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Fluorine in PDB 8pg3: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729, PDB code: 8pg3 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) 34.63 / 1.26
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.52, 67.96, 40.34, 90, 93.78, 90
R / Rfree (%) 14.1 / 15.4

Other elements in 8pg3:

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729 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 2729 (pdb code 8pg3). 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 2729, PDB code: 8pg3:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8pg3

Go back to Fluorine Binding Sites List in 8pg3
Fluorine binding site 1 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729


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 2729 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:20.1
occ:0.54
F14 A:YL9303 0.0 20.1 0.5
H211 A:YL9303 0.4 24.1 0.5
C13 A:YL9303 1.4 20.1 0.5
C21 A:YL9303 1.4 20.1 0.5
C22 A:YL9303 2.3 20.1 0.5
C12 A:YL9303 2.4 20.1 0.5
H181 A:YL9303 2.4 24.1 0.5
C15 A:YL9303 2.4 20.1 0.5
C15 A:YL9303 2.4 20.1 0.5
H221 A:YL9303 2.5 24.1 0.5
H121 A:YL9303 2.6 24.1 0.5
O A:HOH460 2.6 13.8 0.5
H162 A:YL9303 2.6 24.1 0.5
HB2 A:HIS240 2.6 15.3 1.0
H182 A:YL9303 2.7 24.1 0.5
H162 A:YL9303 2.7 24.1 0.5
H181 A:YL9303 2.7 24.1 0.5
C18 A:YL9303 2.9 20.1 0.5
C16 A:YL9303 3.0 20.1 0.5
C16 A:YL9303 3.0 20.1 0.5
H182 A:YL9303 3.0 24.1 0.5
O A:HOH666 3.2 23.0 0.8
O A:HOH532 3.2 12.1 0.8
C18 A:YL9303 3.2 20.1 0.5
CB A:HIS240 3.4 12.8 1.0
HB3 A:HIS240 3.4 15.3 1.0
HE1 A:HIS201 3.6 24.0 1.0
C11 A:YL9303 3.6 20.1 0.5
S17 A:YL9303 3.6 20.1 0.5
C11 A:YL9303 3.7 20.1 0.5
C13 A:YL9303 3.7 20.1 0.5
C21 A:YL9303 3.7 20.1 0.5
S17 A:YL9303 3.9 20.1 0.5
H183 A:YL9303 3.9 24.1 0.5
CG A:HIS240 3.9 12.9 1.0
H161 A:YL9303 3.9 24.1 0.5
ND1 A:HIS201 4.0 17.9 1.0
H161 A:YL9303 4.0 24.1 0.5
CE1 A:HIS201 4.1 20.0 1.0
C12 A:YL9303 4.1 20.1 0.5
C22 A:YL9303 4.2 20.1 0.5
H183 A:YL9303 4.3 24.1 0.5
HD2 A:HIS240 4.3 15.0 1.0
CD2 A:HIS240 4.4 12.5 1.0
O A:HIS240 4.4 12.8 1.0
HA2 A:GLY209 4.4 26.7 1.0
HA3 A:GLY209 4.5 26.7 1.0
O A:HOH734 4.5 26.5 0.8
O A:HOH507 4.5 9.8 0.7
O20 A:YL9303 4.6 20.1 0.5
H211 A:YL9303 4.6 24.1 0.5
O08 A:YL9303 4.6 20.1 0.5
O08 A:YL9303 4.7 20.1 0.5
CA A:HIS240 4.7 11.9 1.0
C A:HIS240 4.7 12.4 1.0
O19 A:YL9303 4.8 20.1 0.5
ND1 A:HIS240 4.8 13.5 1.0
F14 A:YL9303 4.8 20.1 0.5
O20 A:YL9303 4.8 20.1 0.5
C10 A:YL9303 4.8 20.1 0.5
C10 A:YL9303 4.9 20.1 0.5
CA A:GLY209 4.9 22.3 1.0
HG2 A:GLU202 4.9 17.0 1.0
O19 A:YL9303 5.0 20.1 0.5
C07 A:YL9303 5.0 20.1 0.5

Fluorine binding site 2 out of 2 in 8pg3

Go back to Fluorine Binding Sites List in 8pg3
Fluorine binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2729


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 2729 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:20.1
occ:0.46
F14 A:YL9303 0.0 20.1 0.5
H211 A:YL9303 0.7 24.1 0.5
C13 A:YL9303 1.4 20.1 0.5
C21 A:YL9303 1.5 20.1 0.5
H161 A:YL9303 2.4 24.1 0.5
C12 A:YL9303 2.4 20.1 0.5
C15 A:YL9303 2.4 20.1 0.5
C15 A:YL9303 2.4 20.1 0.5
C22 A:YL9303 2.5 20.1 0.5
H161 A:YL9303 2.6 24.1 0.5
H121 A:YL9303 2.6 24.1 0.5
H221 A:YL9303 2.8 24.1 0.5
HE1 A:TYR67 2.8 19.0 1.0
C16 A:YL9303 2.8 20.1 0.5
C16 A:YL9303 2.9 20.1 0.5
O20 A:YL9303 3.1 20.1 0.5
O A:HOH620 3.3 24.4 0.4
O A:HOH593 3.3 49.4 1.0
HA2 A:GLY209 3.6 26.7 1.0
CE1 A:TYR67 3.6 15.8 1.0
O20 A:YL9303 3.6 20.1 0.5
C21 A:YL9303 3.6 20.1 0.5
C11 A:YL9303 3.7 20.1 0.5
S17 A:YL9303 3.7 20.1 0.5
C13 A:YL9303 3.7 20.1 0.5
C11 A:YL9303 3.7 20.1 0.5
H162 A:YL9303 3.7 24.1 0.5
H162 A:YL9303 3.9 24.1 0.5
S17 A:YL9303 3.9 20.1 0.5
HD1 A:TYR67 3.9 19.0 1.0
O A:HOH734 4.1 26.5 0.8
C22 A:YL9303 4.1 20.1 0.5
C12 A:YL9303 4.2 20.1 0.5
CD1 A:TYR67 4.2 15.8 1.0
H241 A:YL9303 4.4 24.1 0.5
H241 A:YL9303 4.4 24.1 0.5
CA A:GLY209 4.5 22.3 1.0
H211 A:YL9303 4.5 24.1 0.5
CZ A:TYR67 4.5 15.6 1.0
O A:HOH665 4.6 26.6 0.9
O A:HOH524 4.6 32.7 0.9
OH A:TYR67 4.6 17.3 1.0
H181 A:YL9303 4.6 24.1 0.5
O19 A:YL9303 4.7 20.1 0.5
F14 A:YL9303 4.8 20.1 0.5
C18 A:YL9303 4.9 20.1 0.5
C A:GLY209 4.9 21.9 1.0
O19 A:YL9303 4.9 20.1 0.5
H181 A:YL9303 4.9 24.1 0.5
HA3 A:GLY209 4.9 26.7 1.0
C10 A:YL9303 5.0 20.1 0.5
C10 A:YL9303 5.0 20.1 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 2729 To Be Published.
Page generated: Wed Jul 16 06:32:30 2025

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