Chlorine in PDB 5n5h: Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor

The structure of Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor, PDB code: 5n5h was solved by R.Salimraj, P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.58 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.684, 67.652, 40.217, 90.00, 91.36, 90.00
R / Rfree (%)	15.5 / 16.8

The structure of Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor (pdb code 5n5h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor, PDB code: 5n5h:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:19.4 occ:0.91 CL1 A:S3C303 0.0 19.4 0.9 C2 A:S3C303 1.7 17.7 0.9 C3 A:S3C303 2.6 16.1 0.9 C15 A:S3C303 2.7 16.4 0.9 C4 A:S3C303 2.8 13.1 0.9 H2 A:S3C303 2.8 15.7 0.9 HB3 A:ASN210 2.8 28.4 1.0 H1 A:S3C303 2.9 19.7 0.9 HE1 A:HIS116 3.1 9.6 1.0 HE1 A:HIS179 3.2 9.9 1.0 CE1 A:HIS116 3.3 8.0 1.0 O A:ASN210 3.4 13.3 1.0 CG A:ASN210 3.4 28.2 1.0 O A:HOH534 3.5 16.3 1.0 CB A:ASN210 3.5 23.6 1.0 OD1 A:ASN210 3.6 32.1 1.0 ND2 A:ASN210 3.8 28.7 1.0 ND1 A:HIS116 3.9 6.4 1.0 CE1 A:HIS179 3.9 8.3 1.0 NE2 A:HIS116 3.9 10.1 1.0 C10 A:S3C303 3.9 13.5 0.9 C14 A:S3C303 4.0 13.0 0.9 C5 A:S3C303 4.0 10.5 0.9 HB2 A:ALA212 4.0 38.6 1.0 HD22 A:ASN210 4.0 34.4 1.0 C A:ASN210 4.1 17.9 1.0 HE2 A:HIS116 4.1 12.1 1.0 HD21 A:ASN210 4.1 34.4 1.0 HB2 A:ASN210 4.2 28.4 1.0 H A:ALA212 4.3 29.4 1.0 CA A:ASN210 4.4 24.0 1.0 NE2 A:HIS179 4.4 6.2 1.0 C12 A:S3C303 4.4 13.7 0.9 H A:ASP213 4.5 18.9 1.0 ZN A:ZN302 4.5 7.7 1.0 HB3 A:ALA212 4.7 38.6 1.0 CG A:HIS116 4.7 6.8 1.0 CD2 A:HIS116 4.7 8.9 1.0 CB A:ALA212 4.7 32.2 1.0 HB2 A:ASP213 4.7 20.2 1.0 OD2 A:ASP213 4.7 31.9 1.0 S9 A:S3C303 4.8 9.7 0.9 H5 A:S3C303 4.8 15.6 0.9 O8 A:S3C303 4.8 19.1 0.9 N A:ALA212 4.9 24.5 1.0 H3 A:S3C303 4.9 11.6 0.9 C6 A:S3C303 4.9 16.4 0.9 H A:ASN210 4.9 30.9 1.0 ND1 A:HIS179 5.0 7.6 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:19.5 occ:0.91 CL2 A:S3C303 0.0 19.5 0.9 C10 A:S3C303 1.8 13.5 0.9 C12 A:S3C303 2.7 13.7 0.9 C3 A:S3C303 2.8 16.1 0.9 CL3 A:S3C303 3.0 35.2 0.9 HZ2 A:TRP87 3.2 13.1 1.0 C4 A:S3C303 3.2 13.1 0.9 C5 A:S3C303 3.2 10.5 0.9 S9 A:S3C303 3.2 9.7 0.9 HH2 A:TRP87 3.4 13.6 1.0 CZ2 A:TRP87 3.4 10.9 1.0 CH2 A:TRP87 3.6 11.4 1.0 HB3 A:ASP118 3.8 8.1 1.0 H2 A:S3C303 3.9 15.7 0.9 C14 A:S3C303 