Fluorine in PDB 4glu: Crystal Structure of the Mirror Image Form of Vegf-A

The structure of Crystal Structure of the Mirror Image Form of Vegf-A, PDB code: 4glu was solved by K.Mandal, M.Uppalapati, D.Ault-Riche, J.Kenney, J.Lowitz, S.Sidhu, S.B.H.Kent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.50 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	231.395, 43.986, 73.514, 90.00, 100.30, 90.00
R / Rfree (%)	17.2 / 20.9

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the Mirror Image Form of Vegf-A (pdb code 4glu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 21 binding sites of Fluorine where determined in the Crystal Structure of the Mirror Image Form of Vegf-A, PDB code: 4glu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:81.9 occ:1.00 F1 A:TFA202 0.0 81.9 1.0 C2 A:TFA202 1.3 78.7 1.0 F2 A:TFA202 2.2 80.2 1.0 F3 A:TFA202 2.2 77.6 1.0 C1 A:TFA202 2.3 73.0 1.0 OXT A:TFA202 2.9 68.3 1.0 O A:TFA202 3.2 71.1 1.0

Fluorine binding site 2 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:80.2 occ:1.00 F2 A:TFA202 0.0 80.2 1.0 C2 A:TFA202 1.3 78.7 1.0 F1 A:TFA202 2.2 81.9 1.0 F3 A:TFA202 2.2 77.6 1.0 C1 A:TFA202 2.3 73.0 1.0 OXT A:TFA202 2.8 68.3 1.0 O A:TFA202 3.3 71.1 1.0 CD1 A:DLE90 3.7 36.5 1.0 OE2 A:DGL66 3.9 35.5 1.0 CG A:DLE90 4.9 30.3 1.0 CD2 A:DLE90 5.0 42.8 1.0

Fluorine binding site 3 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:77.6 occ:1.00 F3 A:TFA202 0.0 77.6 1.0 C2 A:TFA202 1.3 78.7 1.0 F2 A:TFA202 2.2 80.2 1.0 F1 A:TFA202 2.2 81.9 1.0 C1 A:TFA202 2.3 73.0 1.0 O A:TFA202 2.6 71.1 1.0 OXT A:TFA202 3.5 68.3 1.0 OD1 A:DSG68 4.8 54.6 1.0

Fluorine binding site 4 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ D:F203 b:61.0 occ:1.00 F1 D:TFA203 0.0 61.0 1.0 C2 D:TFA203 1.3 54.0 1.0 F2 D:TFA203 2.2 48.5 1.0 F3 D:TFA203 2.2 33.7 1.0 C1 D:TFA203 2.3 63.0 1.0 OXT D:TFA203 3.0 70.9 1.0 O D:TFA203 3.1 63.2 1.0 CG A:MED48 4.0 24.7 1.0 SD A:MED48 4.4 24.9 1.0 CD1 A:DIL69 4.5 32.5 1.0 NE2 A:DGN91 4.6 38.7 1.0 O A:DPR46 4.7 16.8 1.0

Fluorine binding site 5 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ D:F203 b:48.5 occ:1.00 F2 D:TFA203 0.0 48.5 1.0 C2 D:TFA203 1.3 54.0 1.0 F1 D:TFA203 2.2 61.0 1.0 F3 D:TFA203 2.2 33.7 1.0 C1 D:TFA203 2.3 63.0 1.0 OXT D:TFA203 2.7 70.9 1.0 O D:TFA203 3.4 63.2 1.0 O A:DPR46 3.6 16.8 1.0 CD A:DGL23 3.8 30.4 1.0 CG A:DGL23 3.9 17.8 1.0 C A:DPR46 4.0 19.8 1.0 SD A:MED48 4.0 24.9 1.0 OE2 A:DGL23 4.0 29.6 1.0 OE1 A:DGL23 4.2 32.5 1.0 CB A:DPR46 4.3 21.3 1.0 CG A:MED48 4.3 24.7 1.0 NH2 D:DAR16 4.4 53.2 1.0 N A:DLE47 4.4 17.1 1.0 C A:DLE47 4.5 20.5 1.0 CA A:DLE47 4.5 19.1 1.0 N A:MED48 4.5 18.7 1.0 CB A:DGL23 4.7 17.7 1.0 CG A:DPR46 4.7 25.2 1.0 CZ D:DAR16 4.8 56.8 1.0 CA A:DPR46 4.8 16.8 1.0 O A:DLE47 4.9 24.0 1.0

Fluorine binding site 6 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ D:F203 b:33.7 occ:1.00 F3 D:TFA203 0.0 33.7 1.0 C2 D:TFA203 1.3 54.0 1.0 F1 D:TFA203 2.2 61.0 1.0 F2 D:TFA203 2.2 48.5 1.0 C1 D:TFA203 2.3 63.0 1.0 O D:TFA203 2.6 63.2 1.0 O A:DPR46 2.7 16.8 1.0 OXT D:TFA203 3.4 70.9 1.0 C A:DPR46 3.6 19.8 1.0 CA A:DLE47 3.8 19.1 1.0 CD1 A:DIL69 3.9 32.5 1.0 N A:DLE47 4.1 17.1 1.0 CE A:MED71 4.1 22.5 1.0 N A:MED48 4.3 18.7 1.0 C A:DLE47 4.3 20.5 1.0 NE2 A:DGN91 4.5 38.7 1.0 CB A:DPR46 4.7 21.3 1.0 CG A:MED48 4.7 24.7 1.0 CG A:DPR46 4.7 25.2 1.0 CD2 A:DLE47 4.8 20.6 1.0 CA A:DPR46 4.8 16.8 1.0 CG2 A:DIL69 4.9 21.7 1.0

