Fluorine in PDB 8pwm: Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B

The structure of Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B, PDB code: 8pwm was solved by N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.81 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	65.849, 65.849, 264.213, 90, 90, 120
R / Rfree (%)	19.6 / 25.2

The binding sites of Fluorine atom in the Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B (pdb code 8pwm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B, PDB code: 8pwm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B


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 Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:85.5 occ:1.00 F28 A:HXI502 0.0 85.5 1.0 C27 A:HXI502 1.3 92.5 1.0 F29 A:HXI502 2.2 86.3 1.0 F30 A:HXI502 2.2 77.1 1.0 C12 A:HXI502 2.4 79.9 1.0 C11 A:HXI502 2.8 73.8 1.0 O13 A:HXI502 2.8 76.3 1.0 O A:ALA331 3.1 78.9 1.0 NE2 A:HIS333 3.4 79.9 1.0 CD1 A:LEU430 3.5 100.5 1.0 CD1 A:LEU255 3.6 68.6 1.0 C31 A:HXI502 3.7 94.2 1.0 CD2 A:HIS333 3.8 84.3 1.0 F32 A:HXI502 4.1 81.2 1.0 C10 A:HXI502 4.1 98.9 1.0 F34 A:HXI502 4.1 80.8 1.0 CE1 A:HIS333 4.2 75.6 1.0 C A:ALA331 4.2 80.5 1.0 CB A:ALA331 4.2 77.3 1.0 CG A:HIS333 4.7 76.6 1.0 F33 A:HXI502 4.7 95.3 1.0 ND1 A:HIS333 4.9 77.5 1.0 CA A:ALA331 4.9 81.0 1.0 CG A:LEU430 5.0 94.1 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B


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 Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:86.3 occ:1.00 F29 A:HXI502 0.0 86.3 1.0 C27 A:HXI502 1.3 92.5 1.0 F30 A:HXI502 2.2 77.1 1.0 F28 A:HXI502 2.2 85.5 1.0 C12 A:HXI502 2.4 79.9 1.0 F32 A:HXI502 2.5 81.2 1.0 O13 A:HXI502 2.7 76.3 1.0 C31 A:HXI502 2.9 94.2 1.0 CD1 A:LEU430 3.1 100.5 1.0 F34 A:HXI502 3.5 80.8 1.0 CD1 A:LEU255 3.6 68.6 1.0 CD2 A:LEU440 3.6 67.1 1.0 C11 A:HXI502 3.7 73.8 1.0 F33 A:HXI502 4.1 95.3 1.0 CD1 A:TYR427 4.2 74.3 1.0 CE1 A:TYR427 4.4 75.4 1.0 CG A:LEU430 4.5 94.1 1.0 NE2 A:HIS333 4.6 79.9 1.0 O A:ALA331 4.6 78.9 1.0 CB A:LEU430 4.9 78.6 1.0 C10 A:HXI502 4.9 98.9 1.0 CG A:LEU440 4.9 69.5 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B


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 Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:77.1 occ:1.00 F30 A:HXI502 0.0 77.1 1.0 C27 A:HXI502 1.3 92.5 1.0 F29 A:HXI502 2.2 86.3 1.0 F28 A:HXI502 2.2 85.5 1.0 C12 A:HXI502 2.4 79.9 1.0 F34 A:HXI502 2.5 80.8 1.0 C31 A:HXI502 2.8 94.2 1.0 C11 A:HXI502 2.9 73.8 1.0 F32 A:HXI502 3.1 81.2 1.0 CD1 A:LEU255 3.2 68.6 1.0 O13 A:HXI502 3.6 76.3 1.0 CA A:ALA259 3.9 67.0 1.0 N A:ALA259 3.9 68.6 1.0 F33 A:HXI502 4.0 95.3 1.0 CB A:ALA259 4.1 64.5 1.0 CD2 A:LEU440 4.2 67.1 1.0 C10 A:HXI502 4.3 98.9 1.0 C A:LEU258 4.4 70.3 1.0 O A:LEU255 4.5 75.5 1.0 CG A:LEU255 4.6 81.0 1.0 O A:ALA331 4.6 78.9 1.0 O A:LEU258 4.6 74.4 1.0 CB A:LEU258 4.7 68.3 1.0 CD1 A:LEU430 4.8 100.5 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B


