Zinc in PDB 6v1p: Structure of Vim-2 Bound to QPX7728 at 1.20 A

The structure of Structure of Vim-2 Bound to QPX7728 at 1.20 A, PDB code: 6v1p 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)	35.20 / 1.20
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	66.670, 79.120, 77.110, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 16.8

The structure of Structure of Vim-2 Bound to QPX7728 at 1.20 A also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Structure of Vim-2 Bound to QPX7728 at 1.20 A (pdb code 6v1p). 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 Bound to QPX7728 at 1.20 A, PDB code: 6v1p:
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 Bound to QPX7728 at 1.20 A


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 Bound to QPX7728 at 1.20 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:7.9 occ:1.00 O13 A:QNA401 1.9 7.3 1.0 ND1 A:HIS118 2.0 8.2 1.0 NE2 A:HIS196 2.0 7.3 1.0 NE2 A:HIS116 2.1 7.6 1.0 O14 A:QNA401 2.5 8.3 1.0 B12 A:QNA401 2.7 7.8 1.0 CG A:HIS118 2.9 8.4 1.0 CE1 A:HIS196 3.0 7.1 1.0 CD2 A:HIS196 3.0 7.3 1.0 CE1 A:HIS118 3.0 9.3 1.0 CE1 A:HIS116 3.0 7.4 1.0 CD2 A:HIS116 3.1 7.3 1.0 CB A:HIS118 3.2 8.2 1.0 O11 A:QNA401 3.8 7.7 1.0 C15 A:QNA401 4.0 9.9 1.0 CD2 A:HIS118 4.1 10.0 1.0 ND1 A:HIS196 4.1 6.9 1.0 NE2 A:HIS118 4.1 10.0 1.0 CG A:HIS196 4.1 6.6 1.0 ND1 A:HIS116 4.1 7.8 1.0 OD1 A:ASP120 4.1 7.7 1.0 CG A:HIS116 4.2 6.9 1.0 ZN A:ZN403 4.3 7.7 1.0 CB A:CYS221 4.4 6.8 1.0 SG A:CYS221 4.4 7.7 1.0 CA A:HIS118 4.7 8.3 1.0 O A:HOH629 4.7 10.3 1.0 O03 A:QNA401 4.9 7.3 1.0 C10 A:QNA401 4.9 7.8 1.0 OD2 A:ASP120 4.9 7.8 1.0 N A:HIS118 4.9 7.8 1.0 CG A:ASP120 5.0 7.3 1.0

Zinc binding site 2 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


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 Bound to QPX7728 at 1.20 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:7.7 occ:1.00 NE2 A:HIS263 2.1 7.5 1.0 O11 A:QNA401 2.1 7.7 1.0 O03 A:QNA401 2.2 7.3 1.0 OD2 A:ASP120 2.2 7.8 1.0 SG A:CYS221 2.3 7.7 1.0 C10 A:QNA401 2.9 7.8 1.0 O13 A:QNA401 3.0 7.3 1.0 CD2 A:HIS263 3.0 8.3 1.0 C02 A:QNA401 3.1 8.2 1.0 CE1 A:HIS263 3.1 8.2 1.0 B12 A:QNA401 3.2 7.8 1.0 CG A:ASP120 3.3 7.3 1.0 C04 A:QNA401 3.3 8.2 1.0 CB A:CYS221 3.4 6.8 1.0 OD1 A:ASP120 3.8 7.7 1.0 NH2 A:ARG121 4.0 12.9 1.0 C15 A:QNA401 4.1 9.9 1.0 O14 A:QNA401 4.1 8.3 1.0 C09 A:QNA401 4.2 8.9 1.0 ND1 A:HIS263 4.2 8.4 1.0 CG A:HIS263 4.2 8.0 1.0 O01 A:QNA401 4.3 8.2 1.0 O A:HOH556 4.3 8.5 1.0 ZN A:ZN402 4.3 7.9 1.0 CE1 A:HIS196 4.4 7.1 1.0 C16 A:QNA401 4.5 10.5 1.0 C17 A:QNA401 4.5 9.7 1.0 CA A:CYS221 4.5 6.8 1.0 CB A:ASP120 4.5 8.1 1.0 NE A:ARG121 4.6 7.9 1.0 NE2 A:HIS196 4.6 7.3 1.0 C05 A:QNA401 4.6 9.3 1.0 CZ A:ARG121 4.8 9.9 1.0 CE1 A:HIS116 4.9 7.4 1.0

Zinc binding site 3 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


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 Bound to QPX7728 at 1.20 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:14.5 occ:1.00 OXT A:ACT406 1.9 15.3 1.0 ND1 A:HIS285 2.0 10.3 1.0 OXT A:ACT405 2.0 15.8 1.0 O A:ACT406 2.6 16.2 1.0 C A:ACT406 2.6 16.1 1.0 CE1 A:HIS285 3.0 10.0 1.0 C A:ACT405 3.0 16.4 1.0 CG A:HIS285 3.1 8.9 1.0 O A:ACT405 3.3 17.1 1.0 CB A:HIS285 3.5 9.1 1.0 CA A:HIS285 3.8 9.5 1.0 CH3 A:ACT406 4.0 18.4 1.0 NE2 A:HIS285 4.1 9.6 1.0 CD2 A:HIS285 4.2 9.6 1.0 CH3 A:ACT405 4.4 17.2 1.0 ND2 A:ASN288 4.4 14.0 1.0 O A:HIS285 4.5 9.4 1.0 CD2 A:LEU226 4.6 11.8 1.0 C A:HIS285 4.6 8.8 1.0 N A:HIS285 4.9 10.0 1.0

