Fluorine in PDB 5yak: The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr)

Enzymatic activity of The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr)

All present enzymatic activity of The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr):
1.21.1.1;

Protein crystallography data

The structure of The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr), PDB code: 5yak was solved by J.M.Hu, S.E.Rokita, J.Schlessman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.52 / 2.30
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 105.079, 105.079, 300.202, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 22.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr) (pdb code 5yak). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr), PDB code: 5yak:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5yak

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Fluorine binding site 1 out of 6 in the The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:42.1
occ:1.00
 F A:YOF502 0.0 42.1 1.0
CE1 A:YOF502 1.4 48.0 1.0
CZ A:YOF502 2.3 35.0 1.0
CD1 A:YOF502 2.5 45.1 1.0
O2' A:FMN501 2.8 35.2 1.0
OH A:YOF502 2.8 39.2 1.0
N F:ALA130 3.0 36.4 1.0
C10 A:FMN501 3.4 37.3 1.0
N10 A:FMN501 3.6 37.9 1.0
CE2 A:YOF502 3.6 49.7 1.0
CA F:ALA130 3.6 40.4 1.0
C2' A:FMN501 3.6 36.2 1.0
C4A A:FMN501 3.7 36.6 1.0
N1 A:FMN501 3.7 35.2 1.0
CG A:YOF502 3.8 47.1 1.0
CD1 A:LEU176 3.8 43.3 1.0
C9A A:FMN501 4.0 36.2 1.0
C F:GLY129 4.1 35.0 1.0
C1' A:FMN501 4.1 38.5 1.0
CD2 A:YOF502 4.1 52.2 1.0
N5 A:FMN501 4.2 36.7 1.0
CD2 A:LEU173 4.2 43.2 1.0
CA F:GLY129 4.2 37.1 1.0
C5A A:FMN501 4.3 37.5 1.0
C2 A:FMN501 4.3 40.1 1.0
C4 A:FMN501 4.4 39.6 1.0
CB F:ALA130 4.4 36.0 1.0
N3 A:FMN501 4.6 42.7 1.0
O F:SER128 4.6 35.7 1.0
NH2 A:ARG104 4.7 39.5 1.0
C F:ALA130 4.8 35.7 1.0
C9 A:FMN501 4.9 37.4 1.0
N F:HIS131 5.0 38.7 1.0

Fluorine binding site 2 out of 6 in 5yak

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Fluorine binding site 2 out of 6 in the The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:33.6
occ:1.00
 F B:YOF502 0.0 33.6 1.0
CE1 B:YOF502 1.3 33.3 1.0
CZ B:YOF502 2.3 32.6 1.0
CD1 B:YOF502 2.3 36.4 1.0
OH B:YOF502 2.8 30.1 1.0
N C:ALA130 3.5 29.6 1.0
CA C:GLY129 3.6 31.7 1.0
CE2 B:YOF502 3.6 36.5 1.0
CG B:YOF502 3.6 34.7 1.0
CD1 C:TYR212 3.7 35.5 1.0
CE1 C:TYR212 3.7 36.5 1.0
N5 B:FMN501 3.8 34.2 1.0
C C:GLY129 3.9 31.5 1.0
C5A B:FMN501 4.1 32.7 1.0
CD2 B:YOF502 4.1 32.9 1.0
C4A B:FMN501 4.2 29.5 1.0
CB C:TYR211 4.2 33.8 1.0
CA C:ALA130 4.4 31.5 1.0
C6 B:FMN501 4.5 34.2 1.0
NE1 B:TRP169 4.5 34.8 1.0
CB C:ALA130 4.6 33.7 1.0
C9A B:FMN501 4.6 27.6 1.0
CD2 B:LEU173 4.7 36.3 1.0
C10 B:FMN501 4.7 28.5 1.0
C4 B:FMN501 4.8 30.6 1.0
N10 B:FMN501 4.8 24.4 1.0
CG C:TYR211 4.8 34.0 1.0
CB B:YOF502 4.9 35.0 1.0
CZ2 B:TRP169 4.9 31.8 1.0
O4 B:FMN501 4.9 28.4 1.0
N C:GLY129 4.9 32.5 1.0
O C:GLY129 4.9 34.6 1.0
CG C:TYR212 5.0 33.0 1.0
CZ C:TYR212 5.0 36.4 1.0

