Fluorine in PDB 5jid: Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)

The structure of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa), PDB code: 5jid was solved by A.Begum, J.Zhang, A.Olofsson, P.Andersson, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.18 / 1.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.653, 85.674, 63.420, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 16.3

The structure of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) (pdb code 5jid). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 30 binding sites of Fluorine where determined in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa), PDB code: 5jid:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


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 Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:33.8 occ:0.50 F01 A:8PF301 0.0 33.8 0.5 C02 A:8PF301 1.3 34.0 0.5 F03 A:8PF301 2.2 34.3 0.5 C10 A:8PF301 2.3 31.4 0.5 C04 A:8PF301 2.3 36.5 0.5 O08 A:8PF301 2.5 38.4 0.5 F12 A:8PF301 2.6 29.2 0.5 F14 A:8PF301 2.6 34.1 0.5 C07 A:8PF301 2.8 37.5 0.5 HD11 A:LEU17 2.8 21.3 1.0 F05 A:8PF301 2.8 36.2 0.5 C13 A:8PF301 3.0 33.2 0.5 HD12 A:LEU17 3.4 21.3 1.0 F06 A:8PF301 3.5 37.7 0.5 F11 A:8PF301 3.5 29.0 0.5 CD1 A:LEU17 3.5 17.8 1.0 F15 A:8PF301 3.6 33.6 0.5 HD13 A:LEU17 3.9 21.3 1.0 O09 A:8PF301 4.0 37.2 0.5 C16 A:8PF301 4.3 34.2 0.5 F18 A:8PF301 4.3 35.3 0.5 O A:HOH411 4.4 56.2 1.0 HG A:LEU17 4.8 18.7 1.0 CG A:LEU17 4.8 15.6 1.0 F17 A:8PF301 4.8 31.2 0.5 HD21 A:LEU17 5.0 20.4 1.0 HE2 A:LYS15 5.0 37.9 1.0

Fluorine binding site 2 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


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 Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:34.3 occ:0.50 F03 A:8PF301 0.0 34.3 0.5 C02 A:8PF301 1.3 34.0 0.5 F01 A:8PF301 2.2 33.8 0.5 C04 A:8PF301 2.3 36.5 0.5 C10 A:8PF301 2.3 31.4 0.5 F15 A:8PF301 2.5 33.6 0.5 F06 A:8PF301 2.5 37.7 0.5 HD11 A:LEU17 2.5 21.3 1.0 C13 A:8PF301 2.8 33.2 0.5 F11 A:8PF301 2.8 29.0 0.5 HD12 A:LEU17 2.9 21.3 1.0 C07 A:8PF301 3.0 37.5 0.5 O08 A:8PF301 3.0 38.4 0.5 F14 A:8PF301 3.1 34.1 0.5 CD1 A:LEU17 3.1 17.8 1.0 HG A:LEU17 3.3 18.7 1.0 HB1 A:ALA108 3.4 18.9 1.0 F05 A:8PF301 3.4 36.2 0.5 F12 A:8PF301 3.5 29.2 0.5 HD3 A:LYS15 3.8 33.5 1.0 CG A:LEU17 3.8 15.6 1.0 HG2 A:LYS15 3.9 28.3 1.0 HD13 A:LEU17 3.9 21.3 1.0 HE3 A:LYS15 4.1 37.9 1.0 O09 A:8PF301 4.1 37.2 0.5 CB A:ALA108 4.2 15.7 1.0 HB2 A:ALA108 4.2 18.9 1.0 HD21 A:LEU17 4.2 20.4 1.0 C16 A:8PF301 4.3 34.2 0.5 CD A:LYS15 4.4 27.9 1.0 F24 A:8PF301 4.4 39.1 0.5 HE2 A:LYS15 4.5 37.9 1.0 HB3 A:LYS15 4.5 22.4 1.0 CE A:LYS15 4.5 31.6 1.0 HB3 A:ALA108 4.6 18.9 1.0 CG A:LYS15 4.6 23.6 1.0 CD2 A:LEU17 4.6 17.0 1.0 HB2 A:LEU17 4.7 16.7 1.0 F17 A:8PF301 4.8 31.2 0.5 CB A:LEU17 4.9 13.9 1.0 F18 A:8PF301 5.0 35.3 0.5

