Fluorine in PDB 8b1w: Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35

Protein crystallography data

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35, PDB code: 8b1w 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) 36.88 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.19, 73.699, 77.28, 90, 90, 90
R / Rfree (%) 19.2 / 22.2

Other elements in 8b1w:

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Bromine (Br) 2 atoms
Calcium (Ca) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35 (pdb code 8b1w). 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 CP35, PDB code: 8b1w:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8b1w

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Fluorine binding site 1 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35


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 CP35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F305

b:35.9
occ:0.80
 F1 A:OQU305 0.0 35.9 0.8
C1 A:OQU305 1.3 32.4 0.8
F2 A:OQU305 2.1 37.6 0.8
F3 A:OQU305 2.1 31.8 0.8
C2 A:OQU305 2.3 30.3 0.8
N3 A:OQU305 2.9 29.9 0.8
N4 A:OQU305 3.0 34.8 0.8
CG1 A:VAL73 3.3 30.6 1.0
N1 A:OQU305 3.4 27.9 0.8
ND1 A:HIS250 3.9 22.2 1.0
C4 A:OQU305 3.9 34.6 0.8
CG A:HIS250 3.9 22.2 1.0
CB A:HIS250 4.0 21.0 1.0
C3 A:OQU305 4.1 27.2 0.8
N2 A:OQU305 4.4 27.5 0.8
CE1 A:HIS250 4.5 20.2 1.0
CD2 A:HIS250 4.6 20.3 1.0
C6 A:OQU305 4.6 34.4 0.8
CB A:VAL73 4.7 36.2 1.0
C5 A:OQU305 4.8 33.0 0.8
O A:ALA74 4.9 20.5 1.0
NE2 A:HIS250 4.9 20.9 1.0

Fluorine binding site 2 out of 6 in 8b1w

Go back to Fluorine Binding Sites List in 8b1w
Fluorine binding site 2 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35


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 CP35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F305

b:37.6
occ:0.80
 F2 A:OQU305 0.0 37.6 0.8
C1 A:OQU305 1.3 32.4 0.8
F1 A:OQU305 2.1 35.9 0.8
F3 A:OQU305 2.1 31.8 0.8
C2 A:OQU305 2.3 30.3 0.8
N3 A:OQU305 3.0 29.9 0.8
N4 A:OQU305 3.3 34.8 0.8
N1 A:OQU305 3.3 27.9 0.8
C3 A:OQU305 4.2 27.2 0.8
N2 A:OQU305 4.3 27.5 0.8
C4 A:OQU305 4.5 34.6 0.8
CA A:GLY219 4.8 24.3 1.0
CG1 A:VAL73 4.9 30.6 1.0

Fluorine binding site 3 out of 6 in 8b1w

Go back to Fluorine Binding Sites List in 8b1w
Fluorine binding site 3 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35


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 CP35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F305

b:31.8
occ:0.80
 F3 A:OQU305 0.0 31.8 0.8
C1 A:OQU305 1.3 32.4 0.8
F1 A:OQU305 2.1 35.9 0.8
F2 A:OQU305 2.1 37.6 0.8
C2 A:OQU305 2.3 30.3 0.8
N1 A:OQU305 2.7 27.9 0.8
N3 A:OQU305 3.6 29.9 0.8
CB A:HIS250 4.0 21.0 1.0
N2 A:OQU305 4.1 27.5 0.8
N4 A:OQU305 4.4 34.8 0.8
O A:HIS250 4.4 21.6 1.0
C3 A:OQU305 4.4 27.2 0.8
CG A:HIS250 4.6 22.2 1.0

Fluorine binding site 4 out of 6 in 8b1w

Go back to Fluorine Binding Sites List in 8b1w
Fluorine binding site 4 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35


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 CP35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:34.6
occ:0.80
 F1 B:OQU305 0.0 34.6 0.8
C1 B:OQU305 1.3 33.3 0.8
F3 B:OQU305 2.1 34.3 0.8
F2 B:OQU305 2.1 33.5 0.8
C2 B:OQU305 2.3 31.2 0.8
N3 B:OQU305 3.0 28.0 0.8
N4 B:OQU305 3.2 29.1 0.8
N1 B:OQU305 3.4 29.9 0.8
C3 B:OQU305 4.2 29.5 0.8
N2 B:OQU305 4.4 27.7 0.8
C4 B:OQU305 4.4 32.6 0.8
C6 B:OQU305 4.8 38.5 0.8
CG1 B:VAL73 4.8 26.7 1.0
CA B:GLY219 4.9 27.1 1.0

Fluorine binding site 5 out of 6 in 8b1w

Go back to Fluorine Binding Sites List in 8b1w
Fluorine binding site 5 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35


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 CP35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:33.5
occ:0.80
 F2 B:OQU305 0.0 33.5 0.8
C1 B:OQU305 1.3 33.3 0.8
F1 B:OQU305 2.1 34.6 0.8
F3 B:OQU305 2.2 34.3 0.8
C2 B:OQU305 2.3 31.2 0.8
N1 B:OQU305 2.8 29.9 0.8
N3 B:OQU305 3.6 28.0 0.8
CB B:HIS250 4.0 18.3 1.0
N2 B:OQU305 4.1 27.7 0.8
O B:HIS250 4.2 22.6 1.0
N4 B:OQU305 4.3 29.1 0.8
C3 B:OQU305 4.5 29.5 0.8
CG B:HIS250 4.6 16.8 1.0

Fluorine binding site 6 out of 6 in 8b1w

Go back to Fluorine Binding Sites List in 8b1w
Fluorine binding site 6 out of 6 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35


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 CP35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:34.3
occ:0.80
 F3 B:OQU305 0.0 34.3 0.8
C1 B:OQU305 1.3 33.3 0.8
F1 B:OQU305 2.1 34.6 0.8
F2 B:OQU305 2.2 33.5 0.8
C2 B:OQU305 2.3 31.2 0.8
N3 B:OQU305 2.9 28.0 0.8
N4 B:OQU305 2.9 29.1 0.8
CG1 B:VAL73 3.4 26.7 1.0
N1 B:OQU305 3.4 29.9 0.8
ND1 B:HIS250 3.6 19.6 1.0
CG B:HIS250 3.7 16.8 1.0
CB B:HIS250 3.8 18.3 1.0
C4 B:OQU305 4.0 32.6 0.8
C3 B:OQU305 4.1 29.5 0.8
CE1 B:HIS250 4.4 17.7 1.0
N2 B:OQU305 4.4 27.7 0.8
CD2 B:HIS250 4.5 17.5 1.0
C6 B:OQU305 4.6 38.5 0.8
O B:ALA74 4.7 17.3 1.0
CB B:VAL73 4.7 24.9 1.0
C5 B:OQU305 4.7 36.5 0.8
NE2 B:HIS250 4.8 17.3 1.0
O B:HOH469 4.9 35.9 1.0
CA B:HIS250 4.9 19.7 1.0
O B:HIS250 5.0 22.6 1.0

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: Fri Aug 2 16:36:38 2024

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