Iodine in PDB 3gh8: Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)

The structure of Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit), PDB code: 3gh8 was solved by S.R.Thomas, P.M.Mctamney, J.M.Adler, N.Laronde-Leblanc, S.E.Rokita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.610, 112.567, 189.253, 90.00, 89.92, 90.00
R / Rfree (%)	18.1 / 26.4

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) (pdb code 3gh8). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit), PDB code: 3gh8:
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 Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


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 Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:41.0 occ:0.80 I1 A:TYI302 0.0 41.0 0.8 CE1 A:TYI302 2.1 42.0 1.0 CD1 A:TYI302 3.0 41.7 1.0 NH2 A:ARG100 3.1 29.8 1.0 CZ A:TYI302 3.1 41.1 1.0 OH A:TYI302 3.5 39.8 1.0 CD1 A:LEU172 3.6 36.6 1.0 O2' A:FMN301 3.6 19.4 1.0 O2 A:FMN301 3.8 28.4 1.0 C2 A:FMN301 3.8 29.6 1.0 CZ A:ARG100 3.9 29.1 1.0 N1 A:FMN301 3.9 30.6 1.0 CB A:LEU172 4.0 37.7 1.0 CG2 A:THR174 4.2 34.9 1.0 CG A:LEU172 4.2 37.5 1.0 OG1 A:THR174 4.2 34.1 1.0 NE A:ARG100 4.3 30.4 1.0 CG A:TYI302 4.3 40.8 1.0 N3 A:FMN301 4.3 28.7 1.0 CB A:THR174 4.4 35.4 1.0 CE2 A:TYI302 4.4 41.0 1.0 CD1 A:LEU169 4.6 39.7 1.0 C10 A:FMN301 4.6 28.2 1.0 CG A:LEU169 4.7 37.0 1.0 CD2 A:LEU172 4.8 36.1 1.0 NH1 A:ARG100 4.8 30.3 1.0 CD2 A:TYI302 4.9 40.9 1.0 C2' A:FMN301 4.9 22.3 1.0 C4 A:FMN301 5.0 28.2 1.0

Iodine binding site 2 out of 16 in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


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 Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:42.6 occ:0.80 I2 A:TYI302 0.0 42.6 0.8 CE2 A:TYI302 2.1 41.0 1.0 CZ A:TYI302 3.0 41.1 1.0 OH A:TYI302 3.0 39.8 1.0 CD2 A:TYI302 3.1 40.9 1.0 CA B:GLY125 3.6 29.4 1.0 CD1 B:TYR208 3.6 29.7 1.0 CE1 B:TYR208 3.7 30.5 1.0 N B:ALA126 3.7 30.9 1.0 CB B:TYR207 3.8 28.9 1.0 N5 A:FMN301 3.9 28.1 1.0 C B:GLY125 4.0 30.5 1.0 C5A A:FMN301 4.1 28.9 1.0 C6 A:FMN301 4.2 28.6 1.0 NE1 A:TRP165 4.2 35.2 1.0 CZ2 A:TRP165 4.3 37.3 1.0 CE1 A:TYI302 4.4 42.0 1.0 CG A:TYI302 4.4 40.8 1.0 C4A A:FMN301 4.5 28.6 1.0 CG B:TYR207 4.5 28.4 1.0 CE2 A:TRP165 4.6 36.0 1.0 CA B:ALA126 4.8 30.5 1.0 CD1 A:TYI302 4.9 41.7 1.0 N B:GLY125 4.9 30.5 1.0 C9A A:FMN301 4.9 28.7 1.0 C4 A:FMN301 4.9 28.2 1.0 CB B:ALA126 4.9 30.1 1.0 CG B:TYR208 5.0 30.6 1.0 CD1 A:LEU169 5.0 39.7 1.0

Iodine binding site 3 out of 16 in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


