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:
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
|