Atomistry » Iodine » PDB 6rzm-6vu4 » 6tyk
Atomistry »
  Iodine »
    PDB 6rzm-6vu4 »
      6tyk »

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: Mon Aug 12 00:21:18 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy