Zinc in PDB 6zyn: Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B

The structure of Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B, PDB code: 6zyn was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.59 / 1.40
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	67.48, 79.17, 78.07, 90, 90.5, 90
R / Rfree (%)	15 / 17.6

The binding sites of Zinc atom in the Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B (pdb code 6zyn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B, PDB code: 6zyn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.7 occ:1.00 OD2 A:ASP118 2.0 12.7 1.0 NE2 A:HIS240 2.1 12.6 1.0 S01 A:QT2304 2.3 17.2 1.0 SG A:CYS198 2.3 9.5 1.0 HH21 A:ARG119 3.0 16.6 1.0 CE1 A:HIS240 3.0 11.0 1.0 CG A:ASP118 3.0 8.6 1.0 CD2 A:HIS240 3.1 10.5 1.0 HE1 A:HIS240 3.2 13.2 1.0 H18 A:QT2304 3.3 20.7 1.0 HE A:ARG119 3.3 12.4 1.0 HD2 A:HIS240 3.3 12.6 1.0 H2 A:QT2304 3.3 22.9 1.0 C02 A:QT2304 3.4 19.1 1.0 HB3 A:CYS198 3.4 10.9 1.0 OD1 A:ASP118 3.4 12.4 1.0 CB A:CYS198 3.5 9.1 1.0 HE1 A:HIS114 3.6 13.0 1.0 S09 A:QT2304 3.7 21.4 1.0 ZN A:ZN302 3.7 10.3 1.0 NH2 A:ARG119 3.7 13.8 1.0 HB2 A:CYS198 3.9 10.9 1.0 H8 A:QT2304 4.0 26.8 1.0 NE A:ARG119 4.1 10.4 1.0 ND1 A:HIS240 4.1 8.0 1.0 H1 A:QT2304 4.2 22.9 1.0 C03 A:QT2304 4.2 21.1 1.0 CG A:HIS240 4.2 8.2 1.0 CB A:ASP118 4.3 14.4 1.0 HH22 A:ARG119 4.3 16.6 1.0 H14 A:QT2304 4.3 27.1 1.0 CE1 A:HIS114 4.3 10.8 1.0 CZ A:ARG119 4.3 8.4 1.0 HB2 A:ASP118 4.4 17.2 1.0 HB3 A:ASP118 4.5 17.2 1.0 NE2 A:HIS114 4.5 9.7 1.0 O A:HOH577 4.6 24.1 1.0 NE2 A:HIS179 4.6 8.1 1.0 H10 A:QT2304 4.6 26.8 1.0 HE1 A:HIS179 4.6 11.1 1.0 C11 A:QT2304 4.7 22.3 1.0 HA3 A:GLY239 4.7 7.3 1.0 O A:HOH529 4.7 16.7 1.0 HA A:CYS198 4.7 8.4 1.0 C10 A:QT2304 4.8 22.5 1.0 CA A:CYS198 4.8 7.0 1.0 HG2 A:ARG119 4.8 9.3 1.0 CE1 A:HIS179 4.8 9.2 1.0 C13 A:QT2304 4.8 22.5 1.0 HD1 A:HIS240 4.9 9.6 1.0 N17 A:QT2304 4.9 21.9 1.0

