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Fluorine in PDB 5nai: Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1)

Protein crystallography data

The structure of Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1), PDB code: 5nai was solved by G.-B.Li, J.Brem, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 3.89 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.553, 67.555, 40.093, 90.00, 92.66, 90.00
R / Rfree (%) 13.1 / 14.1

Other elements in 5nai:

The structure of Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1) (pdb code 5nai). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1), PDB code: 5nai:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5nai

Go back to Fluorine Binding Sites List in 5nai
Fluorine binding site 1 out of 2 in the Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F306

b:29.0
occ:1.00
ZN A:ZN301 1.7 13.5 0.6
ZN A:ZN302 2.2 30.0 0.5
OD1 A:CYS198 2.2 46.5 0.5
OD1 A:ASP118 2.8 19.6 1.0
OD2 A:ASP118 2.9 17.2 1.0
O A:HOH573 2.9 28.8 0.5
NE2 A:HIS114 3.1 12.7 0.6
O A:HOH573 3.1 21.4 0.5
O A:HOH553 3.1 19.9 0.5
NE2 A:HIS179 3.2 17.0 1.0
O A:HOH640 3.2 42.8 1.0
CG A:ASP118 3.2 14.6 1.0
ND1 A:HIS116 3.2 15.7 1.0
CE1 A:HIS114 3.4 20.6 0.4
CE1 A:HIS114 3.6 13.3 0.6
SG A:CYS198 3.6 43.2 0.5
CB A:HIS116 3.7 14.2 1.0
CE1 A:HIS179 3.7 18.9 1.0
O A:HOH637 3.7 42.3 1.0
SG A:CYS198 3.8 17.9 0.5
CG A:HIS116 3.9 14.8 1.0
NE2 A:HIS114 4.0 12.1 0.4
F A:F307 4.1 45.8 0.5
OD2 A:CYS198 4.2 46.2 0.5
CD2 A:HIS179 4.2 16.2 1.0
NE2 A:HIS240 4.3 15.6 1.0
CE1 A:HIS116 4.3 17.3 1.0
CD2 A:HIS114 4.3 13.1 0.6
CB A:CYS198 4.4 41.5 0.5
CB A:CYS198 4.5 17.0 0.5
ND1 A:HIS114 4.6 20.5 0.4
CB A:ASP118 4.7 13.9 1.0
ND1 A:HIS114 4.9 12.9 0.6
NE A:ARG119 4.9 13.7 1.0
ND1 A:HIS179 4.9 18.9 1.0
O A:HOH604 4.9 32.8 1.0

Fluorine binding site 2 out of 2 in 5nai

Go back to Fluorine Binding Sites List in 5nai
Fluorine binding site 2 out of 2 in the Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F307

b:45.8
occ:0.50
CE1 A:HIS114 1.8 13.3 0.6
NE2 A:HIS114 1.8 12.1 0.4
OD2 A:CYS198 1.9 46.2 0.5
SG A:CYS198 2.1 17.9 0.5
CB A:CYS198 2.4 41.5 0.5
ND1 A:HIS114 2.5 12.9 0.6
CB A:CYS198 2.6 17.0 0.5
O A:HOH454 2.7 17.1 1.0
SG A:CYS198 2.7 43.2 0.5
CD2 A:HIS114 2.8 13.2 0.4
OD1 A:CYS198 2.8 46.5 0.5
CE1 A:HIS114 2.9 20.6 0.4
NE2 A:HIS114 3.0 12.7 0.6
NE A:ARG119 3.0 13.7 1.0
N A:CYS198 3.1 21.8 0.5
N A:CYS198 3.1 11.0 0.5
CA A:CYS198 3.3 11.5 0.5
CA A:CYS198 3.3 40.0 0.5
CD A:ARG119 3.4 14.3 1.0
CZ A:ARG119 3.7 15.3 1.0
CG A:ARG119 3.7 12.6 1.0
CG A:HIS114 3.8 13.5 0.6
CG A:HIS114 3.9 13.0 0.4
ND1 A:HIS114 3.9 20.5 0.4
CD2 A:HIS114 4.0 13.1 0.6
ZN A:ZN302 4.0 30.0 0.5
ZN A:ZN301 4.0 13.5 0.6
F A:F306 4.1 29.0 1.0
NH2 A:ARG119 4.1 19.8 1.0
C A:GLY197 4.2 13.2 1.0
OD2 A:ASP118 4.2 17.2 1.0
CD2 A:HIS179 4.3 16.2 1.0
NH1 A:ARG119 4.5 18.1 1.0
C A:CYS198 4.5 11.6 0.5
NE2 A:HIS179 4.5 17.0 1.0
C A:CYS198 4.6 17.6 0.5
OG1 A:THR113 4.6 11.9 1.0
CA A:GLY197 4.6 16.0 1.0
CG A:ASP118 4.9 14.6 1.0
O A:HOH435 4.9 16.8 1.0
O A:HOH573 5.0 21.4 0.5
CB A:HIS114 5.0 12.1 0.6
OD1 A:ASP118 5.0 19.6 1.0

Reference:

G.B.Li, J.Brem, R.Lesniak, M.I.Abboud, C.T.Lohans, I.J.Clifton, S.Y.Yang, J.C.Jimenez-Castellanos, M.B.Avison, J.Spencer, M.A.Mcdonough, C.J.Schofield. Crystallographic Analyses of Isoquinoline Complexes Reveal A New Mode of Metallo-Beta-Lactamase Inhibition. Chem. Commun. (Camb.) V. 53 5806 2017.
ISSN: ESSN 1364-548X
PubMed: 28470248
DOI: 10.1039/C7CC02394D
Page generated: Sun Dec 13 12:28:36 2020

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