Fluorine in PDB 3qtk: The Crystal Structure of Chemically Synthesized Vegf-A

The structure of The Crystal Structure of Chemically Synthesized Vegf-A, PDB code: 3qtk was solved by K.Mandal, S.B.H.Kent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.51 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	230.922, 44.008, 73.111, 90.00, 99.93, 90.00
R / Rfree (%)	18 / 22.3

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the The Crystal Structure of Chemically Synthesized Vegf-A (pdb code 3qtk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the The Crystal Structure of Chemically Synthesized Vegf-A, PDB code: 3qtk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


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 Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F104 b:87.5 occ:1.00 F1 A:TFA104 0.0 87.5 1.0 C2 A:TFA104 1.3 84.0 1.0 F3 A:TFA104 2.1 81.7 1.0 F2 A:TFA104 2.1 85.5 1.0 C1 A:TFA104 2.3 80.5 1.0 ND1 A:HIS83 2.6 58.9 1.0 O A:TFA104 2.9 75.5 1.0 CE1 A:HIS83 3.0 53.3 1.0 OXT A:TFA104 3.3 79.3 1.0 CG A:HIS83 3.8 54.6 1.0 NE2 A:HIS83 4.2 51.8 1.0 O A:ARG75 4.4 29.2 1.0 CB A:HIS83 4.4 44.0 1.0 N A:HIS83 4.5 34.1 1.0 CD2 A:HIS83 4.6 56.2 1.0 C A:GLN82 4.6 44.5 1.0 CA A:GLN82 4.8 38.7 1.0 O A:HOH119 4.8 32.4 1.0

Fluorine binding site 2 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


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 Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F104 b:85.5 occ:1.00 F2 A:TFA104 0.0 85.5 1.0 C2 A:TFA104 1.3 84.0 1.0 F1 A:TFA104 2.1 87.5 1.0 F3 A:TFA104 2.2 81.7 1.0 C1 A:TFA104 2.3 80.5 1.0 O A:TFA104 2.8 75.5 1.0 N A:GLN82 2.9 39.7 1.0 CA A:GLN82 2.9 38.7 1.0 C A:GLN82 3.0 44.5 1.0 C A:GLY81 3.2 40.1 1.0 OXT A:TFA104 3.2 79.3 1.0 N A:HIS83 3.4 34.1 1.0 O A:GLN82 3.4 42.2 1.0 ND1 A:HIS83 3.4 58.9 1.0 O A:GLY81 3.5 35.0 1.0 O A:ARG75 3.9 29.2 1.0 CA A:GLY81 4.0 40.3 1.0 CB A:HIS83 4.1 44.0 1.0 CG A:HIS83 4.2 54.6 1.0 CA A:HIS83 4.3 37.1 1.0 CB A:GLN82 4.4 36.3 1.0 CE1 A:HIS83 4.4 53.3 1.0 O A:HOH283 4.6 46.6 1.0 N A:GLY81 4.8 45.5 1.0

Fluorine binding site 3 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


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 Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F104 b:81.7 occ:1.00 F3 A:TFA104 0.0 81.7 1.0 C2 A:TFA104 1.3 84.0 1.0 F1 A:TFA104 2.1 87.5 1.0 F2 A:TFA104 2.2 85.5 1.0 C1 A:TFA104 2.3 80.5 1.0 OXT A:TFA104 2.6 79.3 1.0 O A:GLY81 3.4 35.0 1.0 O A:TFA104 3.6 75.5 1.0 O A:ARG75 3.7 29.2 1.0 C A:GLY81 3.8 40.1 1.0 N A:LYS77 4.0 34.2 1.0 CA A:GLN82 4.1 38.7 1.0 CB A:LYS77 4.1 34.6 1.0 N A:GLN82 4.2 39.7 1.0 ND1 A:HIS83 4.2 58.9 1.0 CG A:LYS77 4.2 34.9 1.0 CD A:LYS77 4.3 40.5 1.0 CE2 A:TYR38 4.4 29.6 1.0 C A:ARG75 4.5 35.4 1.0 O A:HOH119 4.6 32.4 1.0 C A:GLN82 4.7 44.5 1.0 C A:ILE76 4.7 31.9 1.0 CA A:GLY81 4.7 40.3 1.0 CA A:LYS77 4.7 30.9 1.0 CE1 A:HIS83 4.7 53.3 1.0 OE1 A:GLN80 4.8 76.0 1.0 N A:HIS83 4.8 34.1 1.0 CA A:ILE76 4.8 32.0 1.0 N A:GLY81 4.8 45.5 1.0 CD2 A:TYR38 4.9 26.1 1.0 N A:ILE76 5.0 29.5 1.0