4.0 13.0 0.9 C2 A:S3C303 4.0 17.7 0.9 HE1 A:HIS240 4.3 8.6 1.0 CE2 A:TRP87 4.3 10.1 1.0 CG A:ASP118 4.3 6.8 1.0 CD2 A:PHE62 4.3 19.6 1.0 C6 A:S3C303 4.4 16.4 0.9 HD2 A:PHE62 4.4 23.6 1.0 OD2 A:ASP118 4.4 8.1 1.0 OD1 A:ASP118 4.5 9.7 1.0 CE2 A:PHE62 4.5 24.4 1.0 CZ3 A:TRP87 4.5 10.1 1.0 H3 A:S3C303 4.5 11.6 0.9 ZN A:ZN301 4.5 9.0 0.9 C15 A:S3C303 4.6 16.4 0.9 CB A:ASP118 4.6 6.7 1.0 HE2 A:PHE62 4.6 29.3 1.0 HB3 A:HIS116 4.7 6.4 1.0 H A:ASP118 4.7 7.3 1.0 CG A:PHE62 4.7 15.9 1.0 CE1 A:HIS240 4.7 7.2 1.0 H5 A:S3C303 4.8 15.6 0.9 NE2 A:HIS240 4.8 6.8 1.0 HZ3 A:TRP87 4.9 12.1 1.0 HE1 A:TRP87 5.0 12.5 1.0 NE1 A:TRP87 5.0 10.4 1.0 CZ A:PHE62 5.0 27.7 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Metallo-Beta-Lactamase Vim-1 in Complex with ML302F Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:35.2 occ:0.91 CL3 A:S3C303 0.0 35.2 0.9 C12 A:S3C303 1.8 13.7 0.9 C10 A:S3C303 2.7 13.5 0.9 C14 A:S3C303 2.8 13.0 0.9 H5 A:S3C303 2.9 15.6 0.9 CL2 A:S3C303 3.0 19.5 0.9 HZ2 A:TRP87 3.2 13.1 1.0 HB3 A:ASP117 3.2 12.2 1.0 HE1 A:TRP87 3.4 12.5 1.0 O A:HOH433 3.4 10.9 1.0 CE1 A:PHE62 3.6 27.1 1.0 CD1 A:PHE62 3.7 21.6 1.0 H A:ASP117 3.7 7.1 1.0 HE1 A:PHE62 3.7 32.5 1.0 CZ2 A:TRP87 3.8 10.9 1.0 CZ A:PHE62 3.8 27.7 1.0 NE1 A:TRP87 3.9 10.4 1.0 H A:ASP118 3.9 7.3 1.0 HB3 A:HIS116 3.9 6.4 1.0 HD1 A:PHE62 3.9 26.0 1.0 O A:HOH561 4.0 8.7 1.0 C3 A:S3C303 4.0 16.1 0.9 CB A:ASP117 4.0 10.2 1.0 C15 A:S3C303 4.0 16.4 0.9 CE2 A:TRP87 4.1 10.1 1.0 CG A:PHE62 4.1 15.9 1.0 HB2 A:ASP117 4.1 12.2 1.0 HZ A:PHE62 4.2 33.2 1.0 CE2 A:PHE62 4.2 24.4 1.0 N A:ASP117 4.3 5.9 1.0 CD2 A:PHE62 4.3 19.6 1.0 HB3 A:ASP118 4.4 8.1 1.0 N A:ASP118 4.5 6.1 1.0 C2 A:S3C303 4.5 17.7 0.9 HB2 A:PHE62 4.6 18.4 1.0 CA A:ASP117 4.7 5.5 1.0 HE2 A:PHE62 4.7 29.3 1.0 CH2 A:TRP87 4.8 11.4 1.0 CB A:HIS116 4.8 5.4 1.0 HD2 A:PHE62 4.9 23.6 1.0 H1 A:S3C303 4.9 19.7 0.9 CB A:PHE62 4.9 15.4 1.0 C A:ASP117 5.0 5.9 1.0 CD1 A:TRP87 5.0 9.4 1.0

R.Salimraj, P.Hinchliffe, M.Kosmopoulou, J.M.Tyrrell, J.Brem, S.S.Van Berkel, A.Verma, R.J.Owens, M.A.Mcdonough, T.R.Walsh, C.J.Schofield, J.Spencer. Crystal Structures of Vim-1 Complexes Explain Active Site Heterogeneity in Vim-Class Metallo-Beta-Lactamases. Febs J. V. 286 169 2019.
ISSN: ISSN 1742-4658
PubMed: 30430727
DOI: 10.1111/FEBS.14695