Chlorine in PDB 6q1l: Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine

Enzymatic activity of Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine

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

Protein crystallography data

The structure of Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine, PDB code: 6q1l 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) 37.91 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.861, 81.232, 103.9, 90, 90, 90
R / Rfree (%) 16.5 / 19.6

Other elements in 6q1l:

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

Iodine (I) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine (pdb code 6q1l). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine, PDB code: 6q1l:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6q1l

Go back to Chlorine Binding Sites List in 6q1l
Chlorine binding site 1 out of 6 in the Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) 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 Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:16.1
occ:1.00
HG1 A:THR13 2.1 20.4 1.0
HH12 A:ARG11 2.2 16.5 1.0
HD3 A:PRO137 2.6 23.3 1.0
HH22 A:ARG11 2.7 15.9 1.0
H1'2 A:FMN301 2.7 13.1 1.0
HG23 A:THR13 2.8 20.5 1.0
HD2 A:PRO137 2.9 23.3 1.0
OG1 A:THR13 3.0 17.0 1.0
HB3 B:PRO38 3.0 17.0 1.0
O3' A:FMN301 3.0 13.3 1.0
NH1 A:ARG11 3.1 13.8 1.0
HA A:THR13 3.1 15.5 1.0
CD A:PRO137 3.2 19.4 1.0
H3' A:FMN301 3.2 14.8 1.0
HB2 B:PRO38 3.4 17.0 1.0
NH2 A:ARG11 3.4 13.3 1.0
HA A:VAL136 3.4 18.5 1.0
CG2 A:THR13 3.5 17.1 1.0
CB A:THR13 3.5 15.0 1.0
C1' A:FMN301 3.6 10.9 1.0
CB B:PRO38 3.6 14.1 1.0
H1'1 A:FMN301 3.6 13.1 1.0
C3' A:FMN301 3.6 12.3 1.0
HO3' A:FMN301 3.7 15.9 1.0
CA A:THR13 3.7 12.9 1.0
CZ A:ARG11 3.7 13.9 1.0
HH11 A:ARG11 3.7 16.5 1.0
HG23 A:VAL136 3.7 19.2 1.0
HG2 A:PRO137 3.9 20.1 1.0
HG21 A:THR13 3.9 20.5 1.0
HG3 B:PRO38 4.0 12.5 1.0
H9 A:FMN301 4.0 14.9 1.0
CG A:PRO137 4.0 16.8 1.0
N A:THR13 4.0 16.6 1.0
H A:THR13 4.1 19.9 1.0
HH21 A:ARG11 4.2 15.9 1.0
HG22 A:THR13 4.3 20.5 1.0
C2' A:FMN301 4.3 11.6 1.0
CG B:PRO38 4.4 10.4 1.0
CA A:VAL136 4.4 15.4 1.0
HG3 A:PRO137 4.4 20.1 1.0
N A:PRO137 4.4 13.5 1.0
O5' A:FMN301 4.5 12.7 1.0
HB A:THR13 4.5 18.0 1.0
O A:SER135 4.5 14.3 1.0
CG2 A:VAL136 4.6 16.0 1.0
H5'1 A:FMN301 4.7 15.2 1.0
N10 A:FMN301 4.7 14.8 1.0
HB A:VAL136 4.8 16.9 1.0
HD13 A:LEU125 4.8 17.7 1.0
C A:LYS12 4.8 18.2 1.0
O2P A:FMN301 4.8 16.1 1.0
C9 A:FMN301 4.8 12.4 1.0
H2' A:FMN301 4.9 13.9 1.0
CB A:VAL136 4.9 14.1 1.0
HA B:PRO38 4.9 16.3 1.0
C4' A:FMN301 4.9 12.9 1.0
CA B:PRO38 4.9 13.6 1.0
HG2 B:PRO38 4.9 12.5 1.0
C A:VAL136 4.9 14.8 1.0
C5' A:FMN301 5.0 12.7 1.0
H A:VAL14 5.0 16.0 1.0
O A:HOH433 5.0 14.5 1.0
HG22 A:VAL136 5.0 19.2 1.0

