Zinc in PDB 4pvt: Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F, PDB code: 4pvt was solved by W.S.Aik, 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)	24.93 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.391, 78.909, 67.742, 90.00, 130.32, 90.00
R / Rfree (%)	16.6 / 21.9

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

Chlorine

(Cl)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F (pdb code 4pvt). 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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F, PDB code: 4pvt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex 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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:15.9 occ:1.00 ND1 A:HIS118 1.9 13.5 1.0 NE2 A:HIS196 2.1 10.3 1.0 S9 A:S3C403 2.2 11.2 0.7 NE2 A:HIS116 2.2 13.7 1.0 CE1 A:HIS118 2.9 13.8 1.0 CG A:HIS118 2.9 13.9 1.0 CE1 A:HIS196 3.0 11.2 1.0 CD2 A:HIS196 3.1 10.0 1.0 CD2 A:HIS116 3.2 13.5 1.0 CE1 A:HIS116 3.2 13.1 1.0 C5 A:S3C403 3.2 27.5 0.7 CB A:HIS118 3.3 13.8 1.0 C3 A:S3C403 3.8 40.0 0.7 ZN A:ZN402 3.9 15.6 1.0 C2 A:S3C403 3.9 42.2 0.7 C4 A:S3C403 3.9 34.0 0.7 NE2 A:HIS118 4.0 15.2 1.0 C6 A:S3C403 4.0 22.6 0.7 CD2 A:HIS118 4.1 15.3 1.0 OD1 A:ASP120 4.1 15.7 1.0 CL1 A:S3C403 4.1 53.8 0.7 ND1 A:HIS196 4.2 11.4 1.0 O8 A:S3C403 4.2 21.5 0.7 CG A:HIS196 4.2 11.4 1.0 ND1 A:HIS116 4.3 12.6 1.0 CG A:HIS116 4.3 13.5 1.0 CB A:CYS221 4.3 13.2 1.0 C10 A:S3C403 4.4 41.9 0.7 C15 A:S3C403 4.5 41.5 0.7 SG A:CYS221 4.5 16.7 1.0 OD2 A:ASP120 4.7 16.5 1.0 CA A:HIS118 4.8 14.6 1.0 CG A:ASP120 4.8 16.4 1.0 O7 A:S3C403 5.0 20.1 0.7 C12 A:S3C403 5.0 41.2 0.7

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex 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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:15.6 occ:1.00 OD2 A:ASP120 2.0 16.5 1.0 NE2 A:HIS263 2.1 13.7 1.0 S9 A:S3C403 2.2 11.2 0.7 SG A:CYS221 2.2 16.7 1.0 O8 A:S3C403 2.4 21.5 0.7 C5 A:S3C403 3.0 27.5 0.7 CE1 A:HIS263 3.0 14.8 1.0 CG A:ASP120 3.1 16.4 1.0 C6 A:S3C403 3.1 22.6 0.7 CD2 A:HIS263 3.1 14.2 1.0 CB A:CYS221 3.4 13.2 1.0 OD1 A:ASP120 3.5 15.7 1.0 ZN A:ZN401 3.9 15.9 1.0 NH2 A:ARG121 3.9 16.3 1.0 NE A:ARG121 4.1 13.5 1.0 ND1 A:HIS263 4.1 14.8 1.0 CG A:HIS263 4.2 14.4 1.0 CE1 A:HIS116 4.2 13.1 1.0 O7 A:S3C403 4.3 20.1 0.7 CB A:ASP120 4.3 17.4 1.0 CZ A:ARG121 4.4 14.4 1.0 CL2 A:S3C403 4.4 37.5 0.7 NE2 A:HIS116 4.5 13.7 1.0 C4 A:S3C403 4.5 34.0 0.7 CA A:CYS221 4.6 12.9 1.0 O A:HOH501 4.6 16.4 1.0 NE2 A:HIS196 4.7 10.3 1.0 O A:HOH658 4.9 27.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex 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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:20.0 occ:1.00 O1 A:FMT405 1.8 21.1 1.0 O2 A:FMT406 2.0 14.2 1.0 ND1 A:HIS285 2.2 18.3 1.0 C A:FMT406 2.6 14.8 1.0 O1 A:FMT406 2.7 15.6 1.0 C A:FMT405 2.8 23.3 1.0 O2 A:FMT405 3.2 24.7 1.0 CG A:HIS285 3.2 17.1 1.0 CE1 A:HIS285 3.2 18.6 1.0 CB A:HIS285 3.4 16.4 1.0 CA A:HIS285 3.7 16.9 1.0 ND2 A:ASN288 4.3 19.8 1.0 NE2 A:HIS285 4.3 18.0 1.0 CD2 A:HIS285 4.3 17.5 1.0 O A:HIS285 4.4 17.6 1.0 C A:HIS285 4.5 16.4 1.0 CD2 A:LEU226 4.8 16.8 1.0 N A:HIS285 4.8 17.3 1.0 CB A:ASN288 5.0 16.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex 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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:14.5 occ:1.00 NE2 B:HIS196 2.0 11.4 1.0 ND1 B:HIS118 2.0 14.5 1.0 NE2 B:HIS116 2.1 13.1 1.0 S9 B:S3C406 2.3 15.0 0.9 CE1 B:HIS196 2.9 12.9 1.0 CG B:HIS118 3.0 14.3 1.0 CE1 B:HIS118 3.0 14.9 1.0 CD2 B:HIS196 3.1 10.4 1.0 CE1 B:HIS116 3.1 13.1 1.0 CD2 B:HIS116 3.1 14.3 1.0 C5 B:S3C406 3.2 25.0 0.9 CB B:HIS118 3.3 13.0 1.0 ZN B:ZN402 3.8 15.5 1.0 C6 B:S3C406 3.9 21.6 0.9 OD1 B:ASP120 3.9 15.5 1.0 C4 B:S3C406 4.0 29.3 0.9 C3 B:S3C406 4.0 33.3 0.9 ND1 B:HIS196 4.1 12.8 1.0 O7 B:S3C406 4.1 19.4 0.9 NE2 B:HIS118 4.1 16.1 1.0 CG B:HIS196 4.1 11.3 1.0 CD2 B:HIS118 4.2 15.7 1.0 C2 B:S3C406 4.2 35.9 0.9 ND1 B:HIS116 4.2 12.8 1.0 CG B:HIS116 4.2 13.5 1.0 CB B:CYS221 4.3 11.3 1.0 CL1 B:S3C406 4.4 47.1 0.9 SG B:CYS221 4.5 13.9 1.0 OD2 B:ASP120 4.6 15.5 1.0 C10 B:S3C406 4.6 34.3 0.9 CG B:ASP120 4.7 15.3 1.0 CA B:HIS118 4.8 13.1 1.0 O8 B:S3C406 4.8 21.0 0.9 C15 B:S3C406 4.9 36.9 0.9

