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Chlorine 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 (I) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 7 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6tyk

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Chlorine binding site 1 out of 7 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 Chlorine with other atoms in the Cl 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:Cl303

b:12.4
occ:1.00
 H1'2 A:FMN301 2.7 12.2 1.0
OG1 A:THR13 3.0 12.6 1.0
O3' A:FMN301 3.0 11.1 1.0
NH1 A:ARG11 3.1 11.7 1.0
H3' A:FMN301 3.2 13.0 1.0
CD A:PRO137 3.2 15.1 1.0
NH2 A:ARG11 3.4 11.8 1.0
CG2 A:THR13 3.6 13.5 1.0
CB A:THR13 3.6 12.5 1.0
C1' A:FMN301 3.6 10.2 1.0
CB B:PRO38 3.6 10.3 1.0
H1'1 A:FMN301 3.6 12.2 1.0
C3' A:FMN301 3.6 10.8 1.0
CA A:THR13 3.7 10.5 1.0
CZ A:ARG11 3.7 11.1 1.0
HO3' A:FMN301 3.7 13.4 1.0
H9 A:FMN301 4.0 13.6 1.0
CG A:PRO137 4.1 14.7 1.0
N A:THR13 4.1 12.2 1.0
C2' A:FMN301 4.3 10.9 1.0
CG B:PRO38 4.4 9.5 1.0
CA A:VAL136 4.4 13.7 1.0
O5' A:FMN301 4.5 11.1 1.0
N A:PRO137 4.5 12.9 1.0
O A:SER135 4.5 10.7 1.0
CG2 A:VAL136 4.7 15.7 1.0
C A:LYS12 4.7 12.3 1.0
N10 A:FMN301 4.8 10.4 1.0
O2P A:FMN301 4.8 13.8 1.0
H5'1 A:FMN301 4.8 12.8 1.0
H2' A:FMN301 4.8 13.1 1.0
C9 A:FMN301 4.9 11.4 1.0
CA B:PRO38 4.9 10.2 1.0
C4' A:FMN301 4.9 11.3 1.0
CB A:VAL136 5.0 14.9 1.0
O A:HOH440 5.0 12.3 1.0

Chlorine binding site 2 out of 7 in 6tyk

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Chlorine binding site 2 out of 7 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 Chlorine with other atoms in the Cl 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
A:Cl304

b:27.1
occ:1.00
 O A:HOH457 3.1 17.8 1.0
NH1 A:ARG157 3.6 25.0 1.0
CD A:ARG157 3.7 17.3 1.0
CD A:ARG114 3.9 15.4 1.0
CG A:LYS108 4.0 17.3 1.0
CG A:ARG114 4.1 15.1 1.0
CB A:LYS108 4.4 15.6 1.0
CA A:LYS108 4.5 15.1 1.0
CZ A:ARG157 4.5 23.7 1.0
NE A:ARG157 4.6 19.6 1.0
O A:HOH497 4.6 38.5 1.0
CB A:ARG157 4.6 13.6 1.0
CG A:ARG157 4.8 15.2 1.0
CD A:LYS108 4.8 21.5 1.0
NE A:ARG114 4.8 14.5 1.0
OG A:SER113 4.9 16.2 1.0
O A:LYS108 4.9 17.7 1.0
O A:HOH559 5.0 42.9 1.0
OG A:SER106 5.0 13.7 1.0

Chlorine binding site 3 out of 7 in 6tyk

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Chlorine binding site 3 out of 7 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 Chlorine with other atoms in the Cl 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
A:Cl305

b:16.1
occ:1.00
 O A:HOH584 3.1 31.4 1.0
O A:HOH458 3.1 22.4 1.0
N A:ARG15 3.2 10.9 1.0
N A:LYS171 3.3 17.5 1.0
CA A:PRO170 3.4 17.6 1.0
N A:ARG16 3.6 13.2 1.0
CB A:PRO170 3.6 16.7 1.0
CG A:ARG16 3.7 15.4 1.0
CB A:ARG15 3.8 12.2 1.0
CA A:ARG15 3.9 11.7 1.0
C A:PRO170 3.9 18.7 1.0
C A:ARG15 4.0 12.5 1.0
CB A:ARG16 4.0 15.4 1.0
CD A:ARG16 4.0 15.0 1.0
CG A:LYS171 4.1 26.6 1.0
C A:VAL14 4.3 11.3 1.0
CB A:LYS171 4.3 22.0 1.0
CA A:VAL14 4.4 11.0 1.0
CA A:ARG16 4.4 15.1 1.0
CA A:LYS171 4.4 18.4 1.0
O A:HOH427 4.5 15.5 1.0
O A:THR13 4.5 12.1 1.0
CG A:ARG15 4.5 12.8 1.0
N A:PRO170 4.7 16.9 1.0
O A:ARG15 4.9 15.7 1.0

Chlorine binding site 4 out of 7 in 6tyk

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Chlorine binding site 4 out of 7 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl306

b:18.2
occ:1.00
 ND2 B:ASN42 3.2 12.7 1.0
NE1 A:TRP82 3.3 16.4 1.0
NZ A:LYS86 3.4 26.2 1.0
CE A:LYS86 3.7 23.7 1.0
CB B:ASN42 3.8 11.3 1.0
CG B:ASN42 4.0 11.9 1.0
CB A:TYR174 4.1 14.1 1.0
CD1 A:TRP82 4.2 15.9 1.0
O B:HOH459 4.3 30.6 1.0
CD2 A:TYR174 4.3 15.2 1.0
CE2 A:TRP82 4.3 15.7 1.0
CG A:TYR174 4.3 14.7 1.0
CD A:PRO175 4.4 16.2 1.0
CZ2 A:TRP82 4.6 15.8 1.0
O A:HOH539 4.7 25.4 1.0
O B:MET41 4.8 12.2 1.0
O B:ASN42 4.8 11.9 1.0

