Zinc in PDB 6dd0: Crystal Structure of Vim-2 Complexed with Compound 8

The structure of Crystal Structure of Vim-2 Complexed with Compound 8, PDB code: 6dd0 was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.39 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.630, 79.130, 67.790, 90.00, 130.50, 90.00
R / Rfree (%)	18.3 / 22.5

The structure of Crystal Structure of Vim-2 Complexed with Compound 8 also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Complexed with Compound 8 (pdb code 6dd0). 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 Complexed with Compound 8, PDB code: 6dd0:
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 Complexed with Compound 8


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 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:10.4 occ:1.00 ND1 A:HIS118 2.0 8.7 1.0 NE2 A:HIS196 2.0 8.3 1.0 NE2 A:HIS116 2.1 7.7 1.0 O07 A:P9T403 2.2 13.3 0.8 CG A:HIS118 3.0 6.0 1.0 CE1 A:HIS196 3.0 7.8 1.0 CE1 A:HIS118 3.0 10.8 1.0 CE1 A:HIS116 3.1 8.3 1.0 CD2 A:HIS196 3.1 6.3 1.0 CD2 A:HIS116 3.1 5.2 1.0 CB A:HIS118 3.3 8.5 1.0 P06 A:P9T403 3.5 19.3 0.8 O09 A:P9T403 3.9 18.3 0.8 OD1 A:ASP120 4.0 11.1 1.0 O08 A:P9T403 4.1 14.9 0.8 CD2 A:HIS118 4.1 10.9 1.0 NE2 A:HIS118 4.1 11.6 1.0 ND1 A:HIS196 4.1 5.7 1.0 ND1 A:HIS116 4.2 7.3 1.0 CG A:HIS196 4.2 5.6 1.0 CG A:HIS116 4.2 7.6 1.0 ZN A:ZN402 4.4 9.9 1.0 O A:HOH705 4.4 34.5 1.0 CB A:CYS221 4.4 7.1 1.0 O A:HOH664 4.7 21.4 1.0 SG A:CYS221 4.7 9.4 1.0 CA A:HIS118 4.7 6.1 1.0 CG A:ASP120 4.8 10.6 1.0 OD2 A:ASP120 4.9 10.7 1.0 C05 A:P9T403 4.9 20.1 0.8 O A:HOH574 5.0 14.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 8


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 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:9.9 occ:0.98 O08 A:P9T403 1.9 14.9 0.8 OD2 A:ASP120 2.0 10.7 1.0 NE2 A:HIS263 2.0 8.7 1.0 SG A:CYS221 2.2 9.4 1.0 P06 A:P9T403 2.9 19.3 0.8 CE1 A:HIS263 3.0 7.9 1.0 CD2 A:HIS263 3.0 7.0 1.0 CG A:ASP120 3.1 10.6 1.0 O07 A:P9T403 3.1 13.3 0.8 CB A:CYS221 3.4 7.1 1.0 OD1 A:ASP120 3.5 11.1 1.0 C05 A:P9T403 3.6 20.1 0.8 NH2 A:ARG121 3.7 17.7 1.0 O A:HOH511 4.0 17.9 1.0 ND1 A:HIS263 4.1 5.8 1.0 NE A:ARG121 4.2 9.0 1.0 CG A:HIS263 4.2 5.2 1.0 O09 A:P9T403 4.2 18.3 0.8 C03 A:P9T403 4.2 27.7 0.8 CB A:ASP120 4.4 9.3 1.0 O A:HOH610 4.4 10.4 1.0 ZN A:ZN401 4.4 10.4 1.0 CZ A:ARG121 4.4 12.6 1.0 C04 A:P9T403 4.4 23.8 0.8 CA A:CYS221 4.5 7.5 1.0 CE1 A:HIS116 4.5 8.3 1.0 NE2 A:HIS196 4.8 8.3 1.0 CE1 A:HIS196 4.8 7.8 1.0 NE2 A:HIS116 4.9 7.7 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 8


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 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:10.6 occ:1.00 OXT A:ACT405 1.9 12.1 1.0 O A:ACT404 1.9 12.0 1.0 ND1 A:HIS285 2.1 8.6 1.0 C A:ACT404 2.4 10.4 1.0 OXT A:ACT404 2.5 11.4 1.0 C A:ACT405 2.8 10.2 1.0 CE1 A:HIS285 2.9 8.2 1.0 CG A:HIS285 3.1 7.4 1.0 O A:ACT405 3.3 9.5 1.0 CB A:HIS285 3.5 7.0 1.0 CA A:HIS285 3.8 7.3 1.0 CH3 A:ACT404 3.9 12.9 1.0 NE2 A:HIS285 4.1 7.3 1.0 CH3 A:ACT405 4.1 9.7 1.0 CD2 A:HIS285 4.2 6.9 1.0 ND2 A:ASN288 4.4 10.3 1.0 O A:HIS285 4.6 7.4 1.0 C A:HIS285 4.7 8.3 1.0 CD2 A:LEU226 4.7 8.8 1.0 N A:HIS285 4.9 8.5 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 8


