 34.8 1.0 CB A:ILE559 4.6 34.9 1.0 CB A:GLU363 4.6 45.2 1.0 O A:HIS558 4.8 36.3 1.0 CA A:THR560 4.8 36.7 1.0 CD2 A:TYR365 4.9 37.0 1.0 O A:LYS561 4.9 33.6 1.0 CB A:LYS561 5.0 35.2 1.0 CG A:LYS561 5.0 37.5 1.0 OE1 A:GLU363 5.0 48.2 1.0 CB A:THR560 5.0 37.5 1.0

Iodine binding site 6 out of 7 in the Crystal Structure of Lactoperoxidase Complex with Cyanide


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 Lactoperoxidase Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:I602 b:21.1 occ:1.00 N A:TRP46 3.4 14.8 1.0 N A:VAL342 3.6 17.2 1.0 CH2 A:TRP452 3.8 19.5 1.0 CB A:ASN341 3.8 20.9 1.0 CA A:ARG45 3.9 14.6 1.0 N A:ASN341 3.9 20.3 1.0 CG1 A:VAL342 4.0 15.3 1.0 CZ2 A:TRP452 4.0 18.7 1.0 CB A:VAL342 4.1 14.5 1.0 O A:ALA44 4.1 17.3 1.0 C A:ARG45 4.1 15.0 1.0 CA A:ASN341 4.2 20.2 1.0 N A:LEU47 4.2 17.7 1.0 CE A:MET446 4.2 19.6 1.0 C A:ASN341 4.3 19.5 1.0 CB A:TRP46 4.3 15.7 1.0 CA A:TRP46 4.3 15.3 1.0 O A:LEU47 4.4 16.6 1.0 CD A:ARG45 4.4 13.5 1.0 CA A:VAL342 4.4 15.2 1.0 SD A:MET446 4.7 23.9 1.0 CB A:SER340 4.7 20.5 1.0 NH1 A:ARG45 4.7 10.8 1.0 CB A:ARG45 4.7 14.5 1.0 C A:TRP46 4.8 16.7 1.0 N A:ARG45 4.9 14.6 1.0 C A:ALA44 4.9 15.5 1.0 OG A:SER340 4.9 18.9 1.0 C A:SER340 4.9 21.7 1.0 CG A:TRP46 4.9 16.9 1.0 CG A:ARG45 5.0 14.9 1.0 CZ3 A:TRP452 5.0 19.6 1.0

Iodine binding site 7 out of 7 in the Crystal Structure of Lactoperoxidase Complex with Cyanide


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 Lactoperoxidase Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:I603 b:61.6 occ:1.00 OG1 A:THR463 3.2 25.3 1.0 N A:LYS462 3.6 26.4 1.0 CA A:GLY466 3.9 23.8 1.0 N A:THR463 4.0 26.1 1.0 CA A:PRO461 4.1 24.0 1.0 CB A:THR463 4.3 25.6 1.0 CG2 A:THR463 4.3 22.5 1.0 C A:PRO461 4.3 24.7 1.0 N A:GLY466 4.5 25.1 1.0 CA A:LYS462 4.5 27.4 1.0 C A:LYS462 4.6 26.5 1.0 CB A:PRO461 4.6 23.1 1.0 CA A:THR463 4.7 25.3 1.0 CB A:LYS462 4.9 28.4 1.0

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