Fluorine in PDB 8pgk: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3016

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3016, PDB code: 8pgk was solved by K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.14 / 1.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.49, 67.89, 40.3, 90, 93.85, 90
R / Rfree (%)	13.4 / 15.1

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3016 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3016 (pdb code 8pgk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3016, PDB code: 8pgk:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3016


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 Metallo-Beta-Lactamase VIM1 with 3016 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:19.7 occ:0.69 F33 A:YVH303 0.0 19.7 0.7 H251 A:YVH303 0.2 20.7 0.3 C25 A:YVH303 1.2 17.2 0.3 C32 A:YVH303 1.4 18.0 0.7 C34 A:YVH303 2.3 16.3 0.7 C26 A:YVH303 2.3 18.0 0.3 C24 A:YVH303 2.3 16.3 0.3 C26 A:YVH303 2.5 18.4 0.7 H341 A:YVH303 2.5 19.5 0.7 H241 A:YVH303 2.6 19.6 0.3 H272 A:YVH303 2.6 23.7 0.7 H293 A:YVH303 2.6 26.2 0.7 HB2 A:HIS240 2.6 15.1 1.0 H292 A:YVH303 2.6 26.6 0.3 H272 A:YVH303 2.6 24.0 0.3 O A:HOH452 2.7 12.1 0.6 H291 A:YVH303 2.9 26.2 0.7 C27 A:YVH303 2.9 20.0 0.3 C27 A:YVH303 2.9 19.7 0.7 H293 A:YVH303 3.0 26.6 0.3 C29 A:YVH303 3.1 21.8 0.7 C29 A:YVH303 3.2 22.2 0.3 O A:HOH512 3.2 10.6 0.7 HD1 A:HIS201 3.3 21.4 1.0 O A:HOH666 3.3 20.7 0.9 CB A:HIS240 3.4 12.6 1.0 HB3 A:HIS240 3.4 15.1 1.0 HE1 A:HIS201 3.5 22.7 1.0 C23 A:YVH303 3.5 15.7 0.3 C32 A:YVH303 3.6 16.9 0.3 C25 A:YVH303 3.7 17.8 0.7 C23 A:YVH303 3.7 15.5 0.7 S28 A:YVH303 3.7 21.9 0.3 S28 A:YVH303 3.7 21.4 0.7 ND1 A:HIS201 3.9 17.8 1.0 H271 A:YVH303 3.9 24.0 0.3 H271 A:YVH303 3.9 23.7 0.7 CG A:HIS240 3.9 12.1 1.0 CE1 A:HIS201 4.0 18.9 1.0 C34 A:YVH303 4.1 16.5 0.3 H292 A:YVH303 4.1 26.2 0.7 H291 A:YVH303 4.2 26.6 0.3 C24 A:YVH303 4.2 16.8 0.7 HD2 A:HIS240 4.3 14.9 1.0 CD2 A:HIS240 4.3 12.4 1.0 O A:HIS240 4.4 13.1 1.0 HA3 A:GLY209 4.4 24.6 1.0 HA2 A:GLY209 4.4 24.6 1.0 O21 A:YVH303 4.5 14.4 0.3 O A:HOH496 4.5 11.1 0.8 H251 A:YVH303 4.6 21.4 0.7 O30 A:YVH303 4.6 21.7 0.7 CA A:HIS240 4.7 12.3 1.0 O21 A:YVH303 4.7 13.7 0.7 O30 A:YVH303 4.7 22.4 0.3 O31 A:YVH303 4.7 22.6 0.7 O A:HOH731 4.7 21.9 0.4 C A:HIS240 4.7 12.4 1.0 F33 A:YVH303 4.8 15.7 0.3 C22 A:YVH303 4.8 14.4 0.3 O31 A:YVH303 4.8 22.8 0.3 ND1 A:HIS240 4.8 12.7 1.0 C22 A:YVH303 4.9 13.3 0.7 CA A:GLY209 4.9 20.5 1.0 HG2 A:GLU202 5.0 16.8 1.0 C19 A:YVH303 5.0 14.1 0.3 O A:HOH501 5.0 10.2 0.5 C19 A:YVH303 5.0 13.1 0.7

Fluorine binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3016


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 Metallo-Beta-Lactamase VIM1 with 3016 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:15.7 occ:0.31 F33 A:YVH303 0.0 15.7 0.3 H251 A:YVH303 0.3 21.4 0.7 C25 A:YVH303 1.3 17.8 0.7 C32 A:YVH303 1.4 16.9 0.3 C26 A:YVH303 2.3 18.4 0.7 C34 A:YVH303 2.3 16.5 0.3 C24 A:YVH303 2.4 16.8 0.7 C26 A:YVH303 2.5 18.0 0.3 H271 A:YVH303 2.5 23.7 0.7 H341 A:YVH303 2.6 19.8 0.3 H271 A:YVH303 2.6 24.0 0.3 H241 A:YVH303 2.7 20.2 0.7 C27 A:YVH303 2.9 19.7 0.7 HE1 A:TYR67 2.9 18.1 1.0 C27 A:YVH303 3.0 20.0 0.3 O A:HOH516 3.2 47.4 1.0 O30 A:YVH303 3.3 21.7 0.7 O30 A:YVH303 3.3 22.4 0.3 HA2 A:GLY209 3.4 24.6 1.0 C23 A:YVH303 3.6 15.5 0.7 C32 A:YVH303 3.7 18.0 0.7 CE1 A:TYR67 3.7 15.1 1.0 C25 A:YVH303 3.7 17.2 0.3 C23 A:YVH303 3.7 15.7 0.3 S28 A:YVH303 3.7 21.4 0.7 S28 A:YVH303 3.8 21.9 0.3 H272 A:YVH303 3.8 23.7 0.7 H272 A:YVH303 3.9 24.0 0.3 HD1 A:TYR67 4.0 17.2 1.0 C34 A:YVH303 4.1 16.3 0.7 C24 A:YVH303 4.2 16.3 0.3 CD1 A:TYR67 4.3 14.4 1.0 H361 A:YVH303 4.3 16.2 0.7 CA A:GLY209 4.4 20.5 1.0 H361 A:YVH303 4.5 17.0 0.3 H251 A:YVH303 4.6 20.7 0.3 CZ A:TYR67 4.6 15.0 1.0 O A:HOH469 4.6 32.8 0.8 O A:HOH731 4.6 21.9 0.4 OH A:TYR67 4.7 15.9 1.0 O31 A:YVH303 4.7 22.6 0.7 H293 A:YVH303 4.7 26.6 0.3 F33 A:YVH303 4.8 19.7 0.7 C A:GLY209 4.8 19.9 1.0 H291 A:YVH303 4.8 26.2 0.7 HA3 A:GLY209 4.8 24.6 1.0 O31 A:YVH303 4.8 22.8 0.3 C22 A:YVH303 4.9 13.3 0.7 C29 A:YVH303 5.0 22.2 0.3 C22 A:YVH303 5.0 14.4 0.3 C29 A:YVH303 5.0 21.8 0.7 H A:GLY209 5.0 26.4 1.0

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3016 To Be Published.