Chlorine in PDB 6ew3: Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F, PDB code: 6ew3 was solved by P.M.Collins, J.Brem, M.A.Mcdonough, S.S.Van Berkel, F.Von Delft, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.31 / 2.14
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.480, 78.910, 67.460, 90.00, 130.48, 90.00
R / Rfree (%)	16.9 / 21

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F (pdb code 6ew3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F, PDB code: 6ew3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


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 the Metallo-Beta-Lactamase Vim-2 with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:24.9 occ:1.00 CL1 A:S3C506 0.0 24.9 1.0 C2 A:S3C506 1.7 26.2 1.0 C3 A:S3C506 2.7 25.6 1.0 C15 A:S3C506 2.7 26.7 1.0 C4 A:S3C506 3.0 22.9 1.0 CE1 A:HIS116 3.3 29.5 1.0 CG A:ASN210 3.4 62.8 1.0 O A:ASN210 3.4 25.9 1.0 OD1 A:ASN210 3.4 68.8 1.0 CB A:ASN210 3.5 47.6 1.0 O A:HOH690 3.6 17.2 1.0 ND1 A:HIS116 3.8 28.2 1.0 C5 A:S3C506 3.9 21.8 1.0 NE2 A:HIS116 3.9 28.4 1.0 CE1 A:HIS179 3.9 17.4 1.0 C10 A:S3C506 4.0 26.9 1.0 ND2 A:ASN210 4.0 68.9 1.0 C14 A:S3C506 4.0 26.5 1.0 C A:ASN210 4.0 27.6 1.0 NE2 A:HIS179 4.3 19.1 1.0 ZN A:ZN501 4.3 17.7 1.0 CA A:ASN210 4.4 35.0 1.0 C12 A:S3C506 4.4 26.8 1.0 CG A:HIS116 4.6 26.7 1.0 CD2 A:HIS116 4.6 28.7 1.0 S9 A:S3C506 4.7 19.0 1.0 C6 A:S3C506 4.8 25.3 1.0 O7 A:S3C506 4.9 22.8 1.0 OD2 A:ASP213 4.9 16.6 1.0 N A:ALA212 4.9 25.7 1.0 N A:VAL211 4.9 26.1 1.0

Chlorine binding site 2 out of 7 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


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 the Metallo-Beta-Lactamase Vim-2 with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:27.3 occ:1.00 CL2 A:S3C506 0.0 27.3 1.0 C10 A:S3C506 1.7 26.9 1.0 C3 A:S3C506 2.7 25.6 1.0 C12 A:S3C506 2.7 26.8 1.0 C4 A:S3C506 3.0 22.9 1.0 CL3 A:S3C506 3.1 28.9 1.0 C5 A:S3C506 3.2 21.8 1.0 S9 A:S3C506 3.3 19.0 1.0 CZ2 A:TRP87 3.5 25.8 1.0 CH2 A:TRP87 3.7 27.4 1.0 C2 A:DMS508 3.8 60.8 1.0 C2 A:S3C506 3.9 26.2 1.0 C14 A:S3C506 4.0 26.5 1.0 S A:DMS508 4.1 63.1 1.0 C2 A:DMS507 4.2 52.0 1.0 C1 A:DMS508 4.2 59.4 1.0 CG A:ASP118 4.2 18.2 1.0 CE2 A:TRP87 4.3 20.9 1.0 C6 A:S3C506 4.3 25.3 1.0 OD2 A:ASP118 4.3 20.4 1.0 CB A:ASP118 4.5 17.9 1.0 ZN A:ZN502 4.5 19.9 1.0 C15 A:S3C506 4.5 26.7 1.0 CZ3 A:TRP87 4.5 24.8 1.0 OD1 A:ASP118 4.5 23.2 1.0 CE1 A:HIS240 4.7 28.2 1.0 NE2 A:HIS240 4.8 26.7 1.0 NE1 A:TRP87 4.9 18.1 1.0 O7 A:S3C506 4.9 22.8 1.0

