Chlorine 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:

Zinc

(Zn)

3 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl502 b:40.6 occ:1.00 CL1 A:93W502 0.0 40.6 1.0 C07 A:93W502 1.8 49.2 1.0 N08 A:93W502 2.6 42.4 1.0 C05 A:93W502 2.8 52.0 1.0 C06 A:93W502 3.1 66.4 1.0 CG A:HIS240 3.4 29.1 1.0 C27 A:93W502 3.5 80.7 1.0 CB A:HIS240 3.6 22.4 1.0 CD1 A:TYR67 3.6 29.9 1.0 ND1 A:HIS240 3.7 38.0 1.0 C09 A:93W502 3.9 41.7 1.0 CD2 A:HIS240 3.9 37.5 1.0 CG A:TYR67 4.0 30.9 1.0 NH2 A:ARG205 4.0 34.0 1.0 C04 A:93W502 4.0 42.8 1.0 C28 A:93W502 4.0 70.8 1.0 CB A:TYR67 4.1 30.0 1.0 CE1 A:HIS240 4.2 33.6 1.0 C26 A:93W502 4.3 67.1 1.0 CE1 A:TYR67 4.3 40.0 1.0 NE2 A:HIS240 4.4 32.5 1.0 C01 A:93W502 4.4 67.3 1.0 O A:PRO68 4.5 25.0 1.0 C10 A:93W502 4.5 38.5 1.0 O A:HOH696 4.5 56.6 1.0 CZ A:ARG205 4.5 37.9 1.0 CD2 A:TYR67 4.9 39.8 1.0 NH1 A:ARG205 4.9 38.2 1.0 CD A:PRO68 5.0 26.4 1.0

Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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 B:Cl502 b:48.0 occ:1.00 CL1 B:93W502 0.0 48.0 1.0 C07 B:93W502 1.8 52.6 1.0 N08 B:93W502 2.7 53.1 1.0 C05 B:93W502 2.8 56.2 1.0 C06 B:93W502 3.1 45.7 1.0 CG B:HIS240 3.3 36.4 1.0 CB B:HIS240 3.4 33.7 1.0 ND1 B:HIS240 3.5 34.5 1.0 CD2 B:TYR67 3.5 55.9 1.0 C27 B:93W502 3.6 33.5 1.0 NH2 B:ARG205 3.8 28.1 1.0 CD2 B:HIS240 3.8 28.4 1.0 CG B:TYR67 3.9 57.7 1.0 C09 B:93W502 4.0 61.0 1.0 CB B:TYR67 4.0 48.7 1.0 CE1 B:HIS240 4.1 38.6 1.0 C04 B:93W502 4.1 61.3 1.0 C28 B:93W502 4.1 37.7 1.0 NE2 B:HIS240 4.2 34.6 1.0 CE2 B:TYR67 4.2 61.8 1.0 CZ B:ARG205 4.3 35.3 1.0 C26 B:93W502 4.3 45.5 1.0 C01 B:93W502 4.4 52.2 1.0 O B:PRO68 4.5 36.1 1.0 C10 B:93W502 4.5 59.7 1.0 NH1 B:ARG205 4.7 34.3 1.0 CD1 B:TYR67 4.9 73.8 1.0 NE B:ARG205 4.9 27.8 1.0 CA B:HIS240 5.0 20.3 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