Chlorine binding site 2 out of 6 in 6q1l

Go back to Chlorine Binding Sites List in 6q1l
Chlorine binding site 2 out of 6 in the Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) 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 Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:32.3
occ:1.00
HH11 A:ARG157 2.6 30.3 1.0
HD2 A:ARG114 3.0 26.2 1.0
O A:HOH450 3.1 19.0 1.0
O A:HOH511 3.1 32.3 1.0
HG2 A:LYS108 3.1 23.2 1.0
HD2 A:ARG157 3.1 22.1 1.0
HD3 A:ARG157 3.3 22.1 1.0
NH1 A:ARG157 3.4 25.2 1.0
CD A:ARG157 3.7 18.4 1.0
HA A:LYS108 3.7 23.2 1.0
HG3 A:ARG114 3.8 21.8 1.0
HH12 A:ARG157 3.8 30.3 1.0
CD A:ARG114 3.9 21.9 1.0
CG A:LYS108 4.0 19.3 1.0
HB3 A:LYS108 4.1 21.1 1.0
HG2 A:ARG114 4.1 21.8 1.0
HB2 A:ARG157 4.1 14.8 1.0
CG A:ARG114 4.1 18.2 1.0
HD3 A:ARG114 4.3 26.2 1.0
CB A:LYS108 4.4 17.6 1.0
HG A:SER113 4.4 21.2 1.0
HB3 A:ARG157 4.4 14.8 1.0
CZ A:ARG157 4.4 27.3 1.0
CA A:LYS108 4.5 19.4 1.0
NE A:ARG157 4.5 22.8 1.0
HD3 A:LYS108 4.6 25.8 1.0
CB A:ARG157 4.6 12.4 1.0
HG3 A:LYS108 4.6 23.2 1.0
HG A:SER106 4.7 22.5 1.0
HE2 A:LYS108 4.7 42.3 1.0
CG A:ARG157 4.8 16.9 1.0
NE A:ARG114 4.8 20.9 1.0
CD A:LYS108 4.8 21.5 1.0
O A:LYS108 4.9 21.2 1.0
OG A:SER113 4.9 17.7 1.0
HE A:ARG114 5.0 25.1 1.0

Chlorine binding site 3 out of 6 in 6q1l

Go back to Chlorine Binding Sites List in 6q1l
Chlorine binding site 3 out of 6 in the Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) 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 Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:20.5
occ:1.00
H A:ARG15 2.4 17.9 1.0
H A:LYS171 2.5 27.5 1.0
HA A:PRO170 2.8 29.0 1.0
O A:HOH547 2.9 32.4 1.0
HG3 A:ARG16 3.0 29.8 1.0
HB2 A:ARG15 3.1 18.9 1.0
O A:HOH435 3.1 26.3 1.0
H A:ARG16 3.2 19.1 1.0
N A:ARG15 3.2 14.9 1.0
N A:LYS171 3.3 22.9 1.0
HB3 A:PRO170 3.3 24.5 1.0
HD3 A:ARG16 3.4 28.8 1.0
CA A:PRO170 3.5 24.1 1.0
HG3 A:LYS171 3.6 51.3 1.0
HA A:VAL14 3.6 14.2 1.0
HB2 A:PRO170 3.6 24.5 1.0
HB2 A:ARG16 3.6 26.4 1.0
N A:ARG16 3.6 15.9 1.0
CB A:PRO170 3.6 20.4 1.0
HB2 A:LYS171 3.7 30.9 1.0
CG A:ARG16 3.7 24.8 1.0
CB A:ARG15 3.8 15.7 1.0
CA A:ARG15 3.9 12.5 1.0
C A:PRO170 3.9 28.3 1.0
C A:ARG15 4.0 14.4 1.0
CD A:ARG16 4.0 24.0 1.0
CB A:ARG16 4.1 22.0 1.0
HG3 A:ARG15 4.2 24.5 1.0
C A:VAL14 4.3 11.2 1.0
CB A:LYS171 4.3 25.8 1.0
CG A:LYS171 4.3 42.8 1.0
HD2 A:ARG16 4.3 28.8 1.0
CA A:VAL14 4.4 11.8 1.0
CA A:LYS171 4.4 21.1 1.0
CA A:ARG16 4.5 17.6 1.0
O A:HOH442 4.5 21.3 1.0
HD2 A:LYS171 4.5 72.5 1.0
O A:THR13 4.6 16.9 1.0
CG A:ARG15 4.6 20.4 1.0
HG2 A:ARG16 4.6 29.8 1.0
HB3 A:ARG15 4.6 18.9 1.0
HD2 A:ARG15 4.6 19.9 1.0
HH11 A:ARG15 4.6 20.8 1.0
HG13 A:VAL14 4.6 22.0 1.0
HE3 A:LYS171 4.7 85.4 1.0
HA A:ARG15 4.8 15.0 1.0
N A:PRO170 4.8 20.9 1.0
CD A:LYS171 4.9 60.4 1.0
O A:ARG15 4.9 19.3 1.0
HB3 A:ARG16 5.0 26.4 1.0