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex 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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:15.5 occ:1.00 NE2 B:HIS263 2.1 13.5 1.0 OD2 B:ASP120 2.1 15.5 1.0 O7 B:S3C406 2.3 19.4 0.9 S9 B:S3C406 2.3 15.0 0.9 SG B:CYS221 2.3 13.9 1.0 CE1 B:HIS263 3.0 14.4 1.0 C6 B:S3C406 3.0 21.6 0.9 C5 B:S3C406 3.0 25.0 0.9 CG B:ASP120 3.1 15.3 1.0 CD2 B:HIS263 3.1 13.7 1.0 CB B:CYS221 3.4 11.3 1.0 OD1 B:ASP120 3.5 15.5 1.0 ZN B:ZN401 3.8 14.5 1.0 NH2 B:ARG121 4.0 16.0 1.0 ND1 B:HIS263 4.1 14.7 1.0 NE B:ARG121 4.2 15.2 1.0 O2 B:GOL407 4.2 49.4 1.0 CG B:HIS263 4.2 14.4 1.0 CE1 B:HIS116 4.2 13.1 1.0 O8 B:S3C406 4.2 21.0 0.9 CB B:ASP120 4.3 16.0 1.0 O B:HOH505 4.4 9.9 1.0 NE2 B:HIS116 4.4 13.1 1.0 CZ B:ARG121 4.5 16.2 1.0 C4 B:S3C406 4.5 29.3 0.9 CL2 B:S3C406 4.5 39.5 0.9 NE2 B:HIS196 4.6 11.4 1.0 CA B:CYS221 4.6 11.3 1.0 CE1 B:HIS196 4.8 12.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex 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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:16.2 occ:1.00 O2 B:FMT404 1.9 17.1 1.0 NE2 B:HIS170 2.1 14.2 1.0 O1 B:FMT405 2.1 14.9 1.0 C B:FMT404 2.7 16.9 1.0 O1 B:FMT404 2.9 16.5 1.0 CE1 B:HIS170 2.9 14.5 1.0 C B:FMT405 3.0 17.0 1.0 O2 B:FMT405 3.1 18.7 1.0 CD2 B:HIS170 3.2 13.4 1.0 CB B:ALA135 4.1 14.1 1.0 ND1 B:HIS170 4.1 13.9 1.0 CG B:HIS170 4.2 13.3 1.0 CA B:ALA135 4.7 13.8 1.0 O B:HOH543 4.8 20.5 1.0 CG2 B:THR169 4.9 17.7 1.0

J.Brem, S.S.Van Berkel, W.S.Aik, A.M.Rydzik, M.B.Avison, I.Pettinati, K.-D.Umland, A.Kawamura, J.Spencer, T.D.W.Claridge, M.A.Mcdonough, C.J.Schofield. Rhodanine Hydrolysis Leads to Potent Thioenolate Mediated Metallo-Beta-Lactamase Inhibition Nat.Chem. 2014.
ISSN: ESSN 1755-4349
DOI: 10.1038/NCHEM.2110