Zinc binding site 2 out of 6 in the Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.3 occ:1.00 ND1 A:HIS116 2.0 10.4 1.0 NE2 A:HIS179 2.1 8.1 1.0 NE2 A:HIS114 2.1 9.7 1.0 S01 A:QT2304 2.3 17.2 1.0 H18 A:QT2304 2.6 20.7 1.0 CE1 A:HIS116 2.9 8.7 1.0 HB2 A:HIS116 3.0 9.4 1.0 CE1 A:HIS114 3.0 10.8 1.0 CG A:HIS116 3.0 9.7 1.0 CD2 A:HIS179 3.0 7.2 1.0 CE1 A:HIS179 3.0 9.2 1.0 H1 A:QT2304 3.1 22.9 1.0 CD2 A:HIS114 3.1 7.5 1.0 HE1 A:HIS116 3.1 10.4 1.0 HE1 A:HIS114 3.2 13.0 1.0 HD2 A:HIS179 3.2 8.6 1.0 HE1 A:HIS179 3.2 11.1 1.0 C02 A:QT2304 3.3 19.1 1.0 HD2 A:HIS114 3.3 9.1 1.0 CB A:HIS116 3.4 7.9 1.0 H2 A:QT2304 3.4 22.9 1.0 HB3 A:HIS116 3.6 9.4 1.0 HB2 A:CYS198 3.6 10.9 1.0 ZN A:ZN301 3.7 13.7 1.0 HB3 A:CYS198 4.0 10.9 1.0 NE2 A:HIS116 4.1 12.3 1.0 OD1 A:ASP118 4.1 12.4 1.0 CB A:CYS198 4.1 9.1 1.0 ND1 A:HIS114 4.1 8.5 1.0 CD2 A:HIS116 4.1 12.4 1.0 ND1 A:HIS179 4.1 8.7 1.0 CG A:HIS179 4.2 7.4 1.0 CG A:HIS114 4.2 8.3 1.0 SG A:CYS198 4.3 9.5 1.0 H A:HIS116 4.6 9.1 1.0 H171 A:QT2304 4.6 26.3 1.0 OD1 A:ASN210 4.7 49.1 1.0 C03 A:QT2304 4.7 21.1 1.0 OD2 A:ASP118 4.7 12.7 1.0 CG A:ASP118 4.8 8.6 1.0 HG2 A:ARG119 4.8 9.3 1.0 HE A:ARG119 4.8 12.4 1.0 HE2 A:HIS116 4.8 14.8 1.0 CA A:HIS116 4.8 7.3 1.0 HD1 A:HIS114 4.9 10.2 1.0 HD1 A:HIS179 4.9 10.5 1.0 HB3 A:SER180 4.9 12.6 1.0 HD2 A:HIS116 5.0 14.9 1.0

Zinc binding site 3 out of 6 in the Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:14.7 occ:1.00 O1 A:FMT305 1.8 16.0 1.0 O1 A:FMT306 2.0 19.3 1.0 ND1 A:HIS251 2.1 14.8 1.0 HO2 A:FMT306 2.3 23.4 1.0 C A:FMT306 2.6 19.4 1.0 O2 A:FMT306 2.7 19.5 1.0 C A:FMT305 2.8 16.4 1.0 HO2 A:FMT305 2.9 20.0 1.0 CE1 A:HIS251 3.0 15.6 1.0 HA A:HIS251 3.1 11.2 1.0 HE1 A:HIS251 3.1 18.7 1.0 CG A:HIS251 3.1 10.9 1.0 HB2 A:HIS251 3.2 12.8 1.0 O2 A:FMT305 3.2 16.6 1.0 CB A:HIS251 3.5 10.7 1.0 HD22 A:ASN254 3.5 18.4 1.0 H A:FMT306 3.6 23.3 1.0 H A:FMT305 3.7 19.7 1.0 CA A:HIS251 3.7 9.3 1.0 HD22 A:LEU203 3.9 12.1 1.0 NE2 A:HIS251 4.1 11.8 1.0 CD2 A:HIS251 4.2 9.8 1.0 HB2 A:ASN254 4.3 14.6 1.0 ND2 A:ASN254 4.4 15.3 1.0 HB3 A:HIS251 4.4 12.8 1.0 O A:HIS251 4.6 8.4 1.0 C A:HIS251 4.6 8.5 1.0 CD2 A:LEU203 4.7 10.1 1.0 HD23 A:LEU203 4.7 12.1 1.0 HG23 A:VAL255 4.7 13.9 1.0 HD21 A:ASN254 4.8 18.4 1.0 HA A:LEU203 4.8 16.5 1.0 N A:HIS251 4.8 9.5 1.0 HE2 A:HIS251 4.9 14.1 1.0

