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Iodine in PDB 6tyk: Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine

Enzymatic activity of Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine

All present enzymatic activity of Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine:
1.21.1.1;

Protein crystallography data

The structure of Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine, PDB code: 6tyk was solved by Z.Sun, J.M.Kavran, S.E.Rokita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.82 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.035, 81.176, 104.146, 90, 90, 90
R / Rfree (%) 15.8 / 19.4

Other elements in 6tyk:

The structure of Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine (pdb code 6tyk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine, PDB code: 6tyk:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 6tyk

Go back to Iodine Binding Sites List in 6tyk
Iodine binding site 1 out of 3 in the Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine


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 Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:20.5
occ:1.00
IE A:IYR302 0.0 20.5 1.0
CE A:IYR302 2.0 13.8 1.0
CD A:IYR302 3.0 13.2 1.0
CF A:IYR302 3.0 12.1 1.0
HD A:IYR302 3.0 15.8 1.0
OF A:IYR302 3.3 12.6 1.0
CA B:GLY40 3.6 11.6 1.0
N B:MET41 3.8 12.1 1.0
CB B:PRO111 4.0 18.9 1.0
HF A:IYR302 4.0 15.1 1.0
N5 A:FMN301 4.0 12.8 1.0
C B:GLY40 4.1 11.3 1.0
CD1 B:TYR112 4.1 22.6 1.0
C5A A:FMN301 4.2 12.3 1.0
H6 A:FMN301 4.3 13.9 1.0
CC A:IYR302 4.3 13.6 1.0
CG A:IYR302 4.3 13.3 1.0
C6 A:FMN301 4.3 11.6 1.0
C4A A:FMN301 4.5 10.9 1.0
OG1 A:THR139 4.6 14.6 1.0
O B:PRO111 4.6 15.7 1.0
CB B:TYR112 4.7 15.4 1.0
CG B:TYR112 4.7 19.4 1.0
CD1 A:LEU79 4.8 22.0 1.0
C B:PRO111 4.8 14.1 1.0
CH A:IYR302 4.8 13.2 1.0
CE1 B:TYR112 4.8 24.7 1.0
C9A A:FMN301 4.8 11.1 1.0
CG B:PRO111 4.9 21.5 1.0
CA B:MET41 4.9 12.6 1.0
O4 A:FMN301 5.0 13.4 1.0
C4 A:FMN301 5.0 12.5 1.0
N B:GLY40 5.0 10.2 1.0

Iodine binding site 2 out of 3 in 6tyk

Go back to Iodine Binding Sites List in 6tyk
Iodine binding site 2 out of 3 in the Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine


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 Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:21.6
occ:1.00
IE B:IYR302 0.0 21.6 1.0
CE B:IYR302 2.0 12.5 1.0
HF B:IYR302 2.7 15.1 1.0
CD B:IYR302 3.0 13.5 1.0
HD B:IYR302 3.0 16.2 1.0
CF B:IYR302 3.0 12.4 1.0
OF B:IYR302 3.3 12.6 1.0
CA A:GLY40 3.6 10.9 1.0
N A:MET41 3.9 12.5 1.0
CD2 A:TYR112 3.9 19.1 1.0
N5 B:FMN301 3.9 11.7 1.0
C A:GLY40 4.1 11.9 1.0
C5A B:FMN301 4.1 10.2 1.0
CB A:PRO111 4.1 17.0 1.0
H6 B:FMN301 4.1 12.8 1.0
CG A:MET41 4.2 32.6 1.0
C6 B:FMN301 4.2 10.7 1.0
CC B:IYR302 4.3 12.8 1.0
CG A:PRO111 4.3 18.0 1.0
CG B:IYR302 4.3 12.2 1.0
C4A B:FMN301 4.5 10.0 1.0
O A:PRO111 4.5 13.2 1.0
O B:HOH471 4.6 45.7 1.0
OG1 B:THR139 4.6 14.2 1.0
CE2 A:TYR112 4.6 20.9 1.0
CB A:TYR112 4.6 13.8 1.0
CG A:TYR112 4.6 17.1 1.0
C A:PRO111 4.7 12.4 1.0
C9A B:FMN301 4.8 9.9 1.0
CH B:IYR302 4.8 11.6 1.0
O4 B:FMN301 4.9 12.5 1.0
N A:GLY40 4.9 11.0 1.0
CA A:MET41 4.9 14.0 1.0
C4 B:FMN301 4.9 12.2 1.0
CB A:MET41 5.0 21.4 1.0

Iodine binding site 3 out of 3 in 6tyk

Go back to Iodine Binding Sites List in 6tyk
Iodine binding site 3 out of 3 in the Crystal Structure of Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine


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 Iodotyrosine Deiodinase (Iyd) in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I305

b:32.2
occ:1.00
IE B:IYR305 0.0 32.2 1.0
CE B:IYR305 2.0 32.2 1.0
CD B:IYR305 3.0 35.9 1.0
CF B:IYR305 3.0 32.3 1.0
HD B:IYR305 3.0 43.0 1.0
OF B:IYR305 3.3 33.4 1.0
HF B:IYR305 3.8 40.0 1.0
CB B:ARG114 4.0 14.1 1.0
N A:GLU115 4.0 10.3 1.0
CB A:ARG114 4.0 12.6 1.0
C B:ARG114 4.0 11.8 1.0
N B:GLU115 4.1 12.4 1.0
CG A:GLU115 4.1 14.4 1.0
O B:ARG114 4.2 12.1 1.0
C A:ARG114 4.2 10.1 1.0
CA A:GLU115 4.2 11.1 1.0
CD1 B:TRP118 4.2 11.3 1.0
CC B:IYR305 4.3 39.9 1.0
CD A:GLU115 4.3 15.1 1.0
CA B:GLU115 4.3 11.6 1.0
CG B:IYR305 4.3 33.4 1.0
O A:ARG114 4.4 11.1 1.0
CG B:GLU115 4.4 14.5 1.0
OE2 A:GLU115 4.6 18.8 1.0
CA B:ARG114 4.6 12.0 1.0
CD1 A:TRP118 4.7 11.5 1.0
OE1 A:GLU115 4.7 14.2 1.0
CD B:GLU115 4.8 16.8 1.0
CA A:ARG114 4.8 10.6 1.0
CB A:GLU115 4.8 12.1 1.0
CH B:IYR305 4.8 37.4 1.0
CG B:TRP118 4.9 9.9 1.0
NE1 B:TRP118 4.9 11.3 1.0

Reference:

Z.Sun, J.M.Kavran, S.E.Rokita. Structure of Tn Iyd Bound in the Semiquinone Form Bound to Fmn and 3-Iodo-L-Tyrosine To Be Published.
Page generated: Sat Apr 17 16:10:40 2021

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