Chlorine binding site 4 out of 6 in 6q1l

Go back to Chlorine Binding Sites List in 6q1l
Chlorine binding site 4 out of 6 in the Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) 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 Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:19.3
occ:1.00
HD22 B:ASN42 2.4 18.4 1.0
HE1 A:TRP82 2.4 22.7 1.0
HZ1 A:LYS86 2.5 39.9 1.0
HB3 B:ASN42 3.0 16.5 1.0
ND2 B:ASN42 3.3 15.3 1.0
HB3 A:TYR174 3.3 20.0 1.0
NE1 A:TRP82 3.3 18.9 1.0
NZ A:LYS86 3.3 33.3 1.0
HE2 A:LYS86 3.4 29.1 1.0
HZ3 A:LYS86 3.6 39.9 1.0
HD2 A:PRO175 3.6 27.0 1.0
CE A:LYS86 3.8 24.3 1.0
CB B:ASN42 3.8 13.7 1.0
HD21 B:ASN42 3.8 18.4 1.0
HE3 A:LYS86 3.8 29.1 1.0
HZ2 A:LYS86 3.9 39.9 1.0
HB2 B:ASN42 3.9 16.5 1.0
HD2 A:TYR174 4.0 23.9 1.0
CG B:ASN42 4.0 14.7 1.0
HZ2 A:TRP82 4.0 17.3 1.0
CB A:TYR174 4.1 16.6 1.0
CD1 A:TRP82 4.2 19.3 1.0
HD1 A:TRP82 4.2 23.2 1.0
CD2 A:TYR174 4.2 19.9 1.0
CE2 A:TRP82 4.3 16.4 1.0
CG A:TYR174 4.3 18.2 1.0
HB2 A:TYR174 4.3 20.0 1.0
O B:HOH450 4.3 24.6 1.0
HG2 A:PRO175 4.5 27.2 1.0
CZ2 A:TRP82 4.5 14.4 1.0
CD A:PRO175 4.6 22.5 1.0
O B:MET41 4.7 16.0 1.0
O A:HOH513 4.7 26.9 1.0
O B:ASN42 4.8 16.8 1.0
O B:HOH429 5.0 25.6 1.0

Chlorine binding site 5 out of 6 in 6q1l

Go back to Chlorine Binding Sites List in 6q1l
Chlorine binding site 5 out of 6 in the Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) 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 Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:17.2
occ:1.00
HH12 B:ARG11 2.2 18.9 1.0
HG1 B:THR13 2.2 20.6 1.0
HD3 B:PRO137 2.6 23.3 1.0
HH22 B:ARG11 2.7 18.5 1.0
HG23 B:THR13 2.7 18.2 1.0
H1'2 B:FMN301 2.8 15.7 1.0
HB3 A:PRO38 2.9 14.9 1.0
HD2 B:PRO137 3.0 23.3 1.0
O3' B:FMN301 3.0 13.7 1.0
NH1 B:ARG11 3.0 15.8 1.0
OG1 B:THR13 3.0 17.1 1.0
CD B:PRO137 3.2 19.4 1.0
H3' B:FMN301 3.2 18.7 1.0
HA B:THR13 3.2 17.5 1.0
HB2 A:PRO38 3.3 14.9 1.0
NH2 B:ARG11 3.4 15.4 1.0
CG2 B:THR13 3.5 15.1 1.0
CB A:PRO38 3.5 12.4 1.0
HA B:VAL136 3.6 18.4 1.0
CB B:THR13 3.6 17.0 1.0
C3' B:FMN301 3.6 15.6 1.0
HG2 B:PRO137 3.6 22.7 1.0
C1' B:FMN301 3.6 13.1 1.0
HO3' B:FMN301 3.6 16.5 1.0
HH11 B:ARG11 3.7 18.9 1.0
CZ B:ARG11 3.7 15.2 1.0
H1'1 B:FMN301 3.7 15.7 1.0
CA B:THR13 3.7 14.6 1.0
CG B:PRO137 3.9 18.9 1.0
HG21 B:THR13 3.9 18.2 1.0
HG23 B:VAL136 3.9 19.9 1.0
HG3 A:PRO38 3.9 13.1 1.0
H9 B:FMN301 4.0 13.8 1.0
N B:THR13 4.0 15.0 1.0
H B:THR13 4.1 18.0 1.0
HG3 B:PRO137 4.1 22.7 1.0
HH21 B:ARG11 4.2 18.5 1.0
HG22 B:THR13 4.3 18.2 1.0
C2' B:FMN301 4.3 17.8 1.0
CG A:PRO38 4.3 10.9 1.0
O5' B:FMN301 4.4 12.7 1.0
N B:PRO137 4.5 14.2 1.0
CA B:VAL136 4.5 15.3 1.0
HB B:THR13 4.5 20.4 1.0
O B:SER135 4.6 13.0 1.0
O3P B:FMN301 4.6 14.8 1.0
H5'1 B:FMN301 4.7 14.5 1.0
O B:HOH426 4.8 15.4 1.0
C B:LYS12 4.8 19.3 1.0
H2' B:FMN301 4.8 21.3 1.0
CG2 B:VAL136 4.8 16.5 1.0
CA A:PRO38 4.8 14.9 1.0
HA A:PRO38 4.8 17.9 1.0
N10 B:FMN301 4.8 14.4 1.0
C9 B:FMN301 4.9 11.5 1.0
C4' B:FMN301 4.9 16.7 1.0
HG2 A:PRO38 4.9 13.1 1.0
C5' B:FMN301 4.9 12.1 1.0
HD13 B:LEU125 4.9 16.6 1.0
HB B:VAL136 5.0 19.7 1.0
NE B:ARG11 5.0 14.2 1.0

