Iodine in PDB 5ko8: Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)

The structure of Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr), PDB code: 5ko8 was solved by N.Ingavat, J.M.Kavran, Z.Sun, S.E.Rokita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.18 / 2.15
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.718, 152.718, 87.286, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 23.2

The binding sites of Iodine atom in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) (pdb code 5ko8). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr), PDB code: 5ko8:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)


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 Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:52.1 occ:0.70 IE A:IYR302 0.0 52.1 0.7 HG A:IYR302 1.0 72.1 0.3 CG A:IYR302 2.0 60.1 0.3 CE A:IYR302 2.0 60.6 0.7 HF A:IYR302 2.3 55.4 0.3 HF A:IYR302 2.9 51.6 0.7 CF A:IYR302 2.9 55.6 0.3 CD A:IYR302 3.0 61.9 0.7 CH A:IYR302 3.0 62.1 0.3 OF A:IYR302 3.0 46.1 0.3 HD A:IYR302 3.0 74.2 0.7 CF A:IYR302 3.0 55.7 0.7 HH A:IYR302 3.1 74.5 0.3 OF A:IYR302 3.4 43.0 0.7 N5 A:FMN301 4.0 45.2 1.0 HE1 A:TRP103 4.1 0.9 1.0 HG23 A:THR173 4.2 71.9 0.9 C5A A:FMN301 4.2 42.2 1.0 CE A:IYR302 4.2 57.1 0.3 CC A:IYR302 4.2 60.9 0.3 HG21 A:THR173 4.3 71.9 0.9 CC A:IYR302 4.3 60.8 0.7 H6 A:FMN301 4.3 58.9 1.0 CG A:IYR302 4.3 57.1 0.7 C6 A:FMN301 4.4 49.0 1.0 HG1 A:THR173 4.4 70.2 0.1 HZ2 A:TRP103 4.5 0.6 1.0 C4A A:FMN301 4.5 45.1 1.0 HG22 A:THR173 4.5 71.9 0.9 CG2 A:THR173 4.6 59.9 0.9 HD21 A:LEU107 4.7 78.3 1.0 CD A:IYR302 4.7 58.6 0.3 OG1 A:THR173 4.7 58.5 0.1 CH A:IYR302 4.8 58.5 0.7 C9A A:FMN301 4.9 45.5 1.0 O4 A:FMN301 4.9 48.0 1.0 NE1 A:TRP103 4.9 85.8 1.0 C4 A:FMN301 4.9 52.5 1.0

Iodine binding site 2 out of 4 in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)