Fluorine binding site 4 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


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 Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F106 b:79.6 occ:1.00 F1 A:TFA106 0.0 79.6 1.0 C2 A:TFA106 1.3 77.9 1.0 F3 A:TFA106 2.1 82.5 1.0 F2 A:TFA106 2.2 71.3 1.0 C1 A:TFA106 2.3 69.1 1.0 OXT A:TFA106 2.8 74.8 1.0 O A:TFA106 3.3 43.5 1.0 O D:GLY52 3.6 28.7 1.0 C D:GLY52 4.3 27.7 1.0 O A:HOH441 4.4 31.9 1.0 N D:GLY52 4.5 24.1 1.0 CA D:GLY52 4.7 24.7 1.0

Fluorine binding site 5 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


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 Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F106 b:71.3 occ:1.00 F2 A:TFA106 0.0 71.3 1.0 C2 A:TFA106 1.3 77.9 1.0 F1 A:TFA106 2.2 79.6 1.0 F3 A:TFA106 2.2 82.5 1.0 C1 A:TFA106 2.3 69.1 1.0 O A:TFA106 2.7 43.5 1.0 O A:LEU25 3.2 34.8 1.0 OXT A:TFA106 3.5 74.8 1.0 C A:LEU25 3.7 32.0 1.0 CB A:CYS44 3.9 22.3 1.0 N A:ASP27 4.1 26.8 1.0 N A:VAL26 4.1 21.0 1.0 CB A:LEU25 4.1 22.0 1.0 N D:GLY52 4.2 24.1 1.0 SG A:CYS44 4.2 25.9 1.0 C A:VAL26 4.3 26.8 1.0 CA A:VAL26 4.3 21.7 1.0 CA D:GLY52 4.4 24.7 1.0 O D:GLY52 4.4 28.7 1.0 O A:HOH193 4.4 38.3 1.0 C D:GLY52 4.5 27.7 1.0 CA A:LEU25 4.5 24.1 1.0 O A:HOH441 4.7 31.9 1.0 CA A:ASP27 4.7 32.1 0.5 CA A:ASP27 4.8 33.0 0.5 O A:HOH412 4.8 54.0 1.0 CB A:ASP27 4.9 35.5 0.5 CB A:ASP27 4.9 37.3 0.5 O A:VAL26 4.9 23.4 1.0

Fluorine binding site 6 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


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 Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F106 b:82.5 occ:1.00 F3 A:TFA106 0.0 82.5 1.0 C2 A:TFA106 1.3 77.9 1.0 F1 A:TFA106 2.1 79.6 1.0 F2 A:TFA106 2.2 71.3 1.0 C1 A:TFA106 2.3 69.1 1.0 OXT A:TFA106 2.9 74.8 1.0 O A:TFA106 3.4 43.5 1.0 O A:HOH193 3.6 38.3 1.0 O A:LEU25 4.2 34.8 1.0 O A:HOH412 4.4 54.0 1.0 N A:ASP27 4.5 26.8 1.0 CB A:ASP27 4.6 37.3 0.5 CB A:ASP27 4.7 35.5 0.5

