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Fluorine in PDB 1y1d: Crystal Structure of Transthyretin in Complex with Iododiflunisal

Protein crystallography data

The structure of Crystal Structure of Transthyretin in Complex with Iododiflunisal, PDB code: 1y1d was solved by L.Gales, S.Macedo-Ribeiro, G.Arsequell, G.Valencia, M.J.Saraiva, A.M.Damas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 43.313, 85.844, 64.865, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.2

Other elements in 1y1d:

The structure of Crystal Structure of Transthyretin in Complex with Iododiflunisal also contains other interesting chemical elements:

Iodine (I) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Transthyretin in Complex with Iododiflunisal (pdb code 1y1d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Transthyretin in Complex with Iododiflunisal, PDB code: 1y1d:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1y1d

Go back to Fluorine Binding Sites List in 1y1d
Fluorine binding site 1 out of 4 in the Crystal Structure of Transthyretin in Complex with Iododiflunisal


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Transthyretin in Complex with Iododiflunisal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2000

b:29.8
occ:0.35
FAT A:FHI2000 0.0 29.8 0.3
CAN A:FHI2000 1.3 29.2 0.3
CAM A:FHI2000 2.4 28.8 0.3
CAO A:FHI2000 2.4 29.4 0.3
CAP A:FHI2000 2.7 29.7 0.3
CAQ A:FHI2000 2.8 30.2 0.3
CAF A:FHI2000 3.6 28.5 0.3
CAH A:FHI2000 3.6 29.4 0.3
CAI A:FHI2000 3.8 29.5 0.3
CAR A:FHI2000 3.9 30.4 0.3
CAG A:FHI2000 4.1 28.8 0.3
CAJ A:FHI2000 4.7 29.5 0.3
FAE A:FHI2000 4.7 28.9 0.3
CAK A:FHI2000 4.7 30.0 0.3

Fluorine binding site 2 out of 4 in 1y1d

Go back to Fluorine Binding Sites List in 1y1d
Fluorine binding site 2 out of 4 in the Crystal Structure of Transthyretin in Complex with Iododiflunisal


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Transthyretin in Complex with Iododiflunisal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2000

b:28.9
occ:0.35
FAE A:FHI2000 0.0 28.9 0.3
CAF A:FHI2000 1.3 28.5 0.3
CAM A:FHI2000 2.4 28.8 0.3
CAG A:FHI2000 2.4 28.8 0.3
CB A:SER117 3.2 15.5 1.0
CAN A:FHI2000 3.6 29.2 0.3
CAH A:FHI2000 3.6 29.4 0.3
OG A:SER117 3.9 17.3 1.0
CAO A:FHI2000 4.1 29.4 0.3
CD2 A:LEU110 4.2 15.7 1.0
CB A:LEU110 4.4 12.7 1.0
CA A:SER117 4.5 14.6 1.0
C A:SER117 4.6 15.4 1.0
FAT A:FHI2000 4.7 29.8 0.3
O A:SER117 4.8 16.1 1.0
OG B:SER1117 5.0 17.6 1.0

Fluorine binding site 3 out of 4 in 1y1d

Go back to Fluorine Binding Sites List in 1y1d
Fluorine binding site 3 out of 4 in the Crystal Structure of Transthyretin in Complex with Iododiflunisal


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Transthyretin in Complex with Iododiflunisal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F3000

b:33.1
occ:0.35
FAT B:FHI3000 0.0 33.1 0.3
CAN B:FHI3000 1.3 33.3 0.3
CAO B:FHI3000 2.4 34.0 0.3
CAM B:FHI3000 2.4 33.1 0.3
CAP B:FHI3000 2.8 34.5 0.3
CAQ B:FHI3000 3.0 35.8 0.3
CAH B:FHI3000 3.6 33.5 0.3
CAF B:FHI3000 3.6 33.3 0.3
CAI B:FHI3000 3.8 34.5 0.3
CAR B:FHI3000 4.1 36.6 0.3
CAG B:FHI3000 4.1 33.5 0.3
FAE B:FHI3000 4.7 34.2 0.3
CAJ B:FHI3000 4.8 34.7 0.3
CAK B:FHI3000 4.9 35.7 0.3

Fluorine binding site 4 out of 4 in 1y1d

Go back to Fluorine Binding Sites List in 1y1d
Fluorine binding site 4 out of 4 in the Crystal Structure of Transthyretin in Complex with Iododiflunisal


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Transthyretin in Complex with Iododiflunisal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F3000

b:34.2
occ:0.35
FAE B:FHI3000 0.0 34.2 0.3
CAF B:FHI3000 1.3 33.3 0.3
CAG B:FHI3000 2.4 33.5 0.3
CAM B:FHI3000 2.4 33.1 0.3
CB B:SER1117 3.2 14.6 1.0
CAH B:FHI3000 3.6 33.5 0.3
CAN B:FHI3000 3.6 33.3 0.3
C B:SER1117 4.1 14.3 1.0
CAO B:FHI3000 4.1 34.0 0.3
O B:SER1117 4.2 15.6 1.0
OG B:SER1117 4.2 17.6 1.0
CB B:LEU1110 4.3 10.8 1.0
CA B:SER1117 4.3 14.2 1.0
N B:THR1118 4.5 13.6 1.0
CD2 B:LEU1110 4.6 13.8 1.0
FAT B:FHI3000 4.7 33.1 0.3
CA B:THR1118 4.9 13.6 1.0
C B:THR1118 4.9 13.6 1.0
OG A:SER115 4.9 10.7 0.5
CB B:THR1119 5.0 13.9 1.0

Reference:

L.Gales, S.Macedo-Ribeiro, G.Arsequell, G.Valencia, M.J.Saraiva, A.M.Damas. Human Transthyretin in Complex with Iododiflunisal: Structural Features Associated with A Potent Amyloid Inhibitor. Biochem.J. V. 388 615 2005.
ISSN: ISSN 0264-6021
PubMed: 15689188
DOI: 10.1042/BJ20042035
Page generated: Sun Dec 13 11:34:12 2020

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