Zinc in PDB 6dd1: Crystal Structure of Vim-2 Complexed with Compound 14

The structure of Crystal Structure of Vim-2 Complexed with Compound 14, PDB code: 6dd1 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 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.480, 79.200, 77.880, 90.00, 138.63, 90.00
R / Rfree (%)	15.2 / 21.6

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Complexed with Compound 14 (pdb code 6dd1). 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 14, PDB code: 6dd1:
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 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:9.7 occ:1.00 ND1 A:HIS118 2.0 10.1 1.0 NE2 A:HIS196 2.1 7.1 1.0 NE2 A:HIS116 2.1 9.8 1.0 O04 A:M3Q403 2.2 8.3 1.0 O01 A:M3Q403 2.9 10.6 1.0 P02 A:M3Q403 2.9 13.8 1.0 CG A:HIS118 2.9 11.1 1.0 CD2 A:HIS196 3.0 7.5 1.0 CE1 A:HIS118 3.0 11.9 1.0 CE1 A:HIS116 3.0 10.1 1.0 CD2 A:HIS116 3.1 8.0 1.0 CE1 A:HIS196 3.1 8.2 1.0 CB A:HIS118 3.3 11.2 1.0 O03 A:M3Q403 3.9 19.2 1.0 OD1 A:ASP120 4.0 16.0 1.0 NE2 A:HIS118 4.1 14.5 1.0 CD2 A:HIS118 4.1 10.4 1.0 ND1 A:HIS116 4.1 8.8 1.0 CG A:HIS196 4.2 5.2 1.0 ND1 A:HIS196 4.2 7.1 1.0 CG A:HIS116 4.2 10.7 1.0 SG A:CYS221 4.3 9.6 1.0 ZN A:ZN402 4.3 17.6 1.0 C05 A:M3Q403 4.4 13.3 1.0 CB A:CYS221 4.4 7.7 1.0 ND2 A:ASN233 4.5 16.1 1.0 CA A:HIS118 4.7 10.1 1.0 OD2 A:ASP120 4.7 17.9 1.0 CG A:ASP120 4.8 13.2 1.0 O A:HOH646 4.8 26.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:17.6 occ:1.00 NE2 A:HIS263 2.0 14.0 1.0 O03 A:M3Q403 2.1 19.2 1.0 SG A:CYS221 2.3 9.6 1.0 OD2 A:ASP120 2.5 17.9 1.0 O01 A:M3Q404 2.5 17.7 0.9 P02 A:M3Q403 3.0 13.8 1.0 CD2 A:HIS263 3.0 8.8 1.0 CE1 A:HIS263 3.0 12.8 1.0 O04 A:M3Q403 3.2 8.3 1.0 CB A:CYS221 3.3 7.7 1.0 P02 A:M3Q404 3.4 14.7 0.9 CG A:ASP120 3.6 13.2 1.0 O01 A:M3Q403 3.8 10.6 1.0 C05 A:M3Q404 3.9 15.0 0.9 O03 A:M3Q404 4.0 12.3 0.9 NH2 A:ARG121 4.1 14.9 1.0 O A:HOH557 4.1 11.6 1.0 OD1 A:ASP120 4.1 16.0 1.0 ND1 A:HIS263 4.1 6.5 1.0 CG A:HIS263 4.2 8.2 1.0 C05 A:M3Q403 4.3 13.3 1.0 ZN A:ZN401 4.3 9.7 1.0 CA A:CYS221 4.4 5.5 1.0 CE1 A:HIS196 4.4 8.2 1.0 NE2 A:HIS196 4.5 7.1 1.0 O04 A:M3Q404 4.5 20.9 0.9 C07 A:M3Q403 4.7 24.9 1.0 NE A:ARG121 4.8 12.1 1.0 C06 A:M3Q403 4.9 20.8 1.0 CZ A:ARG121 4.9 14.4 1.0 CB A:ASP120 4.9 12.3 1.0 CE1 A:HIS116 5.0 10.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:15.0 occ:1.00 OXT A:ACT405 1.9 12.9 1.0 O A:ACT406 1.9 18.4 1.0 NE2 A:HIS170 2.0 11.1 1.0 C A:ACT406 2.5 21.1 1.0 OXT A:ACT406 2.5 20.4 1.0 CE1 A:HIS170 2.8 11.2 1.0 C A:ACT405 2.9 13.6 1.0 CD2 A:HIS170 3.2 12.5 1.0 O A:ACT405 3.4 15.1 1.0 CH3 A:ACT406 3.9 23.6 1.0 ND1 A:HIS170 4.0 10.8 1.0 CH3 A:ACT405 4.2 11.9 1.0 CB A:ALA135 4.2 13.2 1.0 CG A:HIS170 4.2 11.2 1.0 CA A:ALA135 4.8 9.