Zinc binding site 4 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


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 Bound to QPX7728 at 1.20 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:7.7 occ:1.00 O13 B:QNA401 1.9 7.1 1.0 ND1 B:HIS118 2.0 8.0 1.0 NE2 B:HIS196 2.0 6.4 1.0 NE2 B:HIS116 2.1 7.3 1.0 O14 B:QNA401 2.5 8.4 1.0 B12 B:QNA401 2.7 8.2 1.0 CG B:HIS118 2.9 7.6 1.0 CE1 B:HIS118 3.0 9.3 1.0 CE1 B:HIS196 3.0 6.4 1.0 CD2 B:HIS196 3.0 6.4 1.0 CE1 B:HIS116 3.0 6.9 1.0 CD2 B:HIS116 3.1 7.3 1.0 CB B:HIS118 3.2 7.8 1.0 O11 B:QNA401 3.8 7.1 1.0 C15 B:QNA401 4.0 10.3 1.0 NE2 B:HIS118 4.1 10.0 1.0 CD2 B:HIS118 4.1 9.6 1.0 ND1 B:HIS196 4.1 6.8 1.0 CG B:HIS196 4.1 6.5 1.0 OD1 B:ASP120 4.1 7.7 1.0 ND1 B:HIS116 4.2 7.2 1.0 CG B:HIS116 4.2 7.1 1.0 ZN B:ZN403 4.3 7.4 1.0 SG B:CYS221 4.4 7.3 1.0 CB B:CYS221 4.4 6.5 1.0 CA B:HIS118 4.7 8.0 1.0 O B:HOH630 4.7 11.1 1.0 O03 B:QNA401 4.9 7.8 1.0 C10 B:QNA401 4.9 8.1 1.0 OD2 B:ASP120 4.9 7.3 1.0 CG B:ASP120 5.0 7.2 1.0 N B:HIS118 5.0 7.6 1.0

Zinc binding site 5 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


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 Bound to QPX7728 at 1.20 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:7.4 occ:1.00 NE2 B:HIS263 2.1 7.0 1.0 O11 B:QNA401 2.1 7.1 1.0 OD2 B:ASP120 2.2 7.3 1.0 O03 B:QNA401 2.2 7.8 1.0 SG B:CYS221 2.3 7.3 1.0 C10 B:QNA401 2.9 8.1 1.0 O13 B:QNA401 3.0 7.1 1.0 CD2 B:HIS263 3.0 7.1 1.0 CE1 B:HIS263 3.1 7.8 1.0 C02 B:QNA401 3.1 8.2 1.0 B12 B:QNA401 3.2 8.2 1.0 CG B:ASP120 3.3 7.2 1.0 C04 B:QNA401 3.3 8.7 1.0 CB B:CYS221 3.4 6.5 1.0 OD1 B:ASP120 3.8 7.7 1.0 NH2 B:ARG121 4.1 12.9 1.0 C15 B:QNA401 4.1 10.3 1.0 O14 B:QNA401 4.1 8.4 1.0 C09 B:QNA401 4.1 8.7 1.0 ND1 B:HIS263 4.2 7.6 1.0 CG B:HIS263 4.2 7.4 1.0 O01 B:QNA401 4.3 8.3 1.0 O B:HOH557 4.3 7.7 1.0 ZN B:ZN402 4.3 7.7 1.0 CE1 B:HIS196 4.4 6.4 1.0 C16 B:QNA401 4.5 10.5 1.0 C17 B:QNA401 4.5 9.8 1.0 CA B:CYS221 4.5 6.3 1.0 CB B:ASP120 4.5 7.3 1.0 NE2 B:HIS196 4.5 6.4 1.0 NE B:ARG121 4.6 8.0 1.0 C05 B:QNA401 4.6 9.1 1.0 CZ B:ARG121 4.8 9.6 1.0 CE1 B:HIS116 4.9 6.9 1.0

Zinc binding site 6 out of 6 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


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 Bound to QPX7728 at 1.20 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:10.9 occ:1.00 OXT B:ACT405 2.0 11.5 1.0 OXT B:ACT406 2.0 11.4 1.0 ND1 B:HIS285 2.1 8.9 1.0 O B:ACT406 2.6 13.0 1.0 C B:ACT406 2.7 11.8 1.0 C B:ACT405 3.0 12.0 1.0 CE1 B:HIS285 3.0 8.8 1.0 CG B:HIS285 3.1 8.2 1.0 O B:ACT405 3.2 12.4 1.0 CB B:HIS285 3.5 8.5 1.0 CA B:HIS285 3.8 8.3 1.0 CH3 B:ACT406 4.1 14.4 1.0 NE2 B:HIS285 4.2 8.4 1.0 CD2 B:HIS285 4.2 8.3 1.0 CH3 B:ACT405 4.3 12.5 1.0 ND2 B:ASN288 4.4 11.2 1.0 CD2 B:LEU226 4.6 9.8 1.0 O B:HIS285 4.6 8.0 1.0 C B:HIS285 4.6 7.8 1.0 N B:HIS285 4.9 8.7 1.0

S.J.Hecker, K.R.Reddy, O.Lomovskaya, D.C.Griffith, D.Rubio-Aparicio, K.Nelson, R.Tsivkovski, D.Sun, M.Sabet, Z.Tarazi, J.Parkinson, M.Totrov, S.H.Boyer, T.W.Glinka, O.A.Pemberton, Y.Chen, M.N.Dudley. Discovery of Cyclic Boronic Acid QPX7728, An Ultra-Broad-Spectrum Inhibitor of Serine and Metallo Beta-Lactamases. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32150407
DOI: 10.1021/ACS.JMEDCHEM.9B01976