Fluorine binding site 3 out of 6 in 5yak

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Fluorine binding site 3 out of 6 in the The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:41.0
occ:1.00
 F C:YOF502 0.0 41.0 1.0
CE1 C:YOF502 1.3 41.4 1.0
CZ C:YOF502 2.3 43.7 1.0
CD1 C:YOF502 2.4 41.2 1.0
OH C:YOF502 2.7 36.8 1.0
N B:ALA130 3.4 34.3 1.0
CA B:GLY129 3.5 34.5 1.0
CE2 C:YOF502 3.6 47.3 1.0
CG C:YOF502 3.6 43.4 1.0
N5 C:FMN501 3.7 40.1 1.0
C B:GLY129 3.8 34.0 1.0
CD1 B:TYR212 3.8 40.9 1.0
CE1 B:TYR212 4.0 40.6 1.0
C5A C:FMN501 4.0 41.0 1.0
C4A C:FMN501 4.1 36.7 1.0
CD2 C:YOF502 4.1 42.7 1.0
CB B:TYR211 4.3 38.2 1.0
CA B:ALA130 4.4 35.8 1.0
C6 C:FMN501 4.4 40.0 1.0
CB B:ALA130 4.6 37.4 1.0
NE1 C:TRP169 4.6 36.3 1.0
C9A C:FMN501 4.6 39.0 1.0
C10 C:FMN501 4.6 36.0 1.0
C4 C:FMN501 4.6 37.8 1.0
CD2 C:LEU173 4.7 38.0 1.0
O4 C:FMN501 4.8 36.4 1.0
N10 C:FMN501 4.8 36.2 1.0
N B:GLY129 4.9 33.8 1.0
CB C:YOF502 4.9 36.4 1.0
CZ2 C:TRP169 4.9 39.1 1.0
O B:GLY129 4.9 34.9 1.0

Fluorine binding site 4 out of 6 in 5yak

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Fluorine binding site 4 out of 6 in the The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:41.1
occ:1.00
 F D:YOF502 0.0 41.1 1.0
CE1 D:YOF502 1.3 40.0 1.0
CZ D:YOF502 2.3 40.7 1.0
CD1 D:YOF502 2.3 38.7 1.0
OH D:YOF502 2.7 34.0 1.0
CG D:YOF502 3.6 42.3 1.0
CE2 D:YOF502 3.6 41.0 1.0
CE1 E:TYR212 3.6 43.4 1.0
N E:ALA130 3.6 34.6 1.0
CD1 E:TYR212 3.7 43.6 1.0
CA E:GLY129 3.7 34.2 1.0
N5 D:FMN501 3.8 41.6 1.0
C E:GLY129 4.0 30.3 1.0
CD2 D:YOF502 4.1 43.9 1.0
C4A D:FMN501 4.1 40.3 1.0
C5A D:FMN501 4.1 41.2 1.0
CB E:TYR211 4.3 41.2 1.0
NE1 D:TRP169 4.4 40.8 1.0
C6 D:FMN501 4.5 40.8 1.0
C4 D:FMN501 4.6 41.5 1.0
CA E:ALA130 4.6 29.8 1.0
CZ2 D:TRP169 4.6 38.5 1.0
C10 D:FMN501 4.7 42.8 1.0
CD2 D:LEU173 4.7 39.7 1.0
C9A D:FMN501 4.7 37.8 1.0
O4 D:FMN501 4.8 39.2 1.0
CB E:ALA130 4.8 35.8 1.0
CB D:YOF502 4.8 40.5 1.0
CE2 D:TRP169 4.9 40.5 1.0
N10 D:FMN501 4.9 38.2 1.0
CZ E:TYR212 4.9 43.5 1.0
CG E:TYR211 4.9 39.6 1.0

