Zinc in PDB 6zyq: Structure of Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B

All present enzymatic activity of Structure of Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B:
3.5.2.6;

The structure of Structure of Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B, PDB code: 6zyq 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)	38.72 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.18, 73.84, 77.44, 90, 90, 90
R / Rfree (%)	17.8 / 19.8

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

Zinc binding site 1 out of 4 in the Structure of Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-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 Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.6 occ:1.00 OD2 A:ASP124 1.9 23.8 1.0 NE2 A:HIS250 2.0 25.4 1.0 SG A:CYS208 2.3 24.4 1.0 S01 A:QST305 2.3 25.3 1.0 CG A:ASP124 2.9 27.5 1.0 CE1 A:HIS250 3.0 26.2 1.0 CD2 A:HIS250 3.1 25.1 1.0 OD1 A:ASP124 3.3 24.6 1.0 C02 A:QST305 3.3 27.2 1.0 CB A:CYS208 3.5 20.7 1.0 ZN A:ZN302 3.7 24.4 1.0 S09 A:QST305 4.0 33.1 1.0 ND1 A:HIS250 4.1 24.8 1.0 CB A:SER249 4.1 23.1 1.0 CG A:HIS250 4.2 23.2 1.0 C03 A:QST305 4.2 30.3 1.0 CB A:ASP124 4.3 21.6 1.0 CE1 A:HIS120 4.5 23.1 1.0 NE2 A:HIS120 4.5 21.5 1.0 C12 A:QST305 4.5 34.0 1.0 OG A:SER249 4.6 22.2 1.0 NE2 A:HIS189 4.6 23.5 1.0 CA A:CYS208 4.7 18.1 1.0 CE A:LYS125 4.7 28.0 1.0 N17 A:QST305 4.8 28.6 1.0 CE1 A:HIS189 4.9 27.6 1.0 OG A:SER75 4.9 25.4 1.0 CD A:LYS125 4.9 28.5 1.0 C10 A:QST305 4.9 35.1 1.0 CG A:LYS125 5.0 26.5 1.0

Zinc binding site 2 out of 4 in the Structure of Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-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 Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:24.4 occ:1.00 NE2 A:HIS189 2.0 23.5 1.0 NE2 A:HIS120 2.1 21.5 1.0 ND1 A:HIS122 2.1 21.3 1.0 S01 A:QST305 2.2 25.3 1.0 CD2 A:HIS189 3.0 23.4 1.0 CD2 A:HIS120 3.0 23.3 1.0 CE1 A:HIS122 3.0 27.6 1.0 CG A:HIS122 3.1 22.2 1.0 CE1 A:HIS120 3.1 23.1 1.0 CE1 A:HIS189 3.1 27.6 1.0 CB A:HIS122 3.4 22.0 1.0 C02 A:QST305 3.4 27.2 1.0 ZN A:ZN301 3.7 25.6 1.0 SG A:CYS208 4.0 24.4 1.0 CB A:CYS208 4.1 20.7 1.0 CG A:HIS189 4.1 20.3 1.0 ND1 A:HIS120 4.1 23.1 1.0 CG A:HIS120 4.1 18.3 1.0 ND1 A:HIS189 4.2 24.8 1.0 NE2 A:HIS122 4.2 25.1 1.0 CD2 A:HIS122 4.2 24.5 1.0 OD1 A:ASP124 4.2 24.6 1.0 CG2 A:THR190 4.5 22.2 1.0 C03 A:QST305 4.6 30.3 1.0 N17 A:QST305 4.6 28.6 1.0 OD2 A:ASP124 4.9 23.8 1.0 CA A:HIS122 4.9 18.3 1.0 CG A:ASP124 5.0 27.5 1.0

Zinc binding site 3 out of 4 in the Structure of Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-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 Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.6 occ:1.00 ND1 B:HIS122 1.9 19.5 1.0 NE2 B:HIS120 2.0 28.7 1.0 NE2 B:HIS189 2.1 34.4 1.0 S01 B:QST303 2.3 25.1 0.8 CE1 B:HIS122 2.7 29.8 1.0 CG B:HIS122 3.0 28.8 1.0 CD2 B:HIS189 3.0 31.8 1.0 CD2 B:HIS120 3.0 27.4 1.0 CE1 B:HIS120 3.0 31.0 1.0 CE1 B:HIS189 3.1 34.0 1.0 C02 B:QST303 3.4 30.4 0.8 CB B:HIS122 3.4 33.5 1.0 ZN B:ZN302 3.8 31.1 1.0 NE2 B:HIS122 3.9 27.3 1.0 CD2 B:HIS122 4.0 29.3 1.0 SG B:CYS208 4.0 27.6 1.0 ND1 B:HIS120 4.1 27.8 1.0 CG B:HIS120 4.1 22.9 1.0 CG B:HIS189 4.1 26.6 1.0 CB B:CYS208 4.2 20.4 1.0 ND1 B:HIS189 4.2 31.8 1.0 OD1 B:ASP124 4.3 30.1 1.0 CG2 B:THR190 4.5 26.6 1.0 C03 B:QST303 4.6 37.6 0.8 N17 B:QST303 4.7 35.2 0.8 CA B:HIS122 4.9 30.1 1.0 OD2 B:ASP124 5.0 39.0 1.0

Zinc binding site 4 out of 4 in the Structure of Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-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 Ndm-1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:31.1 occ:1.00 NE2 B:HIS250 2.0 31.1 1.0 OD2 B:ASP124 2.1 39.0 1.0 SG B:CYS208 2.2 27.6 1.0 S01 B:QST303 2.3 25.1 0.8 CE1 B:HIS250 3.0 28.1 1.0 CG B:ASP124 3.0 31.7 1.0 CD2 B:HIS250 3.0 28.1 1.0 OD1 B:ASP124 3.3 30.1 1.0 CB B:CYS208 3.4 20.4 1.0 C02 B:QST303 3.5 30.4 0.8 ZN B:ZN301 3.8 30.6 1.0 S09 B:QST303 4.0 35.9 0.8 CB B:SER249 4.1 28.0 1.0 ND1 B:HIS250 4.1 29.7 1.0 CG B:HIS250 4.2 31.3 1.0 C03 B:QST303 4.3 37.6 0.8 CB B:ASP124 4.4 29.2 1.0 CE1 B:HIS120 4.4 31.0 1.0 OG B:SER249 4.4 29.1 1.0 NE2 B:HIS120 4.5 28.7 1.0 NE2 B:HIS189 4.6 34.4 1.0 CA B:CYS208 4.6 20.9 1.0 CE B:LYS125 4.6 28.9 1.0 C12 B:QST303 4.6 31.6 0.8 CD B:LYS125 4.8 30.3 1.0 CE1 B:HIS189 4.8 34.0 1.0 O B:HOH432 4.9 53.4 1.0 CG B:LYS125 4.9 28.5 1.0 N17 B:QST303 4.9 35.2 0.8

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