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 Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:38.2 occ:0.80 I1 B:TYI302 0.0 38.2 0.8 CE1 B:TYI302 2.0 39.9 1.0 CZ B:TYI302 2.9 40.6 1.0 CD1 B:TYI302 3.0 38.9 1.0 OH B:TYI302 3.1 35.2 1.0 NH2 B:ARG100 3.2 26.2 1.0 CD1 B:LEU172 3.3 37.8 1.0 CD2 B:LEU169 3.7 26.6 1.0 O2' B:FMN301 3.7 16.4 1.0 O2 B:FMN301 3.7 25.9 1.0 C2 B:FMN301 3.8 25.9 1.0 CB B:LEU172 3.8 35.5 1.0 CG2 B:THR174 3.8 27.4 1.0 N1 B:FMN301 3.9 25.7 1.0 CZ B:ARG100 4.0 26.2 1.0 CG B:LEU172 4.1 36.8 1.0 OG1 B:THR174 4.2 25.9 1.0 CE2 B:TYI302 4.3 39.7 1.0 CG B:TYI302 4.3 38.6 1.0 NE B:ARG100 4.4 25.0 1.0 N3 B:FMN301 4.4 24.4 1.0 O4' B:FMN301 4.6 18.5 1.0 CD2 B:LEU172 4.6 36.4 1.0 C10 B:FMN301 4.6 23.7 1.0 CB B:THR174 4.6 28.6 1.0 NH1 B:ARG100 4.8 24.0 1.0 CD2 B:TYI302 4.8 37.1 1.0 C2' B:FMN301 4.9 19.7 1.0

Iodine binding site 4 out of 16 in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


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 Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:46.5 occ:1.00 I2 B:TYI302 0.0 46.5 1.0 CE2 B:TYI302 2.1 39.7 1.0 CD2 B:TYI302 3.1 37.1 1.0 CZ B:TYI302 3.1 40.6 1.0 OH B:TYI302 3.4 35.2 1.0 N A:ALA126 3.5 27.6 1.0 CD1 A:TYR208 3.7 30.6 1.0 CA A:GLY125 3.7 26.5 1.0 CB A:TYR207 3.7 24.6 1.0 CE1 A:TYR208 3.7 31.4 1.0 N5 B:FMN301 4.0 23.8 1.0 CZ2 B:TRP165 4.0 31.5 1.0 C A:GLY125 4.0 27.6 1.0 NE1 B:TRP165 4.1 28.3 1.0 C5A B:FMN301 4.2 24.6 1.0 C6 B:FMN301 4.4 24.5 1.0 CG A:TYR207 4.4 24.3 1.0 CG B:TYI302 4.4 38.6 1.0 CE2 B:TRP165 4.4 30.4 1.0 CE1 B:TYI302 4.5 39.9 1.0 C4A B:FMN301 4.5 24.6 1.0 CB A:ALA126 4.5 27.1 1.0 CA A:ALA126 4.5 27.5 1.0 OG1 B:THR235 4.7 33.6 1.0 CD2 A:TYR207 4.9 19.4 1.0 C4 B:FMN301 4.9 26.2 1.0 C9A B:FMN301 5.0 24.1 1.0 CD1 B:TYI302 5.0 38.9 1.0 O4 B:FMN301 5.0 30.2 1.0 CG A:TYR208 5.0 31.3 1.0 O A:TYR207 5.0 28.2 1.0

Iodine binding site 5 out of 16 in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


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 Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ C:I302 b:40.6 occ:0.80 I1 C:TYI302 0.0 40.6 0.8 CE1 C:TYI302 2.1 44.2 1.0 CZ C:TYI302 2.9 43.8 1.0 OH C:TYI302 3.0 39.6 1.0 CD1 C:TYI302 3.1 43.6 1.0 NH2 C:ARG100 3.4 23.8 1.0 CD1 C:LEU172 3.5 44.8 1.0 O2' C:FMN301 3.6 18.6 1.0 C2 C:FMN301 3.8 26.5 1.0 O2 C:FMN301 3.8 26.5 1.0 N1 C:FMN301 3.9 26.6 1.0 CB C:LEU172 4.0 44.9 1.0 CG2 C:THR174 4.0 40.0 1.0 OG1 C:THR174 4.0 41.1 1.0 CZ C:ARG100 4.1 24.8 1.0 CD1 C:LEU169 4.3 39.6 1.0 CG C:LEU172 4.3 44.4 1.0 N3 C:FMN301 4.3 25.2 1.0 CE2 C:TYI302 4.3 45.6 1.0 CG C:LEU169 4.4 42.0 1.0 CG C:TYI302 4.4 42.6 1.0 NE C:ARG100 4.5 27.9 1.0 C10 C:FMN301 4.5 25.9 1.0 CB C:THR174 4.6 39.6 1.0 NH1 C:ARG100 4.8 25.2 1.0 CD2 C:TYI302 4.9 43.5 1.0 C4 C:FMN301 4.9 25.5 1.0 C2' C:FMN301 4.9 19.1 1.0 C4A C:FMN301 5.0 26.1 1.0

Iodine binding site 6 out of 16 in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