Chlorine binding site 5 out of 7 in 6tyk

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Chlorine binding site 5 out of 7 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl307

b:62.5
occ:1.00
 O A:HOH477 2.7 23.9 1.0
O A:HOH469 2.8 28.3 1.0
O A:GLU54 2.9 15.6 1.0
OE1 A:GLU54 3.0 28.6 1.0
N A:GLY58 3.5 13.8 1.0
CB A:LYS57 3.7 14.0 1.0
CA A:GLY58 3.8 14.7 1.0
C A:GLU54 3.8 15.0 1.0
CG A:LYS96 3.9 28.2 1.0
C A:LYS57 4.0 14.7 1.0
CE A:LYS57 4.0 22.8 1.0
CA A:GLU54 4.1 16.8 1.0
CD A:GLU54 4.1 29.8 1.0
CB A:LYS96 4.2 22.9 1.0
CA A:LYS96 4.2 18.9 1.0
NZ A:LYS96 4.3 40.6 1.0
CB A:GLU54 4.3 22.1 1.0
CA A:LYS57 4.4 13.5 1.0
O A:HOH545 4.5 33.2 1.0
CD A:LYS96 4.6 33.1 1.0
O A:LYS96 4.6 19.7 1.0
O A:LYS57 4.7 14.0 1.0
CG A:GLU54 4.8 26.4 1.0
NH2 A:ARG61 4.9 28.4 1.0
CG A:LYS57 4.9 17.0 1.0
N A:LYS57 4.9 13.3 1.0
C A:LYS96 4.9 18.5 1.0
O A:LEU95 5.0 18.6 1.0
NE A:ARG61 5.0 23.6 1.0

Chlorine binding site 6 out of 7 in 6tyk

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Chlorine binding site 6 out of 7 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl303

b:12.9
occ:1.00
 H1'2 B:FMN301 2.8 11.8 1.0
OG1 B:THR13 3.0 12.4 1.0
NH1 B:ARG11 3.0 11.4 1.0
O3' B:FMN301 3.1 11.0 1.0
H3' B:FMN301 3.2 12.7 1.0
CD B:PRO137 3.2 15.7 1.0
NH2 B:ARG11 3.4 13.0 1.0
CG2 B:THR13 3.6 14.1 1.0
CB A:PRO38 3.6 10.0 1.0
CB B:THR13 3.6 12.7 1.0
H1'1 B:FMN301 3.6 11.8 1.0
C1' B:FMN301 3.6 9.8 1.0
C3' B:FMN301 3.6 10.6 1.0
CZ B:ARG11 3.7 12.3 1.0
CA B:THR13 3.7 10.7 1.0
HO3' B:FMN301 3.8 13.2 1.0
CG B:PRO137 3.9 15.5 1.0
H9 B:FMN301 4.0 12.4 1.0
N B:THR13 4.1 11.3 1.0
C2' B:FMN301 4.3 10.2 1.0
CG A:PRO38 4.3 10.6 1.0
O5' B:FMN301 4.4 10.6 1.0
CA B:VAL136 4.5 12.7 1.0
N B:PRO137 4.5 12.4 1.0
O B:SER135 4.6 11.5 1.0
O3P B:FMN301 4.7 12.1 1.0
C B:LYS12 4.8 12.3 1.0
O B:HOH426 4.8 13.2 1.0
CG2 B:VAL136 4.8 15.0 1.0
H5'1 B:FMN301 4.8 13.4 1.0
N10 B:FMN301 4.8 10.6 1.0
H2' B:FMN301 4.9 12.2 1.0
CA A:PRO38 4.9 10.7 1.0
C9 B:FMN301 4.9 10.4 1.0
C4' B:FMN301 4.9 10.3 1.0
NE B:ARG11 5.0 13.6 1.0
C5' B:FMN301 5.0 11.2 1.0

Chlorine binding site 7 out of 7 in 6tyk

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Chlorine binding site 7 out of 7 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl304

b:16.1
occ:1.00
 NZ B:LYS86 3.2 23.5 1.0
ND2 A:ASN42 3.3 11.7 1.0
CE B:LYS86 3.4 21.0 1.0
NE1 B:TRP82 3.4 14.7 1.0
CB A:ASN42 3.9 11.6 1.0
CB B:TYR174 4.1 10.5 1.0
CG A:ASN42 4.1 10.6 1.0
CD2 B:TYR174 4.3 13.6 1.0
CG B:TYR174 4.3 11.3 1.0
CD1 B:TRP82 4.3 15.1 1.0
CD B:PRO175 4.3 15.0 1.0
CE2 B:TRP82 4.4 14.0 1.0
CZ2 B:TRP82 4.6 14.5 1.0
O A:HOH462 4.6 34.4 1.0
O A:HOH491 4.8 32.6 1.0
OE2 B:GLU85 4.8 24.9 1.0
O A:MET41 4.9 11.1 1.0
O B:HOH423 4.9 45.0 1.0
O A:ASN42 4.9 12.0 1.0
CD B:LYS86 4.9 18.5 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 Jul 29 15:38:55 2024

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