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 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:11.5 occ:1.00 ND1 B:HIS118 2.0 8.5 1.0 NE2 B:HIS196 2.0 5.5 1.0 O09 B:P9T403 2.0 12.8 0.8 NE2 B:HIS116 2.1 8.2 1.0 CD2 B:HIS196 3.0 7.1 1.0 CE1 B:HIS116 3.0 8.2 1.0 CG B:HIS118 3.0 6.8 1.0 CE1 B:HIS118 3.0 7.2 1.0 CE1 B:HIS196 3.1 4.9 1.0 CD2 B:HIS116 3.1 6.9 1.0 P06 B:P9T403 3.2 16.7 0.8 CB B:HIS118 3.3 7.9 1.0 O08 B:P9T403 3.6 10.7 0.8 O07 B:P9T403 3.6 18.1 0.8 OD1 B:ASP120 4.0 11.7 1.0 ND1 B:HIS116 4.1 4.9 1.0 NE2 B:HIS118 4.1 8.8 1.0 CG B:HIS196 4.1 5.0 1.0 CD2 B:HIS118 4.1 7.8 1.0 ND1 B:HIS196 4.1 7.2 1.0 CG B:HIS116 4.2 6.1 1.0 ZN B:ZN402 4.4 8.8 0.9 O B:HOH709 4.4 31.7 1.0 CB B:CYS221 4.5 8.6 1.0 O B:HOH674 4.5 18.3 1.0 SG B:CYS221 4.7 7.7 1.0 CA B:HIS118 4.8 8.1 1.0 CG B:ASP120 4.8 10.2 1.0 C05 B:P9T403 4.8 20.2 0.8 OD2 B:ASP120 4.8 8.8 1.0 O B:HOH665 4.9 16.3 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 8


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 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:8.8 occ:0.95 O08 B:P9T403 1.8 10.7 0.8 NE2 B:HIS263 2.0 9.1 1.0 OD2 B:ASP120 2.0 8.8 1.0 SG B:CYS221 2.3 7.7 1.0 P06 B:P9T403 2.9 16.7 0.8 CD2 B:HIS263 2.9 9.2 1.0 CE1 B:HIS263 3.0 8.4 1.0 CG B:ASP120 3.1 10.2 1.0 O09 B:P9T403 3.3 12.8 0.8 CB B:CYS221 3.4 8.6 1.0 C05 B:P9T403 3.5 20.2 0.8 OD1 B:ASP120 3.6 11.7 1.0 NH2 B:ARG121 3.7 12.9 1.0 NE B:ARG121 4.1 10.6 1.0 ND1 B:HIS263 4.1 8.5 1.0 C03 B:P9T403 4.1 20.9 0.8 CG B:HIS263 4.1 7.5 1.0 O07 B:P9T403 4.2 18.1 0.8 CZ B:ARG121 4.3 9.3 1.0 C04 B:P9T403 4.4 21.1 0.8 ZN B:ZN401 4.4 11.5 1.0 CB B:ASP120 4.4 12.0 1.0 CE1 B:HIS116 4.5 8.2 1.0 CA B:CYS221 4.5 5.9 1.0 O B:HOH613 4.6 14.0 1.0 NE2 B:HIS196 4.8 5.5 1.0 CE1 B:HIS196 4.9 4.9 1.0 NE2 B:HIS116 4.9 8.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 8


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 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:9.3 occ:1.00 OXT B:ACT405 2.0 6.5 1.0 O B:ACT404 2.0 10.2 1.0 ND1 B:HIS285 2.1 6.9 1.0 C B:ACT405 2.6 9.2 1.0 O B:ACT405 2.7 10.9 1.0 C B:ACT404 2.9 11.2 1.0 CE1 B:HIS285 3.0 7.7 1.0 CG B:HIS285 3.1 4.8 1.0 OXT B:ACT404 3.2 11.5 1.0 CB B:HIS285 3.5 5.9 1.0 CA B:HIS285 3.8 7.0 1.0 CH3 B:ACT405 4.0 12.4 1.0 NE2 B:HIS285 4.2 8.3 1.0 CD2 B:HIS285 4.2 7.3 1.0 CH3 B:ACT404 4.3 10.4 1.0 ND2 B:ASN288 4.3 7.8 1.0 CD2 B:LEU226 4.4 10.1 1.0 O B:HIS285 4.6 10.1 1.0 C B:HIS285 4.7 7.4 1.0 N B:HIS285 4.9 6.1 1.0

O.A.Pemberton, P.Jaishankar, A.Akhtar, J.L.Adams, L.N.Shaw, A.R.Renslo, Y.Chen. Heteroaryl Phosphonates As Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J.Med.Chem. V. 62 8480 2019.
ISSN: ISSN 0022-2623
PubMed: 31483651
DOI: 10.1021/ACS.JMEDCHEM.9B00728