Fluorine in PDB 8pg7: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755, PDB code: 8pg7 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) 34.48 / 1.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.302, 67.869, 40.101, 90, 93.53, 90
R / Rfree (%) 12.5 / 14.1

Other elements in 8pg7:

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755 (pdb code 8pg7). 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 2755, PDB code: 8pg7:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8pg7

Go back to Fluorine Binding Sites List in 8pg7
Fluorine binding site 1 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755


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 2755 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:17.1
occ:0.50
F14 A:YV3303 0.0 17.1 0.5
H211 A:YV3303 0.3 15.3 0.5
C21 A:YV3303 1.4 12.8 0.5
C13 A:YV3303 1.4 15.2 0.5
C22 A:YV3303 2.3 11.1 0.5
C12 A:YV3303 2.4 13.1 0.5
C15 A:YV3303 2.4 13.4 0.5
C15 A:YV3303 2.4 15.1 0.5
H183 A:YV3303 2.4 22.6 0.5
H162 A:YV3303 2.5 21.0 0.5
H162 A:YV3303 2.5 19.8 0.5
H221 A:YV3303 2.6 13.3 0.5
HB2 A:HIS240 2.6 11.7 1.0
H121 A:YV3303 2.6 15.7 0.5
O A:HOH463 2.7 12.9 0.7
H183 A:YV3303 2.7 21.6 0.5
C16 A:YV3303 2.9 17.5 0.5
C16 A:YV3303 2.9 16.4 0.5
H181 A:YV3303 3.1 21.6 0.5
H181 A:YV3303 3.1 22.6 0.5
C18 A:YV3303 3.1 18.8 0.5
O A:HOH649 3.2 17.5 0.8
O A:HOH517 3.2 12.2 0.9
C18 A:YV3303 3.3 18.0 0.5
HB3 A:HIS240 3.3 11.7 1.0
CB A:HIS240 3.3 9.7 1.0
HD1 A:HIS201 3.4 18.9 0.5
HE1 A:HIS201 3.6 20.8 1.0
C11 A:YV3303 3.6 11.5 0.5
C13 A:YV3303 3.6 13.7 0.5
C11 A:YV3303 3.7 12.7 0.5
C21 A:YV3303 3.7 14.7 0.5
S17 A:YV3303 3.7 18.7 0.5
S17 A:YV3303 3.8 18.1 0.5
H161 A:YV3303 3.8 21.0 0.5
H161 A:YV3303 3.9 19.8 0.5
CG A:HIS240 3.9 9.9 1.0
ND1 A:HIS201 4.0 15.7 1.0
CE1 A:HIS201 4.1 17.3 1.0
H182 A:YV3303 4.1 22.6 0.5
C12 A:YV3303 4.1 13.3 0.5
C22 A:YV3303 4.2 14.2 0.5
HD2 A:HIS240 4.3 11.2 1.0
H182 A:YV3303 4.3 21.6 0.5
CD2 A:HIS240 4.3 9.4 1.0
HA2 A:GLY209 4.4 20.4 1.0
O A:HIS240 4.4 10.6 1.0
HA3 A:GLY209 4.5 20.4 1.0
O A:HOH709 4.5 25.1 0.7
H211 A:YV3303 4.5 17.6 0.5
O A:HOH465 4.6 9.8 0.9
CA A:HIS240 4.6 9.7 1.0
O20 A:YV3303 4.6 18.1 0.5
O09 A:YV3303 4.6 11.4 0.5
O19 A:YV3303 4.7 17.9 0.5
ND1 A:HIS240 4.7 9.9 1.0
C A:HIS240 4.7 9.7 1.0
O09 A:YV3303 4.7 13.4 0.5
O20 A:YV3303 4.8 19.7 0.5
F14 A:YV3303 4.8 14.5 0.5
C10 A:YV3303 4.8 10.0 0.5
C10 A:YV3303 4.8 10.8 0.5
O19 A:YV3303 4.8 19.2 0.5
CA A:GLY209 4.9 17.0 1.0
HD1 A:HIS240 5.0 11.9 0.8
HG2 A:GLU202 5.0 13.8 1.0
C07 A:YV3303 5.0 12.3 0.5

Fluorine binding site 2 out of 2 in 8pg7

Go back to Fluorine Binding Sites List in 8pg7
Fluorine binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755


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 2755 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:14.5
occ:0.51
F14 A:YV3303 0.0 14.5 0.5
H211 A:YV3303 0.2 17.6 0.5
C21 A:YV3303 1.3 14.7 0.5
C13 A:YV3303 1.4 13.7 0.5
C22 A:YV3303 2.3 14.2 0.5
C15 A:YV3303 2.4 15.1 0.5
C15 A:YV3303 2.4 13.4 0.5
C12 A:YV3303 2.4 13.3 0.5
H161 A:YV3303 2.5 19.8 0.5
H161 A:YV3303 2.5 21.0 0.5
H221 A:YV3303 2.5 17.0 0.5
H121 A:YV3303 2.6 15.9 0.5
C16 A:YV3303 2.8 16.4 0.5
HE1 A:TYR67 2.8 13.7 1.0
C16 A:YV3303 2.9 17.5 0.5
O20 A:YV3303 3.2 18.1 0.5
HA2 A:GLY209 3.3 20.4 1.0
O20 A:YV3303 3.3 19.7 0.5
C11 A:YV3303 3.5 12.7 0.5
C13 A:YV3303 3.6 15.2 0.5
C21 A:YV3303 3.6 12.8 0.5
C11 A:YV3303 3.6 11.5 0.5
CE1 A:TYR67 3.6 11.4 1.0
S17 A:YV3303 3.7 18.1 0.5
S17 A:YV3303 3.8 18.7 0.5
H162 A:YV3303 3.8 19.8 0.5
H162 A:YV3303 3.8 21.0 0.5
HD1 A:TYR67 4.0 14.5 1.0
C12 A:YV3303 4.0 13.1 0.5
C22 A:YV3303 4.1 11.1 0.5
CA A:GLY209 4.2 17.0 1.0
CD1 A:TYR67 4.3 12.1 1.0
H241 A:YV3303 4.3 13.7 0.5
H241 A:YV3303 4.4 14.9 0.5
O A:HOH451 4.4 28.5 0.8
O A:HOH632 4.5 18.5 0.6
H211 A:YV3303 4.5 15.3 0.5
O A:HOH709 4.6 25.1 0.7
CZ A:TYR67 4.6 11.4 1.0
O19 A:YV3303 4.6 19.2 0.5
H181 A:YV3303 4.6 22.6 0.5
OH A:TYR67 4.6 13.2 1.0
C A:GLY209 4.7 17.0 1.0
H A:GLY209 4.7 21.4 1.0
HA3 A:GLY209 4.7 20.4 1.0
F14 A:YV3303 4.8 17.1 0.5
C10 A:YV3303 4.8 10.8 0.5
C18 A:YV3303 4.8 18.8 0.5
C10 A:YV3303 4.9 10.0 0.5
O19 A:YV3303 4.9 17.9 0.5
H181 A:YV3303 4.9 21.6 0.5
C18 A:YV3303 5.0 18.0 0.5

Reference:

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2755 To Be Published.
Page generated: Fri Aug 2 22:03:48 2024

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