Zinc 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:

Chlorine

(Cl)

7 atoms

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F, PDB code: 6ew3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn501 b:17.7 occ:1.00 ND1 A:HIS116 2.0 28.2 1.0 NE2 A:HIS179 2.1 19.1 1.0 NE2 A:HIS114 2.1 14.1 1.0 S9 A:S3C506 2.3 19.0 1.0 CE1 A:HIS116 3.0 29.5 1.0 CG A:HIS116 3.0 26.7 1.0 CD2 A:HIS179 3.0 16.1 1.0 CE1 A:HIS114 3.0 11.8 1.0 CD2 A:HIS114 3.1 13.7 1.0 C5 A:S3C506 3.1 21.8 1.0 CE1 A:HIS179 3.1 17.4 1.0 CB A:HIS116 3.3 24.8 1.0 ZN A:ZN502 3.8 19.9 1.0 C4 A:S3C506 3.8 22.9 1.0 C6 A:S3C506 3.9 25.3 1.0 C3 A:S3C506 4.0 25.6 1.0 O8 A:S3C506 4.0 25.0 1.0 OD1 A:ASP118 4.0 23.2 1.0 NE2 A:HIS116 4.1 28.4 1.0 CD2 A:HIS116 4.1 28.7 1.0 ND1 A:HIS114 4.1 13.2 1.0 CG A:HIS179 4.2 15.8 1.0 ND1 A:HIS179 4.2 16.4 1.0 C2 A:S3C506 4.2 26.2 1.0 CG A:HIS114 4.2 12.5 1.0 CL1 A:S3C506 4.3 24.9 1.0 CB A:CYS198 4.4 18.4 1.0 SG A:CYS198 4.4 16.3 1.0 OD2 A:ASP118 4.6 20.4 1.0 C10 A:S3C506 4.7 26.9 1.0 CG A:ASP118 4.7 18.2 1.0 CA A:HIS116 4.7 20.2 1.0 O7 A:S3C506 5.0 22.8 1.0 N A:HIS116 5.0 16.2 1.0 C15 A:S3C506 5.0 26.7 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn502 b:19.9 occ:1.00 NE2 A:HIS240 2.1 26.7 1.0 OD2 A:ASP118 2.1 20.4 1.0 SG A:CYS198 2.2 16.3 1.0 O8 A:S3C506 2.3 25.0 1.0 S9 A:S3C506 2.3 19.0 1.0 C6 A:S3C506 2.9 25.3 1.0 C5 A:S3C506 3.0 21.8 1.0 CD2 A:HIS240 3.1 26.4 1.0 CE1 A:HIS240 3.1 28.2 1.0 CG A:ASP118 3.2 18.2 1.0 CB A:CYS198 3.3 18.4 1.0 OD1 A:ASP118 3.7 23.2 1.0 ZN A:ZN501 3.8 17.7 1.0 NH2 A:ARG119 3.8 40.2 1.0 NE A:ARG119 4.1 24.9 1.0 ND1 A:HIS240 4.2 25.8 1.0 O7 A:S3C506 4.2 22.8 1.0 CG A:HIS240 4.2 25.5 1.0 CE1 A:HIS114 4.3 11.8 1.0 C4 A:S3C506 4.3 22.9 1.0 CB A:ASP118 4.4 17.9 1.0 O A:HOH634 4.4 10.6 1.0 CZ A:ARG119 4.4 32.8 1.0 CL2 A:S3C506 4.5 27.3 1.0 NE2 A:HIS179 4.5 19.1 1.0 CA A:CYS198 4.5 20.8 1.0 NE2 A:HIS114 4.5 14.1 1.0 CE1 A:HIS179 4.9 17.4 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn503 b:17.7 occ:1.00 O2 A:FMT504 1.8 19.1 1.0 NE2 A:HIS153 2.0 22.3 1.0 O2 A:FMT505 2.1 17.7 1.0 O1 A:FMT505 2.4 15.5 1.0 C A:FMT505 2.5 18.4 1.0 C A:FMT504 2.9 25.1 1.0 CE1 A:HIS153 2.9 21.9 1.0 CD2 A:HIS153 3.1 18.5 1.0 O1 A:FMT504 3.3 21.8 1.0 CB A:ALA132 4.1 31.3 1.0 ND1 A:HIS153 4.1 21.4 1.0 CG A:HIS153 4.2 18.9 1.0 O A:HOH613 4.7 27.4 1.0 CG2 A:THR152 4.7 16.5 1.0 CA A:ALA132 4.8 23.