Fluorine binding site 3 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


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 Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:36.2 occ:0.50 F05 A:8PF301 0.0 36.2 0.5 C04 A:8PF301 1.3 36.5 0.5 F06 A:8PF301 2.2 37.7 0.5 C07 A:8PF301 2.3 37.5 0.5 C02 A:8PF301 2.3 34.0 0.5 F12 A:8PF301 2.6 29.2 0.5 C10 A:8PF301 2.7 31.4 0.5 O09 A:8PF301 2.7 37.2 0.5 F01 A:8PF301 2.8 33.8 0.5 F11 A:8PF301 2.9 29.0 0.5 O08 A:8PF301 3.3 38.4 0.5 F03 A:8PF301 3.4 34.3 0.5 C13 A:8PF301 4.2 33.2 0.5 F14 A:8PF301 4.6 34.1 0.5 F17 A:8PF301 4.8 31.2 0.5 F15 A:8PF301 4.8 33.6 0.5 HD3 A:LYS15 4.8 33.5 1.0 HG21 A:VAL121 4.9 27.0 1.0 C16 A:8PF301 5.0 34.2 0.5

Fluorine binding site 4 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


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 Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:37.7 occ:0.50 F06 A:8PF301 0.0 37.7 0.5 C04 A:8PF301 1.3 36.5 0.5 F05 A:8PF301 2.2 36.2 0.5 C07 A:8PF301 2.3 37.5 0.5 C02 A:8PF301 2.3 34.0 0.5 F03 A:8PF301 2.5 34.3 0.5 F11 A:8PF301 2.6 29.0 0.5 O09 A:8PF301 2.8 37.2 0.5 C10 A:8PF301 2.9 31.4 0.5 HB2 A:ALA108 3.1 18.9 1.0 HD3 A:LYS15 3.2 33.5 1.0 HB1 A:ALA108 3.3 18.9 1.0 O08 A:8PF301 3.3 38.4 0.5 F01 A:8PF301 3.5 33.8 0.5 CB A:ALA108 3.6 15.7 1.0 F12 A:8PF301 3.7 29.2 0.5 HB3 A:ALA108 3.9 18.9 1.0 HB3 A:LYS15 4.0 22.4 1.0 CD A:LYS15 4.1 27.9 1.0 F15 A:8PF301 4.2 33.6 0.5 C13 A:8PF301 4.2 33.2 0.5 HG2 A:LYS15 4.5 28.3 1.0 HG21 A:THR106 4.5 24.0 1.0 HE2 A:LYS15 4.6 37.9 1.0 HD2 A:LYS15 4.7 33.5 1.0 CG A:LYS15 4.7 23.6 1.0 CB A:LYS15 4.7 18.6 1.0 HG21 A:VAL121 4.8 27.0 1.0 HG22 A:THR106 4.8 24.0 1.0 CE A:LYS15 4.8 31.6 1.0 HD11 A:LEU17 4.8 21.3 1.0 F14 A:8PF301 4.9 34.1 0.5 HE3 A:LYS15 4.9 37.9 1.0 HB2 A:LYS15 4.9 22.4 1.0 CA A:ALA108 5.0 14.1 1.0 HA A:ALA108 5.0 16.9 1.0

Fluorine binding site 5 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:29.0 occ:0.50 F11 A:8PF301 0.0 29.0 0.5 C10 A:8PF301 1.3 31.4 0.5 F12 A:8PF301 2.2 29.2 0.5 C13 A:8PF301 2.3 33.2 0.5 C02 A:8PF301 2.3 34.0 0.5 F06 A:8PF301 2.6 37.7 0.5 F17 A:8PF301 2.6 31.2 0.5 F15 A:8PF301 2.6 33.6 0.5 C04 A:8PF301 2.7 36.5 0.5 F03 A:8PF301 2.8 34.3 0.5 F05 A:8PF301 2.9 36.2 0.5 C16 A:8PF301 2.9 34.2 0.5 HB1 A:ALA108 3.0 18.9 1.0 F24 A:8PF301 3.1 39.1 0.5 HB3 A:ALA108 3.1 18.9 1.0 CB A:ALA108 3.4 15.7 1.0 F14 A:8PF301 3.4 34.1 0.5 F01 A:8PF301 3.5 33.8 0.5 HB2 A:ALA108 3.5 18.9 1.0 HG22 A:THR119 3.5 18.9 1.0 HG21 A:THR119 3.8 18.9 1.0 F18 A:8PF301 3.8 35.3 0.5 CG2 A:THR119 4.0 15.8 1.0 C19 A:8PF301 4.0 36.3 0.5 C22 A:8PF301 4.1 37.9 0.5 C07 A:8PF301 4.2 37.5 0.5 HG23 A:THR119 4.3 18.9 1.0 F25 A:8PF301 4.6 37.4 0.5 F21 A:8PF301 4.7 38.2 0.5 CA A:ALA108 4.8 14.1 1.0 O08 A:8PF301 4.9 38.4 0.5 O09 A:8PF301 5.0 37.2 0.5 HD12 A:LEU17 5.0 21.3 1.0