Fluorine binding site 5 out of 6 in 5yak

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Fluorine binding site 5 out of 6 in the The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F502

b:43.0
occ:1.00
 F E:YOF502 0.0 43.0 1.0
CE1 E:YOF502 1.3 41.7 1.0
CZ E:YOF502 2.4 41.7 1.0
CD1 E:YOF502 2.4 38.7 1.0
OH E:YOF502 2.7 37.9 1.0
N D:ALA130 3.4 43.2 1.0
CA D:GLY129 3.6 47.3 1.0
CE2 E:YOF502 3.6 40.9 1.0
CG E:YOF502 3.6 40.0 1.0
CD1 D:TYR212 3.9 45.5 1.0
C D:GLY129 3.9 49.6 1.0
N5 E:FMN501 3.9 45.7 1.0
CE1 D:TYR212 4.0 44.1 1.0
CB D:TYR211 4.1 43.4 1.0
CD2 E:YOF502 4.1 37.4 1.0
C5A E:FMN501 4.2 41.1 1.0
C4A E:FMN501 4.2 40.9 1.0
NE1 E:TRP169 4.3 46.7 1.0
CA D:ALA130 4.4 41.6 1.0
CD2 E:LEU173 4.5 43.2 1.0
C6 E:FMN501 4.6 42.8 1.0
CZ2 E:TRP169 4.6 47.8 1.0
CB D:ALA130 4.6 41.5 1.0
C4 E:FMN501 4.7 41.5 1.0
C10 E:FMN501 4.8 38.3 1.0
C9A E:FMN501 4.8 40.2 1.0
CG D:TYR211 4.8 41.2 1.0
CE2 E:TRP169 4.8 46.8 1.0
O4 E:FMN501 4.8 40.2 1.0
CB E:YOF502 4.9 39.2 1.0
O D:GLY129 5.0 41.0 1.0
O D:HOH631 5.0 41.3 1.0

Fluorine binding site 6 out of 6 in 5yak

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Fluorine binding site 6 out of 6 in the The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Crystal Structure of Human Iyd THR239 Mutant with Ligand 3- Fluorotyrosine (F-Tyr) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F502

b:37.8
occ:1.00
 F F:YOF502 0.0 37.8 1.0
CE1 F:YOF502 1.4 37.2 1.0
CZ F:YOF502 2.3 35.9 1.0
CD1 F:YOF502 2.4 35.2 1.0
OH F:YOF502 2.7 31.3 1.0
N A:ALA130 3.3 34.0 1.0
CA A:GLY129 3.6 32.2 1.0
CE2 F:YOF502 3.6 35.7 1.0
CG F:YOF502 3.7 35.8 1.0
CD1 A:TYR212 3.8 37.8 1.0
CE1 A:TYR212 3.8 32.1 1.0
N5 F:FMN501 3.8 38.1 1.0
C A:GLY129 3.9 31.6 1.0
C5A F:FMN501 4.1 33.2 1.0
C4A F:FMN501 4.1 35.3 1.0
CD2 F:YOF502 4.1 37.0 1.0
CB A:TYR211 4.2 38.9 1.0
CA A:ALA130 4.3 35.7 1.0
NE1 F:TRP169 4.4 46.4 1.0
C6 F:FMN501 4.5 33.9 1.0
CB A:ALA130 4.6 40.0 1.0
C9A F:FMN501 4.6 33.0 1.0
CD2 F:LEU173 4.6 44.2 1.0
C4 F:FMN501 4.7 34.1 1.0
C10 F:FMN501 4.7 34.7 1.0
O4 F:FMN501 4.8 32.8 1.0
N10 F:FMN501 4.8 36.8 1.0
CZ2 F:TRP169 4.9 41.3 1.0
CG A:TYR211 4.9 38.6 1.0
N A:GLY129 4.9 31.2 1.0
O A:GLY129 5.0 34.8 1.0
CB F:YOF502 5.0 36.1 1.0

Reference:

J.Hu, Q.Su, J.L.Schlessman, S.E.Rokita. Redox Control of Iodotyrosine Deiodinase Protein Sci. V. 28 68 2019.
ISSN: ESSN 1469-896X
PubMed: 30052294
DOI: 10.1002/PRO.3479
Page generated: Sun Dec 13 12:43:10 2020

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