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 Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ C:I302 b:49.1 occ:1.00 I2 C:TYI302 0.0 49.1 1.0 CE2 C:TYI302 2.1 45.6 1.0 CZ C:TYI302 3.1 43.8 1.0 CD2 C:TYI302 3.1 43.5 1.0 OH C:TYI302 3.3 39.6 1.0 CA D:GLY125 3.5 26.9 1.0 N D:ALA126 3.6 28.0 1.0 CB D:TYR207 3.7 31.6 1.0 CD1 D:TYR208 3.7 35.3 1.0 CE1 D:TYR208 3.7 36.9 1.0 N5 C:FMN301 3.9 26.4 1.0 C D:GLY125 3.9 28.2 1.0 C5A C:FMN301 4.1 26.2 1.0 C6 C:FMN301 4.1 25.4 1.0 NE1 C:TRP165 4.3 33.0 1.0 CG D:TYR207 4.3 31.4 1.0 CZ2 C:TRP165 4.3 35.0 1.0 CG C:TYI302 4.4 42.6 1.0 CE1 C:TYI302 4.5 44.2 1.0 C4A C:FMN301 4.5 26.1 1.0 CE2 C:TRP165 4.6 33.1 1.0 OG1 C:THR235 4.7 34.0 1.0 CA D:ALA126 4.7 27.2 1.0 CB D:ALA126 4.8 26.4 1.0 C9A C:FMN301 4.8 25.0 1.0 CD2 D:TYR207 4.8 29.8 1.0 O4 C:FMN301 4.9 25.8 1.0 N D:GLY125 4.9 27.9 1.0 O D:GLY125 4.9 28.2 1.0 C7 C:FMN301 4.9 26.0 1.0 C4 C:FMN301 4.9 25.5 1.0 CD1 D:TYR207 5.0 28.6 1.0 CA D:TYR207 5.0 32.0 1.0 O D:TYR207 5.0 30.6 1.0 CD1 C:TYI302 5.0 43.6 1.0

Iodine binding site 7 out of 16 in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


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 Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ D:I302 b:41.6 occ:0.80 I1 D:TYI302 0.0 41.6 0.8 CE1 D:TYI302 2.1 43.8 1.0 CZ D:TYI302 3.0 43.1 1.0 OH D:TYI302 3.1 42.4 1.0 CD1 D:TYI302 3.1 43.8 1.0 NH2 D:ARG100 3.3 35.3 1.0 CD1 D:LEU172 3.4 44.4 1.0 O2' D:FMN301 3.5 29.5 1.0 CG2 D:THR174 3.7 36.7 1.0 C2 D:FMN301 3.8 29.5 1.0 O2 D:FMN301 3.9 30.0 1.0 CD2 D:LEU169 3.9 40.0 1.0 N1 D:FMN301 3.9 28.6 1.0 CB D:LEU172 4.0 41.9 1.0 OG1 D:THR174 4.0 36.7 1.0 CZ D:ARG100 4.1 34.0 1.0 CG D:LEU172 4.3 41.7 1.0 CE2 D:TYI302 4.4 44.6 1.0 N3 D:FMN301 4.4 28.0 1.0 CG D:TYI302 4.4 42.7 1.0 NE D:ARG100 4.5 34.4 1.0 CB D:THR174 4.5 36.8 1.0 C10 D:FMN301 4.5 29.0 1.0 C2' D:FMN301 4.8 27.2 1.0 CD2 D:TYI302 4.9 43.5 1.0 CD2 D:LEU172 4.9 41.2 1.0

Iodine binding site 8 out of 16 in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ D:I302 b:50.9 occ:1.00 I2 D:TYI302 0.0 50.9 1.0 CE2 D:TYI302 2.1 44.6 1.0 CZ D:TYI302 3.0 43.1 1.0 CD2 D:TYI302 3.1 43.5 1.0 OH D:TYI302 3.2 42.4 1.0 N C:ALA126 3.7 29.4 1.0 CA C:GLY125 3.7 29.0 1.0 CB C:TYR207 3.7 34.6 1.0 CE1 C:TYR208 3.9 35.2 1.0 CD1 C:TYR208 3.9 35.9 1.0 C C:GLY125 4.0 30.0 1.0 N5 D:FMN301 4.1 28.1 1.0 C5A D:FMN301 4.3 29.0 1.0 CG C:TYR207 4.3 34.0 1.0 CG D:TYI302 4.4 42.7 1.0 C6 D:FMN301 4.4 29.5 1.0 CB C:ALA126 4.4 28.6 1.0 NE1 D:TRP165 4.4 35.7 1.0 CE1 D:TYI302 4.4 43.8 1.0 CZ2 D:TRP165 4.4 36.1 1.0 CA C:ALA126 4.6 29.9 1.0 C4A D:FMN301 4.6 29.7 1.0 CD2 C:TYR207 4.8 33.5 1.0 CE2 D:TRP165 4.8 37.5 1.0 OG1 D:THR235 4.9 35.9 1.0 CD1 D:TYI302 4.9 43.8 1.0 O C:GLY125 4.9 31.1 1.0

