Zinc in PDB 6o5t: Crystal Structure of Vim-2 with Compound 16

The structure of Crystal Structure of Vim-2 with Compound 16, PDB code: 6o5t was solved by A.Akhtar, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.59 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.389, 79.185, 67.501, 90.00, 130.60, 90.00
R / Rfree (%)	17.9 / 23.6

The structure of Crystal Structure of Vim-2 with Compound 16 also contains other interesting chemical elements:

Bromine

(Br)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Vim-2 with Compound 16 (pdb code 6o5t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Vim-2 with Compound 16, PDB code: 6o5t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Vim-2 with Compound 16


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 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:22.7 occ:1.00 ND1 A:HIS116 1.9 19.1 1.0 NE2 A:HIS179 2.0 16.6 1.0 O A:HOH601 2.1 22.7 1.0 NE2 A:HIS114 2.2 14.6 1.0 CG A:HIS116 2.9 17.8 1.0 CE1 A:HIS116 3.0 22.9 1.0 CD2 A:HIS179 3.0 13.0 1.0 CE1 A:HIS179 3.1 17.2 1.0 CE1 A:HIS114 3.1 11.4 1.0 CD2 A:HIS114 3.2 19.3 1.0 CB A:HIS116 3.2 17.9 1.0 O13 A:L8J503 3.6 27.9 0.8 CD2 A:HIS116 4.0 17.7 1.0 NE2 A:HIS116 4.0 24.3 1.0 OD1 A:ASP118 4.1 22.7 1.0 CG A:HIS179 4.1 15.9 1.0 ND1 A:HIS179 4.2 21.0 1.0 ND1 A:HIS114 4.2 17.6 1.0 CG A:HIS114 4.3 15.9 1.0 O14 A:L8J503 4.4 29.9 0.8 ZN A:ZN502 4.4 22.9 1.0 CB A:CYS198 4.5 16.7 1.0 SG A:CYS198 4.6 16.7 1.0 CA A:HIS116 4.6 19.9 1.0 P11 A:L8J503 4.7 39.9 0.8 OD2 A:ASP118 4.8 24.8 1.0 CG A:ASP118 4.8 19.9 1.0 N A:HIS116 4.9 22.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Vim-2 with Compound 16


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 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:22.9 occ:1.00 OD2 A:ASP118 2.0 24.8 1.0 SG A:CYS198 2.1 16.7 1.0 O13 A:L8J503 2.1 27.9 0.8 NE2 A:HIS240 2.2 24.9 1.0 CE1 A:HIS240 3.1 28.1 1.0 P11 A:L8J503 3.2 39.9 0.8 O12 A:L8J503 3.2 45.6 0.8 CG A:ASP118 3.2 19.9 1.0 CD2 A:HIS240 3.2 20.4 1.0 CB A:CYS198 3.2 16.7 1.0 O A:HOH601 3.3 22.7 1.0 NH2 A:ARG119 3.5 31.1 1.0 OD1 A:ASP118 3.8 22.7 1.0 NE A:ARG119 4.1 20.8 1.0 C10 A:L8J503 4.2 47.3 0.8 ND1 A:HIS240 4.2 16.6 1.0 CZ A:ARG119 4.3 24.6 1.0 CG A:HIS240 4.3 22.0 1.0 CA A:CYS198 4.3 21.8 1.0 O14 A:L8J503 4.3 29.9 0.8 CB A:ASP118 4.4 23.1 1.0 ZN A:ZN501 4.4 22.7 1.0 CE1 A:HIS114 4.6 11.4 1.0 NE2 A:HIS179 4.7 16.6 1.0 BR05 A:L8J503 4.8 68.0 0.8 CE1 A:HIS179 4.8 17.2 1.0 NE2 A:HIS114 5.0 14.6 1.0 N A:CYS198 5.0 12.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Vim-2 with Compound 16