Chlorine binding site 3 out of 7 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


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 the Metallo-Beta-Lactamase Vim-2 with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:28.9 occ:1.00 CL3 A:S3C506 0.0 28.9 1.0 C12 A:S3C506 1.7 26.8 1.0 C14 A:S3C506 2.6 26.5 1.0 C10 A:S3C506 2.7 26.9 1.0 CL2 A:S3C506 3.1 27.3 1.0 CB A:ASP117 3.9 26.7 0.5 C15 A:S3C506 3.9 26.7 1.0 CZ2 A:TRP87 4.0 25.8 1.0 C3 A:S3C506 4.0 25.6 1.0 CE2 A:PHE62 4.0 59.2 1.0 NE1 A:TRP87 4.0 18.1 1.0 CB A:ASP117 4.1 28.0 0.5 CE2 A:TRP87 4.3 20.9 1.0 O A:HOH672 4.4 21.5 1.0 N A:ASP117 4.4 16.9 0.5 N A:ASP117 4.4 16.9 0.5 C2 A:S3C506 4.4 26.2 1.0 CD2 A:PHE62 4.5 55.8 1.0 N A:ASP118 4.6 14.6 1.0 OD2 A:ASP117 4.6 42.2 0.5 CA A:ASP117 4.7 18.6 0.5 CA A:ASP117 4.7 18.5 0.5 CG A:ASP117 4.8 33.5 0.5 CZ A:PHE62 4.9 63.9 1.0 C1 A:DMS508 4.9 59.4 1.0 C A:ASP117 5.0 15.0 0.5

Chlorine binding site 4 out of 7 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl506 b:29.1 occ:1.00 CL1 B:S3C506 0.0 29.1 1.0 C2 B:S3C506 1.7 31.4 1.0 C3 B:S3C506 2.7 30.1 1.0 C15 B:S3C506 2.7 33.7 1.0 C4 B:S3C506 3.0 27.9 1.0 CE1 B:HIS116 3.2 22.1 1.0 CG B:ASN210 3.4 35.1 1.0 CB B:ASN210 3.5 32.7 1.0 OD1 B:ASN210 3.5 28.5 1.0 O B:HOH675 3.5 17.1 1.0 O B:ASN210 3.5 22.4 1.0 ND1 B:HIS116 3.8 23.2 1.0 NE2 B:HIS116 3.8 21.7 1.0 C5 B:S3C506 3.9 27.2 1.0 CE1 B:HIS179 3.9 18.1 1.0 C10 B:S3C506 3.9 32.0 1.0 ND2 B:ASN210 4.0 46.0 1.0 C14 B:S3C506 4.0 32.6 1.0 C B:ASN210 4.1 24.7 1.0 CA B:ASN210 4.4 32.2 1.0 NE2 B:HIS179 4.4 19.9 1.0 ZN B:ZN501 4.4 17.4 1.0 C12 B:S3C506 4.5 34.7 1.0 OD2 B:ASP213 4.6 28.5 1.0 C1 B:DMS508 4.6 58.9 0.7 CD2 B:HIS116 4.6 22.6 1.0 CG B:HIS116 4.6 17.6 1.0 S9 B:S3C506 4.8 22.7 1.0 O8 B:S3C506 4.8 27.3 1.0 C6 B:S3C506 4.8 28.6 1.0 ND1 B:HIS179 4.9 17.5 1.0

