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

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

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:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc 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 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)-D-Tryptophan (Compound 1), PDB code: 5nai:
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)-D-Tryptophan (Compound 1)


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)-D-Tryptophan (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.5 occ:0.60 F A:F306 1.7 29.0 1.0 NE2 A:HIS179 2.0 17.0 1.0 NE2 A:HIS114 2.0 12.7 0.6 ND1 A:HIS116 2.0 15.7 1.0 CE1 A:HIS114 2.5 20.6 0.4 CD2 A:HIS179 2.9 16.2 1.0 CE1 A:HIS179 2.9 18.9 1.0 OD1 A:CYS198 3.0 46.5 0.5 CE1 A:HIS114 3.0 13.3 0.6 CE1 A:HIS116 3.0 17.3 1.0 CG A:HIS116 3.0 14.8 1.0 CD2 A:HIS114 3.0 13.1 0.6 NE2 A:HIS114 3.3 12.1 0.4 CB A:HIS116 3.4 14.2 1.0 ND1 A:HIS114 3.4 20.5 0.4 O A:HOH640 3.5 42.8 1.0 ZN A:ZN302 3.6 30.0 0.5 OD1 A:ASP118 3.9 19.6 1.0 O A:HOH573 4.0 21.4 0.5 O A:HOH573 4.0 28.8 0.5 ND1 A:HIS179 4.0 18.9 1.0 F A:F307 4.0 45.8 0.5 CG A:HIS179 4.1 16.4 1.0 ND1 A:HIS114 4.1 12.9 0.6 NE2 A:HIS116 4.1 19.6 1.0 CD2 A:HIS116 4.1 18.7 1.0 CG A:HIS114 4.2 13.5 0.6 SG A:CYS198 4.2 43.2 0.5 CB A:CYS198 4.3 41.5 0.5 CB A:CYS198 4.3 17.0 0.5 OD2 A:ASP118 4.4 17.2 1.0 SG A:CYS198 4.4 17.9 0.5 CD2 A:HIS114 4.5 13.2 0.4 CG A:HIS114 4.5 13.0 0.4 CG A:ASP118 4.6 14.6 1.0 O A:HOH553 4.7 19.9 0.5 CA A:HIS116 4.8 12.5 1.0 O A:HOH637 4.8 42.3 1.0 OD2 A:CYS198 4.8 46.2 0.5

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)-D-Tryptophan (Compound 1)


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)-D-Tryptophan (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:30.0 occ:0.50 OD1 A:CYS198 1.6 46.5 0.5 OD2 A:ASP118 2.0 17.2 1.0 NE2 A:HIS240 2.1 15.6 1.0 F A:F306 2.2 29.0 1.0 O A:HOH573 2.2 21.4 0.5 O A:HOH573 2.4 28.8 0.5 O A:HOH553 2.5 19.9 0.5 SG A:CYS198 2.5 43.2 0.5 SG A:CYS198 2.7 17.9 0.5 CE1 A:HIS240 3.0 14.5 1.0 CG A:ASP118 3.1 14.6 1.0 OD2 A:CYS198 3.1 46.2 0.5 CD2 A:HIS240 3.2 14.4 1.0 OD1 A:ASP118 3.5 19.6 1.0 ZN A:ZN301 3.6 13.5 0.6 NH2 A:ARG119 3.9 19.8 1.0 CB A:CYS198 3.9 41.5 0.5 F A:F307 4.0 45.8 0.5 CB A:CYS198 4.1 17.0 0.5 ND1 A:HIS240 4.2 12.8 1.0 CG A:HIS240 4.3 12.8 1.0 CB A:ASP118 4.3 13.9 1.0 O A:HOH640 4.3 42.8 1.0 NE A:ARG119 4.3 13.7 1.0 NE2 A:HIS179 4.4 17.0 1.0 CE1 A:HIS114 4.4 13.3 0.6 NE2 A:HIS114 4.6 12.7 0.6 O A:HOH637 4.6 42.3 1.0 CZ A:ARG119 4.6 15.3 1.0 O A:HOH575 4.6 23.2 1.0 CE1 A:HIS179 4.6 18.9 1.0 O A:HOH604 4.7 32.8 1.0 CE1 A:HIS114 4.8 20.6 0.4 NE2 A:HIS114 4.8 12.1 0.4 O A:HOH605 5.0 29.9 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)-D-Tryptophan (Compound 1)


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)-D-Tryptophan (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:66.5 occ:1.00 O11 A:93W304 1.9 21.9 1.0 O13 A:93W304 2.0 21.1 1.0 O A:HOH523 2.0 27.0 1.0 O A:HOH546 2.1 23.2 1.0 O A:HOH460 2.1 25.5 1.0 O A:HOH508 2.3 31.6 1.0 C12 A:93W304 2.9 20.1 1.0 C10 A:93W304 2.9 21.1 1.0 C09 A:93W304 3.3 20.5 1.0 O A:HOH550 3.7 42.3 1.0 N14 A:93W304 4.1 20.0 1.0 C04 A:93W304 4.2 21.1 1.0 OH A:TYR67 4.2 18.9 1.0 O A:HOH651 4.3 38.3 1.0 N08 A:93W304 4.6 20.5 1.0 C03 A:93W304 4.6 22.7 1.0 C15 A:93W304 4.6 19.7 1.0 CA A:GLY209 4.6 23.8 1.0 OG A:SER207 4.7 31.3 1.0 O A:HOH666 4.8 43.8 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