Zinc in PDB 5n58: Di-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1)

The structure of Di-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1), PDB code: 5n58 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)	62.12 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.471, 81.540, 95.892, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.7

The structure of Di-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)

2 atoms

The binding sites of Zinc atom in the Di-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1) (pdb code 5n58). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Di-Zinc Vim-5 Metallo-Beta-Lactamase in Complex with (1-Chloro-4- Hydroxyisoquinoline-3-Carbonyl)-D-Tryptophan (Compound 1), PDB code: 5n58:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Di-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 Di-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:Zn501 b:34.1 occ:0.80 NE2 A:HIS179 2.0 29.7 1.0 ND1 A:HIS116 2.1 37.9 1.0 NE2 A:HIS114 2.2 56.7 1.0 O A:HOH644 2.4 32.6 1.0 CD2 A:HIS179 2.9 26.5 1.0 CE1 A:HIS114 3.0 63.6 1.0 CE1 A:HIS116 3.0 38.0 1.0 CG A:HIS116 3.1 29.0 1.0 CE1 A:HIS179 3.1 36.8 1.0 CD2 A:HIS114 3.2 45.1 1.0 CB A:HIS116 3.4 22.9 1.0 O A:HOH712 3.7 47.0 1.0 CG A:HIS179 4.1 35.0 1.0 OD1 A:ASP118 4.1 37.6 1.0 ND1 A:HIS179 4.1 37.5 1.0 NE2 A:HIS116 4.1 40.4 1.0 ND1 A:HIS114 4.2 52.0 1.0 CD2 A:HIS116 4.2 41.5 1.0 ZN A:ZN505 4.2 0.5 1.0 CG A:HIS114 4.3 39.3 1.0 SG A:CYS198 4.4 39.8 1.0 CB A:CYS198 4.5 54.5 1.0 O A:HOH678 4.5 41.7 1.0 OD2 A:ASP118 4.6 40.5 1.0 CG A:ASP118 4.8 30.6 1.0 CA A:HIS116 4.8 21.0 1.0

Zinc binding site 2 out of 3 in the Di-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 Di-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:Zn505 b:0.5 occ:1.00 OD2 A:ASP118 2.1 40.5 1.0 NE2 A:HIS240 2.2 32.5 1.0 SG A:CYS198 2.4 39.8 1.0 O A:HOH644 2.8 32.6 1.0 CE1 A:HIS240 3.0 33.6 1.0 CD2 A:HIS240 3.3 37.5 1.0 CG A:ASP118 3.3 30.6 1.0 NH2 A:ARG119 3.6 68.0 1.0 CB A:CYS198 3.8 54.5 1.0 OD1 A:ASP118 3.8 37.6 1.0 O A:HOH712 3.9 47.0 1.0 ND1 A:HIS240 4.2 38.0 1.0 ZN A:ZN501 4.2 34.1 0.8 NE A:ARG119 4.2 20.5 1.0 CG A:HIS240 4.3 29.1 1.0 CZ A:ARG119 4.4 44.2 1.0 O A:HOH696 4.4 56.6 1.0 CB A:ASP118 4.5 32.5 1.0 O A:HOH707 4.6 63.6 1.0 CE1 A:HIS114 4.7 63.6 1.0 O A:HOH703 4.8 47.8 1.0 CA A:CYS198 4.8 39.5 1.0 NE2 A:HIS179 4.9 29.7 1.0

Zinc binding site 3 out of 3 in the Di-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 Di-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 B:Zn501 b:37.2 occ:0.50 ND1 B:HIS116 2.0 36.3 1.0 NE2 B:HIS179 2.1 36.5 1.0 NE2 B:HIS114 2.2 70.7 1.0 CD2 B:HIS179 2.8 36.7 1.0 CG B:HIS116 3.0 41.5 1.0 CE1 B:HIS116 3.0 49.2 1.0 CE1 B:HIS114 3.1 83.4 1.0 CD2 B:HIS114 3.2 54.1 1.0 CE1 B:HIS179 3.2 40.9 1.0 CB B:HIS116 3.3 28.9 1.0 CG B:HIS179 4.0 30.6 1.0 NE2 B:HIS116 4.1 41.9 1.0 OD1 B:ASP118 4.1 82.8 0.8 CD2 B:HIS116 4.1 39.8 1.0 ND1 B:HIS179 4.2 38.5 1.0 ND1 B:HIS114 4.2 63.5 1.0 CG B:HIS114 4.3 43.0 1.0 SG B:CYS198 4.3 58.3 1.0 CB B:CYS198 4.6 70.9 1.0 OD2 B:ASP118 4.6 74.8 0.8 CA B:HIS116 4.7 37.9 1.0 CG B:ASP118 4.8 71.4 0.8 N B:HIS116 5.0 26.8 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