Zinc binding site 4 out of 6 in the Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:14.5 occ:1.00 H18 B:QT2304 1.9 22.3 1.0 OD2 B:ASP118 2.0 15.7 1.0 NE2 B:HIS240 2.1 11.1 1.0 S01 B:QT2304 2.3 18.6 1.0 SG B:CYS198 2.4 10.2 1.0 CG B:ASP118 3.0 9.6 1.0 HH21 B:ARG119 3.0 22.4 1.0 CE1 B:HIS240 3.0 9.0 1.0 CD2 B:HIS240 3.1 8.7 1.0 HE1 B:HIS240 3.2 10.8 1.0 HE B:ARG119 3.3 12.3 1.0 HD2 B:HIS240 3.3 10.4 1.0 H1 B:QT2304 3.3 24.6 1.0 HB3 B:CYS198 3.4 8.2 1.0 C02 B:QT2304 3.4 20.5 1.0 OD1 B:ASP118 3.4 11.5 1.0 CB B:CYS198 3.5 6.9 1.0 S09 B:QT2304 3.6 22.6 1.0 HE1 B:HIS114 3.6 10.7 1.0 ZN B:ZN302 3.7 9.4 1.0 NH2 B:ARG119 3.8 18.7 1.0 HB2 B:CYS198 3.9 8.2 1.0 H9 B:QT2304 3.9 27.7 1.0 NE B:ARG119 4.0 10.3 1.0 ND1 B:HIS240 4.2 9.7 1.0 C03 B:QT2304 4.2 22.5 1.0 H2 B:QT2304 4.2 24.6 1.0 CG B:HIS240 4.2 8.3 1.0 H14 B:QT2304 4.2 28.3 1.0 CB B:ASP118 4.3 10.3 1.0 CE1 B:HIS114 4.3 8.9 1.0 CZ B:ARG119 4.3 9.1 1.0 HH22 B:ARG119 4.3 22.4 1.0 HB2 B:ASP118 4.4 12.4 1.0 NE2 B:HIS114 4.4 8.0 1.0 HB3 B:ASP118 4.5 12.4 1.0 C11 B:QT2304 4.6 23.1 1.0 HA3 B:GLY239 4.6 10.1 1.0 C10 B:QT2304 4.6 23.2 1.0 H10 B:QT2304 4.6 27.7 1.0 HE1 B:HIS179 4.7 10.8 1.0 NE2 B:HIS179 4.7 8.5 1.0 HA B:CYS198 4.7 8.0 1.0 O B:HOH517 4.7 12.8 1.0 HG2 B:ARG119 4.8 11.3 1.0 CA B:CYS198 4.8 6.7 1.0 C13 B:QT2304 4.8 23.6 1.0 O B:HOH479 4.8 42.3 1.0 CE1 B:HIS179 4.8 9.0 1.0 HD1 B:HIS240 4.9 11.7 1.0 HB2 B:HIS116 5.0 8.9 1.0

Zinc binding site 5 out of 6 in the Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:9.4 occ:1.00 H18 B:QT2304 1.9 22.3 1.0 ND1 B:HIS116 2.0 9.9 1.0 NE2 B:HIS114 2.0 8.0 1.0 NE2 B:HIS179 2.1 8.5 1.0 S01 B:QT2304 2.3 18.6 1.0 CE1 B:HIS116 2.9 11.7 1.0 H2 B:QT2304 3.0 24.6 1.0 HB2 B:HIS116 3.0 8.9 1.0 CE1 B:HIS179 3.0 9.0 1.0 CD2 B:HIS114 3.0 7.2 1.0 CE1 B:HIS114 3.0 8.9 1.0 CG B:HIS116 3.0 8.9 1.0 CD2 B:HIS179 3.1 6.9 1.0 HE1 B:HIS116 3.1 14.1 1.0 C02 B:QT2304 3.1 20.5 1.0 HE1 B:HIS179 3.2 10.8 1.0 HD2 B:HIS114 3.2 8.6 1.0 HE1 B:HIS114 3.2 10.7 1.0 H1 B:QT2304 3.2 24.6 1.0 HD2 B:HIS179 3.3 8.2 1.0 CB B:HIS116 3.4 7.4 1.0 HB2 B:CYS198 3.6 8.2 1.0 HB3 B:HIS116 3.7 8.9 1.0 ZN B:ZN301 3.7 14.5 1.0 HB3 B:CYS198 3.9 8.2 1.0 OD1 B:ASP118 4.0 11.5 1.0 NE2 B:HIS116 4.1 14.0 1.0 ND1 B:HIS114 4.1 9.2 1.0 CB B:CYS198 4.1 6.9 1.0 ND1 B:HIS179 4.1 11.6 1.0 CG B:HIS114 4.1 8.1 1.0 CD2 B:HIS116 4.1 10.2 1.0 CG B:HIS179 4.2 7.0 1.0 SG B:CYS198 4.3 10.2 1.0 H B:HIS116 4.5 8.9 1.0 OD2 B:ASP118 4.6 15.7 1.0 C03 B:QT2304 4.7 22.5 1.0 H171 B:QT2304 4.7 27.8 1.0 HG2 B:ARG119 4.8 11.3 1.0 CG B:ASP118 4.8 9.6 1.0 H14 B:QT2304 4.8 28.3 1.0 HB3 B:SER180 4.8 9.6 1.0 HE2 B:HIS116 4.8 16.8 1.0 O B:HOH429 4.9 39.5 1.0 CA B:HIS116 4.9 7.1 1.0 HD1 B:HIS114 4.9 11.0 1.0 HE B:ARG119 4.9 12.3 1.0 HD1 B:HIS179 4.9 13.9 1.0 O B:HOH583 5.0 48.6 1.0