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 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:29.5 occ:0.38 O A:ACT506 2.2 22.9 0.8 ND1 A:HIS251 2.4 18.6 1.0 CB A:HIS251 2.7 13.7 1.0 C A:ACT506 2.8 22.3 0.8 CG A:HIS251 2.9 18.8 1.0 OXT A:ACT506 3.0 27.7 0.8 CA A:HIS251 3.0 20.9 1.0 CE1 A:HIS251 3.6 23.1 1.0 N A:HIS251 3.9 21.8 1.0 ND2 A:ASN254 4.0 23.0 1.0 C A:HIS251 4.1 20.6 1.0 CH3 A:ACT506 4.2 44.9 0.8 CD2 A:HIS251 4.2 15.0 1.0 O A:HIS251 4.3 23.5 1.0 CD2 A:LEU203 4.4 13.2 1.0 NE2 A:HIS251 4.5 20.0 1.0 C A:LYS250 4.8 20.4 1.0 O A:LYS250 5.0 13.2 1.0 CB A:ASN254 5.0 19.8 1.0 CG A:ASN254 5.0 23.2 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Vim-2 with Compound 16


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 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:12.4 occ:0.57 NE2 A:HIS153 2.0 25.2 1.0 O A:ACT508 2.8 36.8 0.7 CE1 A:HIS153 2.9 28.9 1.0 CD2 A:HIS153 3.0 19.5 1.0 OXT A:ACT508 3.3 42.5 0.7 C A:ACT508 3.3 25.3 0.7 ND1 A:HIS153 4.0 24.2 1.0 CG A:HIS153 4.1 23.4 1.0 OXT A:ACT507 4.2 62.5 0.6 CB A:ALA132 4.2 21.5 1.0 CH3 A:ACT508 4.7 22.3 0.7 CA A:ALA132 4.9 19.2 1.0 C A:ACT507 5.0 60.2 0.6

Zinc binding site 5 out of 8 in the Crystal Structure of Vim-2 with Compound 16


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 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:23.7 occ:1.00 NE2 B:HIS179 1.9 20.9 1.0 ND1 B:HIS116 2.0 34.1 1.0 O13 B:L8J503 2.2 23.0 0.5 NE2 B:HIS114 2.3 12.4 1.0 CE1 B:HIS179 2.7 16.3 1.0 CG B:HIS116 2.8 26.4 1.0 CE1 B:HIS116 2.9 36.5 1.0 O14 B:L8J503 3.0 47.4 0.5 P11 B:L8J503 3.1 49.6 0.5 CD2 B:HIS179 3.1 17.1 1.0 CE1 B:HIS114 3.1 15.4 1.0 O13 B:L8J503 3.1 48.1 0.5 CD2 B:HIS114 3.2 21.3 1.0 CB B:HIS116 3.2 23.4 1.0 O12 B:L8J503 3.6 42.1 0.5 NE2 B:HIS116 3.8 26.7 1.0 CD2 B:HIS116 3.8 26.8 1.0 ND1 B:HIS179 3.9 27.4 1.0 P11 B:L8J503 4.1 53.9 0.5 CG B:HIS179 4.1 20.6 1.0 OD1 B:ASP118 4.1 28.6 1.0 O14 B:L8J503 4.2 42.1 0.5 ND1 B:HIS114 4.2 16.9 1.0 CG B:HIS114 4.3 21.6 1.0 ZN B:ZN502 4.4 27.0 1.0 O12 B:L8J503 4.4 42.5 0.5 SG B:CYS198 4.5 20.3 1.0 CB B:CYS198 4.5 18.6 1.0 OD2 B:ASP118 4.6 30.1 1.0 CA B:HIS116 4.7 18.9 1.0 C10 B:L8J503 4.7 45.9 0.5 CG B:ASP118 4.8 26.2 1.0 C15 B:L8J503 4.9 40.6 0.5 ND2 B:ASN210 5.0 51.8 1.0 O B:HOH649 5.0 32.4 1.0 N B:HIS116 5.0 20.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Vim-2 with Compound 16


