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Fluorine in PDB 8b1z: Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56

Protein crystallography data

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56, PDB code: 8b1z was solved by F.Vascon, L.Lazzarato, M.Bersani, E.Gianquinto, J.D.Docquier, F.Spyrakis, D.Tondi, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.19 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.61, 73.964, 77.115, 90, 90, 90
R / Rfree (%) 17.3 / 20.9

Other elements in 8b1z:

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 (pdb code 8b1z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56, PDB code: 8b1z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8b1z

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Fluorine binding site 1 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:30.7
occ:0.72
 F1 A:ORL304 0.0 30.7 0.7
C14 A:ORL304 1.3 27.6 0.7
F2 A:ORL304 2.1 33.5 0.7
F3 A:ORL304 2.1 31.6 0.7
C13 A:ORL304 2.3 21.0 0.7
C15 A:ORL304 2.8 21.6 0.7
NE2 A:GLN123 3.1 21.8 0.5
C12 A:ORL304 3.5 20.2 0.7
CD2 A:LEU65 3.9 35.2 1.0
CD A:GLN123 4.1 21.7 0.5
C16 A:ORL304 4.2 18.5 0.7
OE1 A:GLN123 4.5 25.3 0.5
CG A:GLN123 4.5 20.3 0.5
CB A:GLN123 4.6 18.3 0.5
C11 A:ORL304 4.7 19.7 0.7
CZ3 A:TRP93 4.8 19.4 1.0
CB A:GLN123 4.9 19.0 0.5
C10 A:ORL304 4.9 17.2 0.7
C12 A:1PE306 5.0 47.8 1.0

Fluorine binding site 2 out of 6 in 8b1z

Go back to Fluorine Binding Sites List in 8b1z
Fluorine binding site 2 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:33.5
occ:0.72
 F2 A:ORL304 0.0 33.5 0.7
C14 A:ORL304 1.3 27.6 0.7
F1 A:ORL304 2.1 30.7 0.7
F3 A:ORL304 2.1 31.6 0.7
C13 A:ORL304 2.3 21.0 0.7
C12 A:ORL304 2.7 20.2 0.7
C15 A:ORL304 3.6 21.6 0.7
CG A:MET67 3.7 53.4 1.0
CD2 A:LEU65 3.7 35.2 1.0
SD A:MET67 3.8 65.5 1.0
CE A:MET67 3.9 71.0 1.0
C11 A:ORL304 4.1 19.7 0.7
C12 A:1PE306 4.2 47.8 1.0
OH2 A:1PE306 4.3 51.8 1.0
C16 A:ORL304 4.7 18.5 0.7
CG A:LEU65 4.8 34.5 1.0
CZ3 A:TRP93 4.8 19.4 1.0
C10 A:ORL304 4.9 17.2 0.7

Fluorine binding site 3 out of 6 in 8b1z

Go back to Fluorine Binding Sites List in 8b1z
Fluorine binding site 3 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:31.6
occ:0.72
 F3 A:ORL304 0.0 31.6 0.7
C14 A:ORL304 1.3 27.6 0.7
F1 A:ORL304 2.1 30.7 0.7
F2 A:ORL304 2.1 33.5 0.7
C13 A:ORL304 2.3 21.0 0.7
C15 A:ORL304 3.1 21.6 0.7
C12 A:ORL304 3.2 20.2 0.7
C16 A:ORL304 4.4 18.5 0.7
C11 A:ORL304 4.5 19.7 0.7
CE A:MET67 4.8 71.0 1.0
OH2 A:1PE306 4.9 51.8 1.0
NE2 A:GLN123 4.9 21.8 0.5
C10 A:ORL304 4.9 17.2 0.7

Fluorine binding site 4 out of 6 in 8b1z

Go back to Fluorine Binding Sites List in 8b1z
Fluorine binding site 4 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:35.7
occ:0.82
 F1 B:ORL303 0.0 35.7 0.8
C14 B:ORL303 1.3 30.2 0.8
F3 B:ORL303 2.1 36.0 0.8
F2 B:ORL303 2.1 33.1 0.8
C13 B:ORL303 2.3 23.3 0.8
C12 B:ORL303 2.7 23.6 0.8
C15 B:ORL303 3.6 21.5 0.8
CE B:MET67 3.7 58.4 1.0
CG B:MET67 3.7 50.0 1.0
SD B:MET67 3.8 64.0 1.0
C11 B:ORL303 4.1 20.4 0.8
CD2 B:LEU65 4.3 28.9 1.0
C16 B:ORL303 4.7 18.8 0.8
CB B:MET67 4.8 45.2 1.0
C10 B:ORL303 4.9 18.7 0.8

Fluorine binding site 5 out of 6 in 8b1z

Go back to Fluorine Binding Sites List in 8b1z
Fluorine binding site 5 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:33.1
occ:0.82
 F2 B:ORL303 0.0 33.1 0.8
C14 B:ORL303 1.3 30.2 0.8
F3 B:ORL303 2.1 36.0 0.8
F1 B:ORL303 2.1 35.7 0.8
C13 B:ORL303 2.3 23.3 0.8
C15 B:ORL303 2.9 21.5 0.8
C12 B:ORL303 3.4 23.6 0.8
C16 B:ORL303 4.2 18.8 0.8
OE1 B:GLN123 4.3 19.5 0.6
O B:HOH421 4.3 34.6 1.0
C11 B:ORL303 4.6 20.4 0.8
C10 B:ORL303 4.9 18.7 0.8

Fluorine binding site 6 out of 6 in 8b1z

Go back to Fluorine Binding Sites List in 8b1z
Fluorine binding site 6 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:36.0
occ:0.82
 F3 B:ORL303 0.0 36.0 0.8
C14 B:ORL303 1.3 30.2 0.8
F2 B:ORL303 2.1 33.1 0.8
F1 B:ORL303 2.1 35.7 0.8
C13 B:ORL303 2.3 23.3 0.8
C15 B:ORL303 3.0 21.5 0.8
OE1 B:GLN123 3.2 19.5 0.6
CD2 B:LEU65 3.3 28.9 1.0
C12 B:ORL303 3.3 23.6 0.8
CD B:GLN123 4.0 18.6 0.6
C16 B:ORL303 4.3 18.8 0.8
NE2 B:GLN123 4.5 20.1 0.6
CG B:GLN123 4.5 20.0 0.4
CZ3 B:TRP93 4.5 18.5 1.0
C11 B:ORL303 4.5 20.4 0.8
O B:HOH421 4.6 34.6 1.0
CB B:GLN123 4.7 18.9 0.4
CG B:LEU65 4.7 26.4 1.0
CE3 B:TRP93 4.7 16.9 1.0
C10 B:ORL303 4.9 18.7 0.8
CB B:GLN123 5.0 17.9 0.6

Reference:

F.Vascon, L.Lazzarato, M.Bersani, E.Gianquinto, J.D.Docquier, F.Spyrakis, D.Tondi, L.Cendron. Structural Characterization of Triazole-Based Inhibitors of Metallo-Beta-Lactamases To Be Published.
Page generated: Wed Jul 16 02:46:52 2025

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