Zinc binding site 6 out of 6 in the Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Vim-2 with 2-Mercaptomethyl-Thiazolidine L-Anti-1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:15.6 occ:1.00 HO2 B:FMT305 1.4 18.9 1.0 O2 B:FMT305 2.0 15.7 1.0 O1 B:FMT306 2.0 18.0 1.0 ND1 B:HIS251 2.1 13.1 1.0 C B:FMT305 2.6 16.1 1.0 HO2 B:FMT306 2.7 22.0 1.0 O1 B:FMT305 2.7 16.3 1.0 C B:FMT306 2.8 18.2 1.0 CE1 B:HIS251 3.0 10.9 1.0 HA B:HIS251 3.1 10.4 1.0 HE1 B:HIS251 3.1 13.1 1.0 HB2 B:HIS251 3.1 11.2 1.0 O2 B:FMT306 3.1 18.4 1.0 CG B:HIS251 3.2 9.7 1.0 CB B:HIS251 3.5 9.3 1.0 HD22 B:ASN254 3.5 15.5 1.0 HD22 B:LEU203 3.6 19.7 1.0 H B:FMT305 3.7 19.4 1.0 CA B:HIS251 3.8 8.7 1.0 H B:FMT306 3.8 21.9 1.0 NE2 B:HIS251 4.1 10.2 1.0 CD2 B:HIS251 4.2 9.5 1.0 ND2 B:ASN254 4.4 12.9 1.0 HB2 B:ASN254 4.4 12.1 1.0 HB3 B:HIS251 4.4 11.2 1.0 CD2 B:LEU203 4.5 16.4 1.0 HD23 B:LEU203 4.5 19.7 1.0 HA B:LEU203 4.6 13.5 1.0 O B:HIS251 4.6 9.5 1.0 C B:HIS251 4.7 8.7 1.0 HD21 B:ASN254 4.7 15.5 1.0 HG23 B:VAL255 4.8 14.0 1.0 N B:HIS251 4.8 8.9 1.0 HD21 B:LEU203 4.8 19.7 1.0 HE2 B:HIS251 4.9 12.2 1.0 HG22 B:THR206 5.0 25.4 1.0 HB3 B:LEU203 5.0 11.6 1.0

M.Rossi, V.Martinez, P.Hinchliffe, M.F.Mojica, V.Castillo, D.M.Moreno, R.Smith, B.Spellberg, G.L.Drusano, C.Banchio, R.A.Bonomo, J.Spencer, A.J.Vila, G.Mahler. 2-Mercaptomethyl-Thiazolidines Use Conserved Aromatic-S Interactions to Achieve Broad-Range Inhibition of Metallo-Beta-Lactamases Chem Sci 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC05172A