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 Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:80.1 occ:0.30 IE A:IYR302 0.0 80.1 0.3 HG A:IYR302 0.9 68.5 0.7 CG A:IYR302 1.9 57.1 0.7 CE A:IYR302 2.0 57.1 0.3 HH21 A:ARG38 2.8 50.6 1.0 CF A:IYR302 2.9 55.7 0.7 CH A:IYR302 2.9 58.5 0.7 CD A:IYR302 2.9 58.6 0.3 OF A:IYR302 3.0 43.0 0.7 HD A:IYR302 3.0 70.3 0.3 HH A:IYR302 3.0 70.2 0.7 CF A:IYR302 3.0 55.6 0.3 O2' A:FMN301 3.2 39.5 1.0 NH2 A:ARG38 3.3 42.2 1.0 HO2' A:FMN301 3.3 47.5 1.0 CD2 A:PHE110 3.3 53.3 1.0 OF A:IYR302 3.3 46.1 0.3 HD2 A:PHE110 3.3 64.0 1.0 HH22 A:ARG38 3.4 50.6 1.0 CG A:PHE110 3.4 60.0 1.0 HB3 A:PHE110 3.5 72.3 1.0 HB2 A:PHE110 3.5 72.3 1.0 N1 A:FMN301 3.6 39.0 1.0 O2 A:FMN301 3.6 42.4 1.0 C2 A:FMN301 3.6 49.4 1.0 HD22 A:LEU107 3.6 78.3 1.0 CB A:PHE110 3.7 60.2 1.0 HF A:IYR302 3.9 51.6 0.7 CE2 A:PHE110 3.9 59.3 1.0 HG21 A:THR112 4.0 76.2 1.0 CD1 A:PHE110 4.1 48.8 1.0 CZ A:ARG38 4.2 45.5 1.0 CE A:IYR302 4.2 60.6 0.7 CC A:IYR302 4.2 60.8 0.7 HE A:ARG38 4.2 60.6 1.0 HE2 A:PHE110 4.3 71.1 1.0 CC A:IYR302 4.3 60.9 0.3 HD23 A:LEU107 4.3 78.3 1.0 C10 A:FMN301 4.3 41.9 1.0 N3 A:FMN301 4.3 48.1 1.0 HF A:IYR302 4.3 55.4 0.3 CG A:IYR302 4.3 60.1 0.3 CD2 A:LEU107 4.4 65.2 1.0 CZ A:PHE110 4.5 49.1 1.0 NE A:ARG38 4.5 50.5 1.0 OG1 A:THR112 4.5 59.5 1.0 HD1 A:PHE110 4.5 58.6 1.0 HG23 A:THR112 4.5 76.2 1.0 CE1 A:PHE110 4.6 56.5 1.0 C2' A:FMN301 4.6 42.3 1.0 H1'1 A:FMN301 4.6 47.7 1.0 HD21 A:LEU107 4.7 78.3 1.0 CD A:IYR302 4.7 61.9 0.7 CG2 A:THR112 4.7 63.5 1.0 HN3 A:FMN301 4.7 57.7 1.0 O4' A:FMN301 4.8 40.1 1.0 CH A:IYR302 4.8 62.1 0.3 C4A A:FMN301 4.9 45.1 1.0 C4 A:FMN301 4.9 52.5 1.0 N10 A:FMN301 4.9 38.0 1.0 C1' A:FMN301 4.9 39.7 1.0 HA A:LEU107 5.0 79.4 1.0

Iodine binding site 3 out of 4 in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)


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 Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:62.2 occ:0.67 IE B:IYR302 0.0 62.2 0.7 HG B:IYR302 1.1 71.6 0.3 CE B:IYR302 2.0 60.2 0.7 CG B:IYR302 2.1 59.7 0.3 HF B:IYR302 2.3 59.2 0.3 HF B:IYR302 2.8 56.2 0.7 CD B:IYR302 3.0 57.2 0.7 CF B:IYR302 3.0 51.6 0.3 CH B:IYR302 3.0 57.6 0.3 HD B:IYR302 3.0 68.6 0.7 OF B:IYR302 3.0 49.4 0.3 CF B:IYR302 3.0 51.3 0.7 HH B:IYR302 3.1 69.2 0.3 OF B:IYR302 3.4 46.8 0.7 N5 B:FMN301 3.9 41.3 1.0 HE1 B:TRP103 4.0 0.3 1.0 HG21 B:THR173 4.1 70.9 0.7 HZ2 B:TRP103 4.2 1.0 1.0 HG23 B:THR173 4.2 70.9 0.7 C5A B:FMN301 4.2 50.8 1.0 CE B:IYR302 4.3 57.5 0.3 CC B:IYR302 4.3 59.6 0.3 CC B:IYR302 4.3 59.5 0.7 HG1 B:THR173 4.3 69.8 0.3 CG B:IYR302 4.3 57.5 0.7 C4A B:FMN301 4.4 39.4 1.0 H6 B:FMN301 4.4 43.1 1.0 HG22 B:THR173 4.4 70.9 0.7 C6 B:FMN301 4.4 35.9 1.0 CG2 B:THR173 4.5 59.1 0.7 OG1 B:THR173 4.7 58.2 0.3 O4 B:FMN301 4.7 45.6 1.0 HD21 B:LEU107 4.7 85.8 1.0 C4 B:FMN301 4.8 47.5 1.0 CD B:IYR302 4.8 58.0 0.3 NE1 B:TRP103 4.8 96.1 1.0 CH B:IYR302 4.8 57.6 0.7 C9A B:FMN301 4.9 44.1 1.0 CZ2 B:TRP103 5.0 0.5 1.0 C10 B:FMN301 5.0 37.7 1.0