Chlorine binding site 5 out of 7 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl506 b:31.3 occ:1.00 CL2 B:S3C506 0.0 31.3 1.0 C10 B:S3C506 1.7 32.0 1.0 C3 B:S3C506 2.7 30.1 1.0 C12 B:S3C506 2.7 34.7 1.0 C4 B:S3C506 3.0 27.9 1.0 CL3 B:S3C506 3.1 37.7 1.0 C5 B:S3C506 3.2 27.2 1.0 S9 B:S3C506 3.3 22.7 1.0 CZ2 B:TRP87 3.6 21.2 1.0 CH2 B:TRP87 3.7 18.2 1.0 C2 B:DMS508 3.7 47.1 0.7 C1 B:DMS508 3.8 58.9 0.7 C2 B:S3C506 3.9 31.4 1.0 C14 B:S3C506 4.0 32.6 1.0 C2 B:DMS507 4.2 50.9 1.0 C6 B:S3C506 4.3 28.6 1.0 CG B:ASP118 4.3 19.9 1.0 CE2 B:TRP87 4.4 16.6 1.0 OD2 B:ASP118 4.5 24.5 1.0 C15 B:S3C506 4.5 33.7 1.0 OD1 B:ASP118 4.5 18.5 1.0 ZN B:ZN502 4.6 20.2 1.0 CZ3 B:TRP87 4.6 16.2 1.0 CB B:ASP118 4.6 18.6 1.0 S B:DMS508 4.6 53.0 0.7 CE1 B:HIS240 4.8 19.1 1.0 NE2 B:HIS240 4.8 20.5 1.0 O7 B:S3C506 5.0 23.9 1.0 O8 B:S3C506 5.0 27.3 1.0

Chlorine binding site 6 out of 7 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl506 b:37.7 occ:1.00 CL3 B:S3C506 0.0 37.7 1.0 C12 B:S3C506 1.7 34.7 1.0 C10 B:S3C506 2.7 32.0 1.0 C14 B:S3C506 2.7 32.6 1.0 CL2 B:S3C506 3.1 31.3 1.0 O B:HOH651 3.7 26.1 1.0 O B:HOH684 3.7 54.5 1.0 O B:HOH706 3.8 13.8 1.0 CE1 B:PHE62 3.9 59.8 1.0 C3 B:S3C506 4.0 30.1 1.0 C15 B:S3C506 4.0 33.7 1.0 CZ2 B:TRP87 4.0 21.2 1.0 CB B:ASP117 4.0 32.3 1.0 CD1 B:PHE62 4.1 53.9 1.0 NE1 B:TRP87 4.1 15.3 1.0 N B:ASP117 4.3 17.1 1.0 CE2 B:TRP87 4.3 16.6 1.0 C2 B:S3C506 4.4 31.4 1.0 N B:ASP118 4.5 16.6 1.0 CA B:ASP117 4.7 18.5 1.0 CZ B:PHE62 4.7 69.1 1.0 CB B:HIS116 4.9 14.0 1.0

Chlorine binding site 7 out of 7 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl509 b:45.7 occ:1.00 NE B:ARG141 3.9 71.7 1.0 OG B:SER138 4.1 23.9 0.5 CD B:ARG141 4.2 61.1 1.0 N B:SER138 4.2 19.6 0.5 N B:SER138 4.2 19.6 0.5 C B:PRO137 4.2 17.1 1.0 O B:PRO137 4.3 17.4 1.0 CA B:SER138 4.3 22.2 0.5 CA B:SER138 4.3 22.2 0.5 CB B:PRO137 4.3 19.9 1.0 O B:HOH603 4.6 13.1 0.5 CB B:ARG141 4.8 26.6 1.0 CB B:SER138 4.8 22.8 0.5 CB B:SER138 4.9 22.8 0.5 CA B:PRO137 4.9 19.3 1.0 CZ B:ARG141 5.0 67.2 1.0

D.Zhang, M.S.Markoulides, D.Stepanovs, A.M.Rydzik, A.El-Hussein, C.Bon, J.J.A.G.Kamps, K.D.Umland, P.M.Collins, S.T.Cahill, D.Y.Wang, F.Von Delft, J.Brem, M.A.Mcdonough, C.J.Schofield. Structure Activity Relationship Studies on Rhodanines and Derived Enethiol Inhibitors of Metallo-Beta-Lactamases. Bioorg. Med. Chem. V. 26 2928 2018.
ISSN: ESSN 1464-3391
PubMed: 29655609
DOI: 10.1016/J.BMC.2018.02.043