Fluorine binding site 7 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of The Crystal Structure of Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F107 b:46.2 occ:1.00 F1 A:TFA107 0.0 46.2 1.0 C2 A:TFA107 1.3 53.9 1.0 F3 A:TFA107 2.2 59.5 1.0 F2 A:TFA107 2.2 37.3 1.0 C1 A:TFA107 2.3 62.9 1.0 O A:TFA107 2.6 70.3 1.0 OXT A:TFA107 3.5 63.9 1.0 O A:PRO46 3.7 23.0 1.0 CD A:GLU23 4.0 35.1 1.0 SD A:MET48 4.0 25.6 1.0 C A:PRO46 4.1 24.2 1.0 CG A:GLU23 4.1 27.4 1.0 OE1 A:GLU23 4.2 35.5 1.0 OE2 A:GLU23 4.2 32.8 1.0 CG A:MET48 4.2 23.9 1.0 OE1 A:GLN91 4.4 38.5 1.0 CB A:PRO46 4.4 23.8 1.0 N A:LEU47 4.5 24.3 1.0 CA A:LEU47 4.5 20.0 1.0 C A:LEU47 4.5 21.7 1.0 N A:MET48 4.6 22.0 1.0 NE D:ARG16 4.6 59.3 1.0 CB A:GLU23 4.7 20.5 1.0 CZ D:ARG16 4.8 62.9 1.0 CG A:PRO46 4.9 29.3 1.0 CA A:PRO46 4.9 22.1 1.0 CD D:ARG16 4.9 54.0 1.0

Fluorine binding site 8 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of The Crystal Structure of Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F107 b:37.3 occ:1.00 F2 A:TFA107 0.0 37.3 1.0 C2 A:TFA107 1.3 53.9 1.0 F3 A:TFA107 2.2 59.5 1.0 F1 A:TFA107 2.2 46.2 1.0 C1 A:TFA107 2.3 62.9 1.0 O A:PRO46 2.7 23.0 1.0 OXT A:TFA107 2.8 63.9 1.0 OE1 A:GLN91 2.9 38.5 1.0 O A:TFA107 3.1 70.3 1.0 C A:PRO46 3.7 24.2 1.0 CA A:LEU47 3.8 20.0 1.0 CD1 A:ILE69 3.9 30.5 1.0 CD A:GLN91 3.9 47.4 1.0 CE A:MET71 4.1 29.3 1.0 N A:LEU47 4.1 24.3 1.0 NE2 A:GLN91 4.3 40.1 1.0 N A:MET48 4.3 22.0 1.0 C A:LEU47 4.4 21.7 1.0 CG A:MET48 4.7 23.9 1.0 CD2 A:LEU47 4.8 24.6 1.0 CB A:PRO46 4.8 23.8 1.0 CG A:PRO46 4.8 29.3 1.0 CA A:PRO46 4.8 22.1 1.0 CG2 A:ILE69 4.9 31.4 1.0

Fluorine binding site 9 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of The Crystal Structure of Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F107 b:59.5 occ:1.00 F3 A:TFA107 0.0 59.5 1.0 C2 A:TFA107 1.3 53.9 1.0 F2 A:TFA107 2.2 37.3 1.0 F1 A:TFA107 2.2 46.2 1.0 C1 A:TFA107 2.3 62.9 1.0 OXT A:TFA107 2.8 63.9 1.0 O A:TFA107 3.5 70.3 1.0 OE1 A:GLN91 3.7 38.5 1.0 CG A:MET48 4.0 23.9 1.0 NE2 A:GLN91 4.1 40.1 1.0 CD1 A:ILE69 4.3 30.5 1.0 CD A:GLN91 4.4 47.4 1.0 SD A:MET48 4.5 25.6 1.0 O A:PRO46 4.8 23.0 1.0

Fluorine binding site 10 out of 18 in the The Crystal Structure of Chemically Synthesized Vegf-A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of The Crystal Structure of Chemically Synthesized Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ D:F104 b:47.3 occ:1.00 F1 D:TFA104 0.0 47.3 1.0 C2 D:TFA104 1.3 61.9 1.0 F2 D:TFA104 2.1 71.1 1.0 F3 D:TFA104 2.2 55.5 1.0 C1 D:TFA104 2.3 60.1 1.0 O D:TFA104 2.6 52.5 1.0 OE1 D:GLU66 3.0 42.5 1.0 OXT D:TFA104 3.4 63.7 1.0 CD D:GLU66 3.5 43.8 1.0 OE2 D:GLU66 4.1 44.5 1.0 CG D:GLU66 4.2 40.3 1.0 CB D:GLU66 4.7 29.4 1.0 O D:HOH354 4.7 52.9 1.0

K.Mandal, S.B.Kent. Total Chemical Synthesis of Biologically Active Vascular Endothelial Growth Factor. Angew.Chem.Int.Ed.Engl. V. 50 8029 2011.
ISSN: ISSN 1433-7851
PubMed: 21744452
DOI: 10.1002/ANIE.201103237