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn501 b:17.4 occ:1.00 NE2 B:HIS179 2.0 19.9 1.0 ND1 B:HIS116 2.0 23.2 1.0 NE2 B:HIS114 2.1 17.4 1.0 S9 B:S3C506 2.3 22.7 1.0 CE1 B:HIS114 3.0 12.3 1.0 CD2 B:HIS179 3.0 17.4 1.0 CE1 B:HIS179 3.0 18.1 1.0 CE1 B:HIS116 3.0 22.1 1.0 CG B:HIS116 3.0 17.6 1.0 C5 B:S3C506 3.1 27.2 1.0 CD2 B:HIS114 3.1 15.9 1.0 CB B:HIS116 3.4 14.0 1.0 ZN B:ZN502 3.8 20.2 1.0 C4 B:S3C506 3.8 27.9 1.0 C6 B:S3C506 3.9 28.6 1.0 C3 B:S3C506 4.0 30.1 1.0 OD1 B:ASP118 4.1 18.5 1.0 O7 B:S3C506 4.1 23.9 1.0 ND1 B:HIS179 4.1 17.5 1.0 ND1 B:HIS114 4.1 17.4 1.0 NE2 B:HIS116 4.1 21.7 1.0 CG B:HIS179 4.1 17.6 1.0 CD2 B:HIS116 4.1 22.6 1.0 CG B:HIS114 4.2 17.9 1.0 C2 B:S3C506 4.3 31.4 1.0 CB B:CYS198 4.3 17.5 1.0 SG B:CYS198 4.4 15.6 1.0 CL1 B:S3C506 4.4 29.1 1.0 OD2 B:ASP118 4.6 24.5 1.0 C10 B:S3C506 4.6 32.0 1.0 CG B:ASP118 4.7 19.9 1.0 CA B:HIS116 4.8 13.2 1.0 O8 B:S3C506 4.9 27.3 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 with ML302F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn502 b:20.2 occ:1.00 NE2 B:HIS240 2.1 20.5 1.0 OD2 B:ASP118 2.2 24.5 1.0 O7 B:S3C506 2.2 23.9 1.0 SG B:CYS198 2.2 15.6 1.0 S9 B:S3C506 2.3 22.7 1.0 C6 B:S3C506 2.9 28.6 1.0 CD2 B:HIS240 3.0 18.7 1.0 C5 B:S3C506 3.0 27.2 1.0 CE1 B:HIS240 3.1 19.1 1.0 CG B:ASP118 3.3 19.9 1.0 CB B:CYS198 3.3 17.5 1.0 OD1 B:ASP118 3.7 18.5 1.0 ZN B:ZN501 3.8 17.4 1.0 NH2 B:ARG119 3.9 18.1 1.0 NE B:ARG119 4.1 15.9 1.0 ND1 B:HIS240 4.2 18.8 1.0 O8 B:S3C506 4.2 27.3 1.0 CG B:HIS240 4.2 20.5 1.0 CE1 B:HIS114 4.3 12.3 1.0 C4 B:S3C506 4.3 27.9 1.0 CZ B:ARG119 4.4 18.1 1.0 CB B:ASP118 4.5 18.6 1.0 NE2 B:HIS179 4.5 19.9 1.0 O B:HOH624 4.5 12.6 1.0 CA B:CYS198 4.5 19.4 1.0 NE2 B:HIS114 4.6 17.4 1.0 CL2 B:S3C506 4.6 31.3 1.0 C2 B:DMS507 4.8 50.9 1.0 CE1 B:HIS179 4.9 18.1 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn503 b:21.2 occ:1.00 O1 B:FMT505 2.0 20.8 1.0 O1 B:FMT504 2.0 17.0 1.0 NE2 B:HIS153 2.0 23.7 1.0 O2 B:FMT504 2.6 18.3 1.0 C B:FMT504 2.6 18.0 1.0 CE1 B:HIS153 2.8 23.9 1.0 C B:FMT505 2.9 27.2 1.0 O2 B:FMT505 3.2 24.0 1.0 CD2 B:HIS153 3.2 23.0 1.0 ND1 B:HIS153 4.0 23.3 1.0 CB B:ALA132 4.1 15.8 1.0 CG B:HIS153 4.2 20.4 1.0 CA B:ALA132 4.7 16.2 1.0 O B:HOH639 5.0 18.7 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