Iodine in PDB 8k5m: Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl

The structure of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl, PDB code: 8k5m was solved by V.Viswanathan, A.K.Singh, N.Pandey, M.Sinha, 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)	43.52 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.35, 80.332, 73.391, 90, 103.94, 90
R / Rfree (%)	16.8 / 20.8

The structure of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom
Iron	(Fe)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iodine atom in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl (pdb code 8k5m). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl, PDB code: 8k5m:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I603 b:32.3 occ:0.35 I A:IOD603 0.0 32.3 0.3 I A:IOD603 0.9 25.9 0.3 CG A:PRO145 3.3 25.3 1.0 ND2 A:ASN80 3.4 22.1 1.0 O A:HOH716 3.4 52.7 1.0 CB A:PRO145 3.7 26.3 1.0 CB A:ASN80 4.0 19.3 1.0 O A:LYS146 4.2 37.7 1.0 CG A:ASN80 4.2 20.2 1.0 CG A:GLU77 4.3 23.6 1.0 CE A:LYS81 4.4 31.1 1.0 CA A:GLU77 4.5 17.6 1.0 CD A:GLU77 4.6 30.5 1.0 CB A:GLU77 4.7 20.0 1.0 CD A:PRO145 4.7 24.4 1.0 OE2 A:GLU77 4.8 31.9 1.0 CG A:LYS81 4.9 26.1 1.0 O A:GLU77 4.9 14.8 1.0

Iodine binding site 2 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I603 b:25.9 occ:0.35 I A:IOD603 0.0 25.9 0.3 I A:IOD603 0.9 32.3 0.3 ND2 A:ASN80 3.7 22.1 1.0 O A:HOH716 3.7 52.7 1.0 CE A:LYS81 3.8 31.1 1.0 CB A:ASN80 3.8 19.3 1.0 CG A:PRO145 4.2 25.3 1.0 CG A:LYS81 4.2 26.1 1.0 CG A:ASN80 4.3 20.2 1.0 CG A:GLU77 4.4 23.6 1.0 CD A:LYS81 4.5 28.9 1.0 CB A:PRO145 4.6 26.3 1.0 O A:LYS146 4.7 37.7 1.0 NZ A:LYS81 4.8 35.5 1.0 O A:GLU77 4.8 14.8 1.0 CD A:GLU77 4.8 30.5 1.0 CA A:GLU77 4.8 17.6 1.0 OE2 A:GLU77 4.9 31.9 1.0

Iodine binding site 3 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I604 b:60.2 occ:0.50 O A:HOH1035 2.6 55.6 1.0 O A:PRO424 3.0 55.4 1.0 CA A:PRO236 3.7 31.9 1.0 CB A:PRO236 3.9 34.5 1.0 C A:PRO424 4.0 43.9 1.0 N A:PRO236 4.1 38.5 1.0 CB A:PHE239 4.5 40.5 1.0 O A:HIS426 4.5 49.4 1.0 CA A:THR425 4.6 55.3 1.0 C A:THR425 4.6 55.4 1.0 CG A:PHE239 4.6 41.6 1.0 CD A:PRO236 4.6 38.1 1.0 O A:THR425 4.6 55.6 1.0 N A:THR425 4.7 42.4 1.0 C A:SER235 4.7 44.2 1.0 CG A:PRO236 4.8 37.1 1.0 CB A:PRO234 4.8 78.9 1.0 O A:SER235 4.8 41.1 1.0 CA A:PRO424 4.8 40.5 1.0 CD1 A:PHE239 4.9 41.9 1.0 CZ A:PHE422 5.0 33.0 1.0 C A:PRO236 5.0 27.3 1.0

Iodine binding site 4 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I605 b:16.4 occ:0.30 I A:IOD605 0.0 16.4 0.3 I A:IOD605 0.7 29.8 0.5 N A:GLN217 3.3 25.3 1.0 CA A:ASN216 3.8 22.1 1.0 OD1 A:ASN216 3.8 24.6 1.0 CG A:ASN216 3.8 22.0 1.0 N A:PHE229 3.9 24.8 1.0 ND2 A:ASN216 4.0 21.7 1.0 C A:ASN216 4.1 22.3 1.0 CA A:PRO228 4.2 22.2 1.0 CA A:GLN217 4.3 29.0 1.0 CG A:GLU218 4.3 38.6 1.0 CB A:GLN217 4.3 29.0 1.0 N A:GLU218 4.3 30.5 1.0 CD2 A:PHE229 4.4 20.6 1.0 CB A:ASN216 4.4 21.8 1.0 CB A:PRO228 4.4 21.1 1.0 OE2 A:GLU218 4.5 59.0 1.0 CB A:PHE229 4.6 23.0 1.0 C A:PRO228 4.6 24.5 1.0 CD A:GLU218 4.6 50.6 1.0 O A:VAL215 4.7 24.6 1.0 CG A:PHE229 4.8 21.6 1.0 C A:GLN217 4.8 32.6 1.0 CA A:PHE229 4.8 23.5 1.0 O A:HOH987 4.8 53.3 1.0 CG A:GLN217 4.8 31.7 1.0 N A:ASN216 4.8 22.7 1.0 ND2 A:ASN231 4.8 63.4 1.0 CB A:GLU218 4.9 34.3 1.0