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 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:27.0 occ:1.00 NE2 B:HIS240 2.0 28.8 1.0 O12 B:L8J503 2.0 42.1 0.5 SG B:CYS198 2.1 20.3 1.0 OD2 B:ASP118 2.1 30.1 1.0 O12 B:L8J503 2.3 42.5 0.5 CE1 B:HIS240 2.8 29.8 1.0 CD2 B:HIS240 3.1 24.0 1.0 O13 B:L8J503 3.2 48.1 0.5 P11 B:L8J503 3.3 53.9 0.5 P11 B:L8J503 3.3 49.6 0.5 CG B:ASP118 3.3 26.2 1.0 CB B:CYS198 3.3 18.6 1.0 O13 B:L8J503 3.5 23.0 0.5 NH2 B:ARG119 3.8 29.2 1.0 OD1 B:ASP118 4.0 28.6 1.0 ND1 B:HIS240 4.0 22.5 1.0 CG B:HIS240 4.2 25.1 1.0 O B:HOH607 4.2 40.5 1.0 NE B:ARG119 4.2 23.8 1.0 O B:HOH652 4.2 25.1 1.0 BR05 B:L8J503 4.3 73.3 0.5 C10 B:L8J503 4.3 54.8 0.5 O14 B:L8J503 4.3 47.4 0.5 ZN B:ZN501 4.4 23.7 1.0 CA B:CYS198 4.4 14.8 1.0 CB B:ASP118 4.4 28.1 1.0 CZ B:ARG119 4.5 27.3 1.0 C10 B:L8J503 4.5 45.9 0.5 O14 B:L8J503 4.5 42.1 0.5 CE1 B:HIS114 4.6 15.4 1.0 CE1 B:HIS179 4.8 16.3 1.0 NE2 B:HIS179 4.8 20.9 1.0 NE2 B:HIS114 5.0 12.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Vim-2 with Compound 16


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Vim-2 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:22.4 occ:0.06 OXT B:ACT507 1.6 26.1 0.8 C B:ACT507 1.9 23.2 0.8 O B:ACT507 1.9 20.5 0.8 NE2 B:HIS153 2.0 26.0 1.0 CE1 B:HIS153 2.4 22.2 1.0 CD2 B:HIS153 3.2 24.4 1.0 CH3 B:ACT507 3.3 28.6 0.8 OXT B:ACT506 3.6 23.3 0.1 ND1 B:HIS153 3.6 19.9 1.0 O B:HOH604 3.7 26.9 1.0 CB B:ALA132 3.8 17.6 1.0 CG B:HIS153 4.0 21.5 1.0 C B:ACT506 4.4 23.4 0.1 O B:ACT506 4.5 23.0 0.1 OH B:TYR134 4.6 27.9 1.0 CA B:ALA132 4.9 24.4 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Vim-2 with Compound 16


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Vim-2 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:23.3 occ:0.95 O B:ACT509 1.8 19.5 1.0 ND1 B:HIS251 2.1 17.0 1.0 C B:ACT509 3.0 25.5 1.0 CE1 B:HIS251 3.1 25.2 1.0 CG B:HIS251 3.1 21.9 1.0 CB B:HIS251 3.5 11.8 1.0 OXT B:ACT509 3.6 33.1 1.0 OXT B:ACT508 3.7 25.4 0.3 CA B:HIS251 3.8 18.1 1.0 NE2 B:HIS251 4.2 20.6 1.0 CH3 B:ACT509 4.2 25.1 1.0 CD2 B:HIS251 4.2 19.0 1.0 CD2 B:LEU203 4.6 14.1 1.0 O B:HIS251 4.6 18.5 1.0 ND2 B:ASN254 4.6 20.6 1.0 C B:HIS251 4.6 22.9 1.0 C B:ACT508 4.7 25.1 0.3 N B:HIS251 4.9 16.0 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