Fluorine binding site 6 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:29.2 occ:0.50 F12 A:8PF301 0.0 29.2 0.5 C10 A:8PF301 1.3 31.4 0.5 F11 A:8PF301 2.2 29.0 0.5 C13 A:8PF301 2.3 33.2 0.5 C02 A:8PF301 2.3 34.0 0.5 F01 A:8PF301 2.6 33.8 0.5 F05 A:8PF301 2.6 36.2 0.5 F14 A:8PF301 2.6 34.1 0.5 C16 A:8PF301 2.7 34.2 0.5 F18 A:8PF301 2.7 35.3 0.5 F17 A:8PF301 2.7 31.2 0.5 C04 A:8PF301 3.0 36.5 0.5 F15 A:8PF301 3.4 33.6 0.5 F03 A:8PF301 3.5 34.3 0.5 F06 A:8PF301 3.7 37.7 0.5 C19 A:8PF301 4.2 36.3 0.5 C07 A:8PF301 4.2 37.5 0.5 F24 A:8PF301 4.5 39.1 0.5 O08 A:8PF301 4.6 38.4 0.5 F21 A:8PF301 4.7 38.2 0.5 F20 A:8PF301 4.8 35.2 0.5 HG21 A:THR119 4.9 18.9 1.0 C22 A:8PF301 4.9 37.9 0.5 HD12 A:LEU17 5.0 21.3 1.0

Fluorine binding site 7 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:34.1 occ:0.50 F14 A:8PF301 0.0 34.1 0.5 C13 A:8PF301 1.3 33.2 0.5 F15 A:8PF301 2.2 33.6 0.5 C10 A:8PF301 2.3 31.4 0.5 C16 A:8PF301 2.3 34.2 0.5 F18 A:8PF301 2.4 35.3 0.5 F01 A:8PF301 2.6 33.8 0.5 F12 A:8PF301 2.6 29.2 0.5 C02 A:8PF301 2.7 34.0 0.5 HD12 A:LEU17 2.8 21.3 1.0 F21 A:8PF301 2.9 38.2 0.5 F03 A:8PF301 3.1 34.3 0.5 C19 A:8PF301 3.2 36.3 0.5 F11 A:8PF301 3.4 29.0 0.5 F17 A:8PF301 3.4 31.2 0.5 HD11 A:LEU17 3.5 21.3 1.0 CD1 A:LEU17 3.6 17.8 1.0 HD13 A:LEU17 3.9 21.3 1.0 F24 A:8PF301 4.0 39.1 0.5 F20 A:8PF301 4.1 35.2 0.5 C04 A:8PF301 4.2 36.5 0.5 C22 A:8PF301 4.2 37.9 0.5 HB2 A:LEU110 4.3 15.8 1.0 HD13 A:LEU110 4.4 18.2 1.0 HD22 A:LEU110 4.4 22.1 1.0 F05 A:8PF301 4.6 36.2 0.5 CG A:LEU17 4.8 15.6 1.0 HG A:LEU17 4.9 18.7 1.0 F06 A:8PF301 4.9 37.7 0.5 HB2 A:LEU17 4.9 16.7 1.0 F23 A:8PF301 4.9 39.3 0.5 O08 A:8PF301 5.0 38.4 0.5

Fluorine binding site 8 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:33.6 occ:0.50 F15 A:8PF301 0.0 33.6 0.5 C13 A:8PF301 1.4 33.2 0.5 F14 A:8PF301 2.2 34.1 0.5 F24 A:8PF301 2.3 39.1 0.5 C10 A:8PF301 2.3 31.4 0.5 C16 A:8PF301 2.4 34.2 0.5 F03 A:8PF301 2.5 34.3 0.5 F11 A:8PF301 2.6 29.0 0.5 F21 A:8PF301 2.8 38.2 0.5 C19 A:8PF301 2.8 36.3 0.5 C02 A:8PF301 2.9 34.0 0.5 HD12 A:LEU17 3.0 21.3 1.0 C22 A:8PF301 3.0 37.9 0.5 F17 A:8PF301 3.2 31.2 0.5 HB1 A:ALA108 3.2 18.9 1.0 HB2 A:LEU110 3.4 15.8 1.0 F12 A:8PF301 3.4 29.2 0.5 F18 A:8PF301 3.5 35.3 0.5 F23 A:8PF301 3.6 39.3 0.5 F01 A:8PF301 3.6 33.8 0.5 CD1 A:LEU17 3.8 17.8 1.0 HD11 A:LEU17 3.9 21.3 1.0 HB3 A:ALA108 4.0 18.9 1.0 CB A:ALA108 4.0 15.7 1.0 HG A:LEU17 4.1 18.7 1.0 C04 A:8PF301 4.1 36.5 0.5 F20 A:8PF301 4.2 35.2 0.5 F25 A:8PF301 4.2 37.4 0.5 F06 A:8PF301 4.2 37.7 0.5 HB2 A:LEU17 4.4 16.7 1.0 CB A:LEU110 4.4 13.1 1.0 C A:ALA109 4.5 12.8 1.0 HD13 A:LEU110 4.5 18.2 1.0 HD13 A:LEU17 4.5 21.3 1.0 O A:ALA109 4.5 15.0 1.0 CG A:LEU17 4.5 15.6 1.0 HB2 A:ALA108 4.6 18.9 1.0 N A:LEU110 4.6 12.4 1.0 H A:ALA109 4.7 15.5 1.0 N A:ALA109 4.7 12.9 1.0 HG22 A:THR119 4.7 18.9 1.0 HB3 A:LEU110 4.8 15.8 1.0 HD22 A:LEU110 4.8 22.1 1.0 HA A:LEU110 4.8 14.6 1.0 F05 A:8PF301 4.8 36.2 0.5 C A:ALA108 4.8 12.9 1.0 CA A:LEU110 4.9 12.2 1.0 H A:LEU110 4.9 14.8 1.0