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 Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:81.2 occ:1.00 F32 A:HXI502 0.0 81.2 1.0 C31 A:HXI502 1.3 94.2 1.0 F34 A:HXI502 2.2 80.8 1.0 F33 A:HXI502 2.2 95.3 1.0 C12 A:HXI502 2.4 79.9 1.0 F29 A:HXI502 2.5 86.3 1.0 C27 A:HXI502 2.8 92.5 1.0 O13 A:HXI502 2.8 76.3 1.0 F30 A:HXI502 3.1 77.1 1.0 CE1 A:TYR427 3.4 75.4 1.0 CD1 A:TYR427 3.5 74.3 1.0 CG1 A:VAL444 3.6 61.0 1.0 C11 A:HXI502 3.7 73.8 1.0 CD2 A:PHE448 3.9 75.4 1.0 CE2 A:PHE448 4.0 73.6 1.0 F28 A:HXI502 4.1 85.5 1.0 CD2 A:LEU440 4.1 67.1 1.0 C10 A:HXI502 4.5 98.9 1.0 CZ A:TYR427 4.7 69.3 1.0 CG A:TYR427 4.8 62.7 1.0 NE2 A:HIS423 4.8 66.8 1.0 CB A:VAL444 4.8 67.9 1.0 CG2 A:VAL444 4.9 55.2 1.0 CE1 A:HIS423 5.0 76.4 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B


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 Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:95.3 occ:1.00 F33 A:HXI502 0.0 95.3 1.0 C31 A:HXI502 1.3 94.2 1.0 F32 A:HXI502 2.2 81.2 1.0 F34 A:HXI502 2.2 80.8 1.0 C12 A:HXI502 2.4 79.9 1.0 O13 A:HXI502 2.8 76.3 1.0 CE2 A:PHE448 3.0 73.6 1.0 C11 A:HXI502 3.0 73.8 1.0 C10 A:HXI502 3.1 98.9 1.0 CD2 A:PHE448 3.5 75.4 1.0 C9 A:HXI502 3.6 97.8 1.0 NE2 A:HIS423 3.6 66.8 1.0 CG1 A:VAL262 3.6 71.3 1.0 C27 A:HXI502 3.7 92.5 1.0 CG2 A:VAL262 3.8 76.3 1.0 CE1 A:HIS423 3.9 76.4 1.0 CB A:VAL262 4.0 69.5 1.0 CZ A:PHE448 4.0 83.4 1.0 F30 A:HXI502 4.0 77.1 1.0 F29 A:HXI502 4.1 86.3 1.0 C8 A:HXI502 4.3 97.7 1.0 CD1 A:ILE296 4.6 73.8 1.0 CG1 A:VAL444 4.7 61.0 1.0 CD1 A:TYR427 4.7 74.3 1.0 F28 A:HXI502 4.7 85.5 1.0 CD2 A:HIS423 4.8 72.2 1.0 CG A:PHE448 4.9 76.0 1.0 CE1 A:TYR427 4.9 75.4 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B


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 Vdr in Complex with Des-C-Ring and Aromatic-D- Ring Analog 3B within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:80.8 occ:1.00 F34 A:HXI502 0.0 80.8 1.0 C31 A:HXI502 1.3 94.2 1.0 F32 A:HXI502 2.2 81.2 1.0 F33 A:HXI502 2.2 95.3 1.0 C12 A:HXI502 2.4 79.9 1.0 F30 A:HXI502 2.5 77.1 1.0 C11 A:HXI502 2.8 73.8 1.0 C27 A:HXI502 2.9 92.5 1.0 CG2 A:VAL262 3.4 76.3 1.0 F29 A:HXI502 3.5 86.3 1.0 CB A:VAL262 3.5 69.5 1.0 O13 A:HXI502 3.6 76.3 1.0 C10 A:HXI502 3.7 98.9 1.0 CA A:ALA259 3.8 67.0 1.0 CG1 A:VAL262 3.9 71.3 1.0 O A:LEU258 4.1 74.4 1.0 F28 A:HXI502 4.1 85.5 1.0 N A:ALA259 4.4 68.6 1.0 CB A:ALA259 4.4 64.5 1.0 CG1 A:VAL444 4.5 61.0 1.0 C A:LEU258 4.5 70.3 1.0 C9 A:HXI502 4.6 97.8 1.0 O A:ALA259 4.6 64.2 1.0 CE2 A:PHE448 4.6 73.6 1.0 CG2 A:VAL444 4.6 55.2 1.0 C A:ALA259 4.7 71.3 1.0 CD2 A:LEU440 4.9 67.1 1.0 CA A:VAL262 4.9 66.3 1.0

N.Rochel, N.Rochel. N/A N/A.