Zinc in PDB 5n55: Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2)

The structure of Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2), PDB code: 5n55 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)	50.68 / 1.99
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.219, 155.191, 267.733, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 25.3

The structure of Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2) (pdb code 5n55). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2), PDB code: 5n55:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:28.5 occ:1.00 O A:HOH616 1.8 24.8 1.0 ND1 A:HIS116 2.0 29.4 1.0 NE2 A:HIS179 2.1 22.5 1.0 NE2 A:HIS114 2.1 21.3 1.0 CD2 A:HIS179 2.9 20.4 1.0 CG A:HIS116 3.0 22.9 1.0 CE1 A:HIS116 3.0 25.2 1.0 CD2 A:HIS114 3.1 20.1 1.0 CE1 A:HIS114 3.1 22.8 1.0 CE1 A:HIS179 3.1 23.6 1.0 CB A:HIS116 3.3 22.5 1.0 OD2 A:00C198 3.9 37.1 1.0 OD1 A:ASP118 3.9 26.9 1.0 C07 A:8NN502 4.0 25.8 1.0 NE2 A:HIS116 4.1 26.1 1.0 CD2 A:HIS116 4.1 26.3 1.0 CG A:HIS179 4.1 26.5 1.0 ND1 A:HIS179 4.2 25.0 1.0 ND1 A:HIS114 4.2 24.1 1.0 N08 A:8NN502 4.2 29.4 1.0 CG A:HIS114 4.2 19.3 1.0 C05 A:8NN502 4.2 20.4 1.0 OD1 A:00C198 4.3 44.5 1.0 OD2 A:ASP118 4.3 28.1 1.0 CL1 A:8NN502 4.3 33.7 1.0 CG A:ASP118 4.5 32.2 1.0 SG A:00C198 4.5 35.1 1.0 C09 A:8NN502 4.6 27.7 1.0 C06 A:8NN502 4.6 37.2 1.0 C04 A:8NN502 4.7 20.9 1.0 CA A:HIS116 4.7 21.2 1.0 CB A:00C198 4.8 33.1 1.0 C10 A:8NN502 4.8 25.9 1.0 N A:HIS116 5.0 19.5 1.0

Zinc binding site 2 out of 3 in the Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:21.1 occ:1.00 O B:HOH621 1.8 21.5 1.0 ND1 B:HIS116 2.0 23.9 1.0 NE2 B:HIS179 2.0 32.5 1.0 NE2 B:HIS114 2.1 25.8 1.0 CD2 B:HIS179 2.8 22.8 1.0 CE1 B:HIS116 2.9 24.2 1.0 CG B:HIS116 3.0 23.7 1.0 CE1 B:HIS114 3.0 21.1 1.0 CD2 B:HIS114 3.1 23.3 1.0 CE1 B:HIS179 3.2 24.1 1.0 CB B:HIS116 3.4 22.9 1.0 OD1 B:00C198 3.9 36.9 1.0 C07 B:8NN502 3.9 37.8 1.0 OD1 B:ASP118 4.0 23.4 1.0 NE2 B:HIS116 4.0 27.7 1.0 CG B:HIS179 4.1 25.1 1.0 CD2 B:HIS116 4.1 25.1 1.0 CL1 B:8NN502 4.1 38.8 1.0 ND1 B:HIS114 4.1 26.3 1.0 O3 B:00C198 4.2 37.6 1.0 N08 B:8NN502 4.2 37.4 1.0 ND1 B:HIS179 4.2 23.7 1.0 C05 B:8NN502 4.2 24.0 1.0 CG B:HIS114 4.2 21.1 1.0 SG B:00C198 4.4 33.3 1.0 CB B:00C198 4.5 26.3 1.0 C06 B:8NN502 4.6 24.3 1.0 OD2 B:ASP118 4.6 23.2 1.0 C09 B:8NN502 4.7 28.2 1.0 CG B:ASP118 4.7 28.1 1.0 CA B:HIS116 4.8 23.1 1.0 C04 B:8NN502 4.8 27.0 1.0 O B:HOH639 4.9 19.3 1.0

Zinc binding site 3 out of 3 in the Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mono-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-L-Tryptophan (Compound 2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:30.0 occ:1.00 ND1 C:HIS116 1.9 30.9 1.0 NE2 C:HIS179 2.0 28.8 1.0 NE2 C:HIS114 2.1 30.9 1.0 O C:HOH605 2.2 41.3 1.0 CE1 C:HIS116 2.9 32.0 1.0 CE1 C:HIS114 2.9 26.2 1.0 CG C:HIS116 2.9 31.0 1.0 CD2 C:HIS179 2.9 29.0 1.0 CE1 C:HIS179 3.1 29.5 1.0 CD2 C:HIS114 3.2 26.9 1.0 CB C:HIS116 3.3 30.2 1.0 OD2 C:00C198 3.7 38.9 1.0 NE2 C:HIS116 4.0 32.7 1.0 OD1 C:ASP118 4.0 36.9 1.0 C07 C:8NN502 4.0 42.7 1.0 CD2 C:HIS116 4.0 32.7 1.0 ND1 C:HIS114 4.1 25.1 1.0 N08 C:8NN502 4.1 37.6 1.0 O3 C:00C198 4.1 36.4 1.0 CG C:HIS179 4.1 30.0 1.0 ND1 C:HIS179 4.2 30.2 1.0 CG C:HIS114 4.2 31.5 1.0 SG C:00C198 4.3 37.3 1.0 C05 C:8NN502 4.3 38.3 1.0 OD2 C:ASP118 4.4 29.0 1.0 CL1 C:8NN502 4.4 51.5 1.0 C09 C:8NN502 4.5 31.2 1.0 CB C:00C198 4.6 39.4 1.0 CG C:ASP118 4.6 29.3 1.0 CA C:HIS116 4.7 36.9 1.0 C04 C:8NN502 4.7 29.5 1.0 C10 C:8NN502 4.8 29.5 1.0 C06 C:8NN502 4.8 34.8 1.0 O C:HOH627 4.9 22.5 1.0 N C:HIS116 5.0 29.8 1.0

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