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:10.4 occ:1.00 ND1 B:HIS118 2.0 10.8 1.0 O01 B:M3Q403 2.0 13.3 1.0 NE2 B:HIS196 2.0 11.2 1.0 NE2 B:HIS116 2.1 9.8 1.0 P02 B:M3Q403 2.9 15.0 1.0 CG B:HIS118 2.9 10.4 1.0 O04 B:M3Q403 3.0 12.5 1.0 CD2 B:HIS196 3.0 10.6 1.0 CE1 B:HIS118 3.0 14.4 1.0 CE1 B:HIS116 3.0 10.4 1.0 CE1 B:HIS196 3.0 10.4 1.0 CD2 B:HIS116 3.1 9.3 1.0 CB B:HIS118 3.2 10.0 1.0 OD1 B:ASP120 3.9 14.2 1.0 O03 B:M3Q403 4.0 15.1 1.0 CD2 B:HIS118 4.1 11.0 1.0 NE2 B:HIS118 4.1 14.0 1.0 ND1 B:HIS196 4.1 11.6 1.0 ND1 B:HIS116 4.1 10.3 1.0 CG B:HIS196 4.1 10.0 1.0 CG B:HIS116 4.2 8.9 1.0 SG B:CYS221 4.3 11.8 1.0 C05 B:M3Q403 4.3 17.2 1.0 ZN B:ZN402 4.3 17.9 1.0 CB B:CYS221 4.4 9.7 1.0 OD2 B:ASP120 4.6 17.3 1.0 CA B:HIS118 4.7 10.0 1.0 ND2 B:ASN233 4.7 18.3 1.0 CG B:ASP120 4.7 13.0 1.0 O B:HOH624 4.8 21.1 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:17.9 occ:1.00 NE2 B:HIS263 2.0 10.0 1.0 O03 B:M3Q403 2.1 15.1 1.0 SG B:CYS221 2.2 11.8 1.0 OD2 B:ASP120 2.4 17.3 1.0 O03 B:M3Q404 2.6 17.3 0.9 CD2 B:HIS263 3.0 11.5 1.0 CE1 B:HIS263 3.0 8.9 1.0 P02 B:M3Q403 3.0 15.0 1.0 CB B:CYS221 3.4 9.7 1.0 O01 B:M3Q403 3.4 13.3 1.0 P02 B:M3Q404 3.6 14.4 0.9 CG B:ASP120 3.6 13.0 1.0 O04 B:M3Q403 3.8 12.5 1.0 C05 B:M3Q404 3.8 15.6 0.9 NH2 B:ARG121 4.0 13.3 1.0 O01 B:M3Q404 4.1 15.4 0.9 O B:HOH529 4.1 8.3 1.0 ND1 B:HIS263 4.1 8.6 1.0 CG B:HIS263 4.1 8.3 1.0 OD1 B:ASP120 4.2 14.2 1.0 ZN B:ZN401 4.3 10.4 1.0 CE1 B:HIS196 4.4 10.4 1.0 CA B:CYS221 4.4 8.1 1.0 C05 B:M3Q403 4.4 17.2 1.0 NE2 B:HIS196 4.6 11.2 1.0 C07 B:M3Q403 4.7 20.7 1.0 O04 B:M3Q404 4.7 14.8 0.9 NE B:ARG121 4.8 9.8 1.0 CZ B:ARG121 4.9 12.5 1.0 CB B:ASP120 4.9 12.7 1.0 C06 B:M3Q403 4.9 19.4 1.0 CE1 B:HIS116 4.9 10.4 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Complexed with Compound 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn407 b:13.2 occ:1.00 OXT B:ACT406 1.9 11.5 1.0 ND1 B:HIS285 2.0 11.3 1.0 O B:ACT405 2.1 12.8 1.0 C B:ACT405 2.6 15.7 1.0 OXT B:ACT405 2.7 16.5 1.0 C B:ACT406 2.8 11.1 1.0 CE1 B:HIS285 3.0 12.1 1.0 CG B:HIS285 3.1 9.8 1.0 O B:ACT406 3.2 14.1 1.0 CB B:HIS285 3.4 7.6 1.0 CA B:HIS285 3.8 9.3 1.0 CH3 B:ACT405 4.1 13.3 1.0 NE2 B:HIS285 4.1 11.7 1.0 CD2 B:HIS285 4.2 12.4 1.0 CH3 B:ACT406 4.2 9.9 1.0 ND2 B:ASN288 4.3 8.7 1.0 CD2 B:LEU226 4.5 10.4 1.0 O B:HIS285 4.6 9.0 1.0 C B:HIS285 4.6 11.5 1.0 N B:HIS285 4.9 9.0 1.0 CB B:ASN288 5.0 7.8 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