Iodine binding site 9 out of 16 in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ E:I302 b:43.1 occ:0.80 I1 E:TYI302 0.0 43.1 0.8 CE1 E:TYI302 2.1 39.2 1.0 CD1 E:TYI302 3.0 40.3 1.0 CZ E:TYI302 3.1 39.7 1.0 NH2 E:ARG100 3.3 25.0 1.0 OH E:TYI302 3.4 35.3 1.0 O2 E:FMN301 3.6 25.0 1.0 O2' E:FMN301 3.7 18.0 1.0 C2 E:FMN301 3.7 25.4 1.0 N1 E:FMN301 3.8 25.9 1.0 CD1 E:LEU172 3.8 37.5 1.0 CZ E:ARG100 3.9 27.3 1.0 CB E:LEU172 4.0 37.7 1.0 CG2 E:THR174 4.1 36.0 1.0 NE E:ARG100 4.4 26.2 1.0 CG E:LEU172 4.4 37.5 1.0 CG E:TYI302 4.4 39.7 1.0 CE2 E:TYI302 4.4 41.7 1.0 CB E:THR174 4.4 36.2 1.0 OG1 E:THR174 4.4 34.9 1.0 N3 E:FMN301 4.4 26.0 1.0 NH1 E:ARG100 4.5 26.3 1.0 C10 E:FMN301 4.5 24.7 1.0 CD1 E:LEU169 4.5 38.2 1.0 CG E:LEU169 4.7 36.5 1.0 CD2 E:LEU172 4.8 36.7 1.0 CD2 E:TYI302 4.9 39.7 1.0 O4' E:FMN301 4.9 26.4 1.0

Iodine binding site 10 out of 16 in the Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Mus Musculus Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Di-Iodotyrosine (Dit) within 5.0Å range: probe atom residue distance (Å) B Occ E:I302 b:40.4 occ:0.80 I2 E:TYI302 0.0 40.4 0.8 CE2 E:TYI302 2.1 41.7 1.0 CZ E:TYI302 3.0 39.7 1.0 OH E:TYI302 3.0 35.3 1.0 CD2 E:TYI302 3.0 39.7 1.0 CA F:GLY125 3.5 26.9 1.0 N F:ALA126 3.7 28.7 1.0 CD1 F:TYR208 3.7 26.3 1.0 CE1 F:TYR208 3.8 25.5 1.0 CB F:TYR207 3.8 28.3 1.0 C F:GLY125 3.9 27.8 1.0 N5 E:FMN301 4.1 23.9 1.0 C5A E:FMN301 4.2 25.2 1.0 NE1 E:TRP165 4.3 31.6 1.0 CG E:TYI302 4.3 39.7 1.0 CE1 E:TYI302 4.3 39.2 1.0 CZ2 E:TRP165 4.4 33.0 1.0 C6 E:FMN301 4.4 26.4 1.0 CG F:TYR207 4.5 30.6 1.0 C4A E:FMN301 4.6 25.4 1.0 CE2 E:TRP165 4.7 32.7 1.0 CA F:ALA126 4.7 27.8 1.0 CB F:ALA126 4.7 28.4 1.0 CD1 E:TYI302 4.8 40.3 1.0 O F:TYR207 4.8 29.1 1.0 C9A E:FMN301 4.8 24.9 1.0 N F:GLY125 4.9 27.2 1.0 O F:GLY125 5.0 27.9 1.0 CG F:TYR208 5.0 28.1 1.0 O4 E:FMN301 5.0 25.0 1.0 OG1 E:THR235 5.0 31.1 1.0

S.R.Thomas, P.M.Mctamney, J.M.Adler, N.Laronde-Leblanc, S.E.Rokita. Crystal Structure of Iodotyrosine Deiodinase, A Novel Flavoprotein Responsible For Iodide Salvage in Thyroid Glands. J.Biol.Chem. V. 284 19659 2009.
ISSN: ISSN 0021-9258
PubMed: 19436071
DOI: 10.1074/JBC.M109.013458