Iodine binding site 5 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I605 b:29.8 occ:0.50 I A:IOD605 0.0 29.8 0.5 I A:IOD605 0.7 16.4 0.3 N A:PHE229 3.6 24.8 1.0 N A:GLN217 4.1 25.3 1.0 ND2 A:ASN231 4.1 63.4 1.0 CA A:PRO228 4.2 22.2 1.0 CB A:PHE229 4.2 23.0 1.0 O A:HOH987 4.2 53.3 1.0 CB A:PRO228 4.2 21.1 1.0 CD2 A:PHE229 4.3 20.6 1.0 CG A:ASN216 4.3 22.0 1.0 OD1 A:ASN216 4.3 24.6 1.0 ND2 A:ASN216 4.4 21.7 1.0 CA A:ASN216 4.4 22.1 1.0 CA A:PHE229 4.4 23.5 1.0 C A:PRO228 4.4 24.5 1.0 O A:PHE229 4.4 29.6 1.0 OE2 A:GLU218 4.4 59.0 1.0 CG A:PHE229 4.5 21.6 1.0 CG A:GLU218 4.6 38.6 1.0 CD A:GLU218 4.7 50.6 1.0 C A:ASN216 4.8 22.3 1.0 C A:PHE229 4.9 27.4 1.0 CB A:GLN217 4.9 29.0 1.0 CB A:ASN216 5.0 21.8 1.0 N A:GLU218 5.0 30.5 1.0 CA A:GLN217 5.0 29.0 1.0

Iodine binding site 6 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I606 b:21.9 occ:0.70 O A:HOH1092 3.4 42.8 1.0 O A:HOH706 3.5 26.3 1.0 O A:HOH988 3.8 34.4 1.0 NE1 A:TRP530 3.8 18.8 1.0 CB A:PHE309 3.8 16.6 1.0 CZ2 A:TRP530 4.0 24.5 1.0 CE2 A:TRP530 4.3 21.2 1.0 N A:ARG310 4.3 21.0 1.0 CB A:ARG310 4.4 22.5 1.0 CA A:ILE306 4.4 16.5 1.0 C A:PHE309 4.6 18.6 1.0 CZ2 A:TRP529 4.6 17.1 1.0 CG1 A:ILE306 4.7 21.8 1.0 O A:ILE306 4.7 17.5 1.0 CA A:ARG310 4.7 20.3 1.0 CA A:PHE309 4.8 16.5 1.0 O A:GLN305 4.8 14.4 1.0 CB A:ILE306 4.9 18.6 1.0 CG A:PHE309 5.0 15.3 1.0 OE1 A:GLU531 5.0 34.2 1.0 CG2 A:ILE306 5.0 18.1 1.0

Iodine binding site 7 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I607 b:17.5 occ:0.40 I A:IOD607 0.0 17.5 0.4 I A:IOD607 0.7 15.8 0.4 NE A:ARG397 3.5 24.6 1.0 NH2 A:ARG397 3.6 25.8 1.0 N A:THR560 3.6 18.1 1.0 CA A:ILE559 3.9 19.5 1.0 CG A:GLU363 3.9 24.7 1.0 CA A:GLU363 4.0 21.2 1.0 CZ A:ARG397 4.0 25.1 1.0 NZ A:LYS561 4.1 39.6 1.0 CD A:LYS561 4.1 37.0 1.0 CB A:GLU363 4.1 23.4 1.0 CG2 A:ILE559 4.1 19.4 1.0 O A:GLU363 4.1 24.9 1.0 O A:HIS558 4.2 29.3 1.0 CE A:LYS561 4.2 40.9 1.0 C A:ILE559 4.3 17.7 1.0 OG1 A:THR560 4.3 20.1 1.0 N A:LYS561 4.3 23.0 1.0 CB A:ILE559 4.4 19.4 1.0 CD A:ARG397 4.5 21.6 1.0 CE1 A:TYR365 4.6 23.7 1.0 C A:GLU363 4.6 23.1 1.0 CG1 A:ILE559 4.6 20.8 1.0 CA A:THR560 4.7 21.5 1.0 N A:ILE559 4.9 19.6 1.0 C A:THR560 5.0 22.5 1.0 C A:HIS558 5.0 24.9 1.0