Fluorine binding site 7 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ D:F204 b:89.2 occ:1.00 F1 D:TFA204 0.0 89.2 1.0 C2 D:TFA204 1.3 84.7 1.0 F2 D:TFA204 2.2 81.7 1.0 F3 D:TFA204 2.2 88.6 1.0 C1 D:TFA204 2.3 72.6 1.0 O D:GLY52 2.9 26.1 1.0 O D:HOH324 3.0 39.4 1.0 O D:TFA204 3.0 78.0 1.0 OXT D:TFA204 3.1 51.6 1.0 C D:GLY52 3.6 22.2 1.0 N D:GLY52 3.9 23.7 1.0 CA D:GLY52 4.1 21.8 1.0 N D:DCY53 4.5 19.3 1.0 O A:HOH311 4.5 28.5 1.0 CA D:DCY53 4.6 18.0 1.0 O D:HOH332 4.7 39.4 1.0 CB D:DCY53 4.9 22.6 1.0 SG A:DCY44 4.9 23.7 1.0 C D:GLY51 4.9 25.8 1.0 O D:HOH316 4.9 40.0 1.0

Fluorine binding site 8 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ D:F204 b:81.7 occ:1.00 F2 D:TFA204 0.0 81.7 1.0 C2 D:TFA204 1.3 84.7 1.0 F1 D:TFA204 2.2 89.2 1.0 F3 D:TFA204 2.2 88.6 1.0 C1 D:TFA204 2.3 72.6 1.0 O D:TFA204 2.7 78.0 1.0 OXT D:TFA204 3.4 51.6 1.0 O A:DLE25 4.1 28.3 1.0 O A:HOH325 4.2 31.6 1.0 N A:DAS27 4.4 18.2 1.0 CB A:DAS27 4.6 28.6 1.0 O A:HOH311 4.6 28.5 1.0 O D:HOH324 4.7 39.4 1.0 C A:DLE25 4.8 25.9 1.0 CA A:DAS27 4.9 26.2 1.0 O D:GLY52 4.9 26.1 1.0 CB A:DCY44 4.9 21.7 1.0 C A:DVA26 5.0 23.0 1.0

Fluorine binding site 9 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ D:F204 b:88.6 occ:1.00 F3 D:TFA204 0.0 88.6 1.0 C2 D:TFA204 1.3 84.7 1.0 F1 D:TFA204 2.2 89.2 1.0 F2 D:TFA204 2.2 81.7 1.0 C1 D:TFA204 2.3 72.6 1.0 OXT D:TFA204 2.6 51.6 1.0 O D:HOH324 3.2 39.4 1.0 O D:TFA204 3.4 78.0 1.0 O D:GLY52 4.6 26.1 1.0 N D:GLY52 5.0 23.7 1.0

Fluorine binding site 10 out of 21 in the Crystal Structure of the Mirror Image Form of Vegf-A


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 the Mirror Image Form of Vegf-A within 5.0Å range: probe atom residue distance (Å) B Occ D:F205 b:61.7 occ:1.00 F1 D:TFA205 0.0 61.7 1.0 C2 D:TFA205 1.3 64.4 1.0 F3 D:TFA205 2.2 69.9 1.0 F2 D:TFA205 2.2 49.0 1.0 C1 D:TFA205 2.3 66.7 1.0 O D:TFA205 2.9 59.3 1.0 OXT D:TFA205 3.2 70.1 1.0 CD D:DGL66 3.5 43.1 1.0 CG D:DGL66 3.6 40.4 1.0 OE1 D:DGL66 3.7 38.3 1.0 N D:DGL65 3.8 32.4 1.0 C D:DTH64 3.9 33.2 1.0 O D:DPR63 3.9 32.6 1.0 OE2 D:DGL66 4.0 54.5 1.0 CA D:DGL65 4.1 33.0 1.0 O D:DTH64 4.1 35.4 1.0 N D:DGL66 4.2 32.5 1.0 C D:DGL65 4.2 31.4 1.0 C D:DPR63 4.3 29.2 1.0 CA D:DTH64 4.3 32.1 1.0 CB D:DGL66 4.4 36.5 1.0 N D:DTH64 4.5 29.8 1.0 CB D:DPR63 4.6 29.9 1.0 O D:DGL65 4.9 29.5 1.0 CG D:DPR63 4.9 36.4 1.0 CA D:DGL66 4.9 31.4 1.0

K.Mandal, M.Uppalapati, D.Ault-Riche, J.Kenney, J.Lowitz, S.S.Sidhu, S.B.Kent. Chemical Synthesis and X-Ray Structure of A Heterochiral {D-Protein Antagonist Plus Vascular Endothelial Growth Factor} Protein Complex By Racemic Crystallography. Proc.Natl.Acad.Sci.Usa V. 109 14779 2012.
ISSN: ISSN 0027-8424
PubMed: 22927390
DOI: 10.1073/PNAS.1210483109