Chlorine binding site 6 out of 6 in 6q1l

Go back to Chlorine Binding Sites List in 6q1l
Chlorine binding site 6 out of 6 in the Crystal Structure of Oxidized Iodotyrosine Deiodinase (Iyd) 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 Oxidized Iodotyrosine Deiodinase (Iyd) Bound to Fmn and 3-Iodo-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:19.2
occ:1.00
HD22 A:ASN42 2.5 16.4 1.0
HZ1 B:LYS86 2.5 39.9 1.0
HE1 B:TRP82 2.6 19.4 1.0
HB3 A:ASN42 3.2 16.6 1.0
HE2 B:LYS86 3.2 28.6 1.0
NZ B:LYS86 3.2 33.3 1.0
HB3 B:TYR174 3.3 17.6 1.0
HE3 B:LYS86 3.3 28.6 1.0
ND2 A:ASN42 3.3 13.7 1.0
HD2 B:PRO175 3.3 23.6 1.0
NE1 B:TRP82 3.4 16.2 1.0
CE B:LYS86 3.5 23.8 1.0
HZ3 B:LYS86 3.7 39.9 1.0
HZ2 B:LYS86 3.8 39.9 1.0
HD21 A:ASN42 3.8 16.4 1.0
HZ2 B:TRP82 4.0 20.7 1.0
CB A:ASN42 4.0 13.8 1.0
HD2 B:TYR174 4.0 19.7 1.0
CB B:TYR174 4.1 14.7 1.0
CG A:ASN42 4.1 13.4 1.0
HB2 A:ASN42 4.2 16.6 1.0
CD B:PRO175 4.3 19.6 1.0
CD2 B:TYR174 4.3 16.4 1.0
CE2 B:TRP82 4.3 18.4 1.0
CG B:TYR174 4.3 13.9 1.0
HB2 B:TYR174 4.4 17.6 1.0
CD1 B:TRP82 4.4 18.7 1.0
HD1 B:TRP82 4.5 22.4 1.0
HD3 B:PRO175 4.5 23.6 1.0
CZ2 B:TRP82 4.5 17.2 1.0
O A:HOH477 4.7 32.6 1.0
O B:HOH419 4.8 33.9 1.0
O A:MET41 4.8 14.0 1.0
OE2 B:GLU85 4.8 30.8 1.0
O A:HOH471 4.8 32.5 1.0
HG2 B:PRO175 4.9 27.7 1.0
O A:ASN42 4.9 14.2 1.0
CD B:LYS86 5.0 23.8 1.0

Reference:

Z.Sun, J.M.Kavran, S.E.Rokita. Crystal Structure of Oxidized Tn Iyd Bound to Fmn and 3-Iodo-L-Tyrosine To Be Published.
Page generated: Sat Apr 17 15:07:13 2021

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