Iodine binding site 8 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I607 b:15.8 occ:0.40 I A:IOD607 0.0 15.8 0.4 I A:IOD607 0.7 17.5 0.4 CD A:LYS561 3.5 37.0 1.0 N A:THR560 3.6 18.1 1.0 CE A:LYS561 3.6 40.9 1.0 NZ A:LYS561 3.7 39.6 1.0 NE A:ARG397 3.8 24.6 1.0 N A:LYS561 3.9 23.0 1.0 O A:GLU363 3.9 24.9 1.0 CG2 A:ILE559 4.1 19.4 1.0 CE1 A:TYR365 4.1 23.7 1.0 CA A:ILE559 4.1 19.5 1.0 OG1 A:THR560 4.1 20.1 1.0 CA A:GLU363 4.2 21.2 1.0 NH2 A:ARG397 4.2 25.8 1.0 CB A:LYS561 4.3 25.7 1.0 C A:ILE559 4.4 17.7 1.0 CG A:GLU363 4.4 24.7 1.0 CB A:GLU363 4.4 23.4 1.0 CG A:LYS561 4.5 31.9 1.0 CZ A:ARG397 4.5 25.1 1.0 CA A:THR560 4.5 21.5 1.0 C A:GLU363 4.5 23.1 1.0 CB A:ILE559 4.6 19.4 1.0 C A:THR560 4.6 22.5 1.0 CA A:LYS561 4.6 23.6 1.0 CD A:ARG397 4.7 21.6 1.0 O A:LYS561 4.7 20.3 1.0 O A:HIS558 4.8 29.3 1.0 OH A:TYR365 4.8 20.3 1.0 CZ A:TYR365 4.9 21.9 1.0 CD1 A:TYR365 4.9 20.5 1.0 CG1 A:ILE559 4.9 20.8 1.0 CB A:THR560 4.9 23.1 1.0

Iodine binding site 9 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I608 b:64.9 occ:0.70 NH1 A:ARG96 3.6 20.8 1.0 ND2 A:ASN95 3.8 34.5 1.0 NH2 A:ARG96 3.8 18.3 1.0 NH1 A:ARG506 3.9 21.7 1.0 NH2 A:ARG506 4.0 19.5 1.0 O5 A:NAG626 4.1 45.2 1.0 O6 A:NAG626 4.1 44.7 1.0 CZ A:ARG96 4.2 20.4 1.0 CA A:ARG504 4.3 28.6 1.0 C1 A:NAG626 4.3 39.5 1.0 CZ A:ARG506 4.4 19.8 1.0 O A:ARG504 4.6 23.2 1.0 C2 A:NAG626 4.6 44.8 1.0 C A:ARG504 4.7 22.2 1.0 CB A:ASN95 4.8 23.9 1.0 CG A:ASN95 4.8 28.9 1.0 O7 A:NAG626 4.9 53.0 1.0 CG A:ARG504 4.9 40.7 1.0 CB A:ARG504 4.9 33.8 1.0

Iodine binding site 10 out of 16 in the Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range: probe atom residue distance (Å) B Occ A:I609 b:28.4 occ:0.35 I A:IOD609 0.0 28.4 0.3 I A:IOD609 1.0 23.9 0.3 O4 A:PEG620 3.7 45.5 1.0 C4 A:PEG620 3.8 46.0 1.0 N A:LYS462 3.9 25.5 1.0 CA A:GLY466 4.0 20.4 1.0 OG1 A:THR463 4.0 24.0 1.0 CA A:PRO461 4.3 23.1 1.0 C3 A:PEG620 4.4 46.8 1.0 N A:GLY466 4.5 20.9 1.0 N A:THR463 4.6 24.8 1.0 C A:PRO461 4.6 22.8 1.0 CA A:LYS462 4.9 29.3 1.0 CG2 A:THR463 4.9 27.9 1.0 CB A:LYS462 4.9 31.1 1.0 CB A:THR463 5.0 25.8 1.0 O A:GLN460 5.0 26.0 1.0 CB A:PRO461 5.0 24.6 1.0

V.Viswanathan, A.K.Singh, N.Pandey, M.Sinha, P.Kaur, S.Sharma, T.P.Singh. Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl To Be Published.