Fluorine binding site 9 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:31.2 occ:0.50 F17 A:8PF301 0.0 31.2 0.5 C16 A:8PF301 1.3 34.2 0.5 F18 A:8PF301 2.2 35.3 0.5 C19 A:8PF301 2.3 36.3 0.5 C13 A:8PF301 2.4 33.2 0.5 F11 A:8PF301 2.6 29.0 0.5 F24 A:8PF301 2.7 39.1 0.5 C10 A:8PF301 2.7 31.4 0.5 C22 A:8PF301 2.7 37.9 0.5 F12 A:8PF301 2.7 29.2 0.5 F20 A:8PF301 2.7 35.2 0.5 F25 A:8PF301 2.9 37.4 0.5 HG21 A:THR119 3.1 18.9 1.0 F15 A:8PF301 3.2 33.6 0.5 HG22 A:THR119 3.3 18.9 1.0 F21 A:8PF301 3.4 38.2 0.5 F14 A:8PF301 3.4 34.1 0.5 CG2 A:THR119 3.6 15.8 1.0 F23 A:8PF301 4.0 39.3 0.5 HB A:THR119 4.1 17.2 1.0 C02 A:8PF301 4.2 34.0 0.5 HG23 A:THR119 4.3 18.9 1.0 HB3 A:ALA108 4.4 18.9 1.0 CB A:THR119 4.5 14.3 1.0 HB1 A:ALA108 4.7 18.9 1.0 F03 A:8PF301 4.8 34.3 0.5 F05 A:8PF301 4.8 36.2 0.5 F01 A:8PF301 4.8 33.8 0.5 C04 A:8PF301 5.0 36.5 0.5

Fluorine binding site 10 out of 30 in the Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Transthyretin in Complex with Perfluorooctanoic Acid (Pfoa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:35.3 occ:0.50 F18 A:8PF301 0.0 35.3 0.5 C16 A:8PF301 1.3 34.2 0.5 F17 A:8PF301 2.2 31.2 0.5 C19 A:8PF301 2.3 36.3 0.5 C13 A:8PF301 2.3 33.2 0.5 F14 A:8PF301 2.4 34.1 0.5 F20 A:8PF301 2.5 35.2 0.5 F12 A:8PF301 2.7 29.2 0.5 F21 A:8PF301 2.8 38.2 0.5 C10 A:8PF301 3.1 31.4 0.5 F15 A:8PF301 3.5 33.6 0.5 C22 A:8PF301 3.6 37.9 0.5 F11 A:8PF301 3.8 29.0 0.5 F24 A:8PF301 4.0 39.1 0.5 F25 A:8PF301 4.1 37.4 0.5 C02 A:8PF301 4.3 34.0 0.5 F01 A:8PF301 4.3 33.8 0.5 HD22 A:LEU110 4.6 22.1 1.0 F23 A:8PF301 4.6 39.3 0.5 F03 A:8PF301 5.0 34.3 0.5

J.Zhang, A.Begum, K.Brannstrom, C.Grundstrom, I.Iakovleva, A.Olofsson, A.E.Sauer-Eriksson, P.L.Andersson. Structure-Based Virtual Screening Protocol For in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin. Environ. Sci. Technol. V. 50 11984 2016.
ISSN: ISSN 1520-5851
PubMed: 27668830
DOI: 10.1021/ACS.EST.6B02771