Iodine binding site 4 out of 4 in the Crystal Structure of Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr)


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 Haliscomenobacter Hydrossis Iodotyrosine Deiodinase (Iyd) Bound to Fmn and Mono-Iodotyrosine (I-Tyr) within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:90.2 occ:0.33 IE B:IYR302 0.0 90.2 0.3 HG B:IYR302 1.0 69.0 0.7 CG B:IYR302 2.0 57.5 0.7 CE B:IYR302 2.0 57.5 0.3 HH22 B:ARG38 2.9 61.3 1.0 CF B:IYR302 2.9 51.3 0.7 CH B:IYR302 2.9 57.6 0.7 CD B:IYR302 2.9 58.0 0.3 OF B:IYR302 3.0 46.8 0.7 HD B:IYR302 3.0 69.7 0.3 CF B:IYR302 3.0 51.6 0.3 HH B:IYR302 3.1 69.1 0.7 HG21 B:THR112 3.2 84.6 1.0 HD2 B:PHE110 3.3 77.0 1.0 CD2 B:PHE110 3.3 64.2 1.0 O2' B:FMN301 3.3 42.2 1.0 OF B:IYR302 3.3 49.4 0.3 HO2' B:FMN301 3.3 50.7 1.0 HD22 B:LEU107 3.4 85.8 1.0 CG B:PHE110 3.4 67.2 1.0 HB2 B:PHE110 3.4 79.5 1.0 NH2 B:ARG38 3.5 51.1 1.0 HB3 B:PHE110 3.5 79.5 1.0 O2 B:FMN301 3.6 51.3 1.0 HH12 B:ARG38 3.6 67.8 1.0 C2 B:FMN301 3.6 51.5 1.0 N1 B:FMN301 3.6 39.6 1.0 CB B:PHE110 3.7 66.3 1.0 CE2 B:PHE110 3.9 68.9 1.0 HH21 B:ARG38 3.9 61.3 1.0 HF B:IYR302 3.9 56.2 0.7 HG23 B:THR112 4.0 84.6 1.0 CG2 B:THR112 4.0 70.5 1.0 NH1 B:ARG38 4.1 56.5 1.0 CZ B:ARG38 4.1 59.3 1.0 CD1 B:PHE110 4.1 59.1 1.0 HE2 B:PHE110 4.2 82.7 1.0 CE B:IYR302 4.2 60.2 0.7 CC B:IYR302 4.2 59.5 0.7 CD2 B:LEU107 4.2 71.5 1.0 CC B:IYR302 4.3 59.6 0.3 HF B:IYR302 4.3 59.2 0.3 HD23 B:LEU107 4.3 85.8 1.0 CG B:IYR302 4.3 59.7 0.3 N3 B:FMN301 4.4 49.0 1.0 C10 B:FMN301 4.4 37.7 1.0 CZ B:PHE110 4.5 59.5 1.0 HG22 B:THR112 4.6 84.6 1.0 HD1 B:PHE110 4.6 70.9 1.0 CE1 B:PHE110 4.6 53.1 1.0 C2' B:FMN301 4.6 39.4 1.0 HD21 B:LEU107 4.7 85.8 1.0 OG1 B:THR112 4.7 75.0 1.0 HB3 B:LEU107 4.7 91.7 1.0 H1'1 B:FMN301 4.7 46.1 1.0 CD B:IYR302 4.7 57.2 0.7 HA B:LEU107 4.8 92.6 1.0 O4' B:FMN301 4.8 43.8 1.0 HH11 B:ARG38 4.8 67.8 1.0 CH B:IYR302 4.8 57.6 0.3 HN3 B:FMN301 4.9 58.7 1.0 CB B:THR112 4.9 75.7 1.0

N.Ingavat, J.M.Kavran, Z.Sun, S.E.Rokita. Active Site Binding Is Not Sufficient For Reductive Deiodination By Iodotyrosine Deiodinase. Biochemistry V. 56 1130 2017.
ISSN: ISSN 1520-4995
PubMed: 28157283
DOI: 10.1021/ACS.BIOCHEM.6B01308