Zinc in PDB 5g3w: Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65

The structure of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65, PDB code: 5g3w was solved by A.Kraemer, F.J.Meyer-Almes, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	125.57 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.270, 130.140, 251.130, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 16.7

The structure of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 also contains other interesting chemical elements:

Potassium

(K)

8 atoms

The binding sites of Zinc atom in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 (pdb code 5g3w). 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 Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65, PDB code: 5g3w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn370 b:10.6 occ:0.60 OD2 A:ASP268 1.9 8.3 1.0 OD1 A:ASP180 2.0 8.1 1.0 ND1 A:HIS182 2.1 8.1 1.0 OAT A:C65376 2.2 15.4 0.6 OAS A:C65376 2.2 11.3 0.6 NAR A:C65376 2.3 14.8 0.6 OD2 A:ASP180 2.5 9.8 1.0 CAQ A:C65376 2.5 17.1 0.6 CG A:ASP180 2.5 8.7 1.0 CG A:ASP268 2.9 8.4 1.0 CE1 A:HIS182 3.0 8.2 1.0 CG A:HIS182 3.2 8.4 1.0 OD1 A:ASP268 3.3 8.9 1.0 CB A:HIS182 3.6 8.4 1.0 CAP A:C65376 3.8 18.9 0.6 N A:HIS182 3.9 7.8 1.0 CB A:ASP180 4.0 8.6 1.0 CAO A:C65376 4.1 17.0 0.6 NE2 A:HIS142 4.1 11.5 1.0 NE2 A:HIS182 4.1 8.2 1.0 CB A:ASP268 4.2 8.4 1.0 CA A:GLY310 4.2 8.1 1.0 CD2 A:HIS182 4.2 8.4 1.0 CG1 A:VAL181 4.3 8.0 1.0 N A:VAL181 4.3 8.0 1.0 CE2 A:TYR312 4.4 8.6 1.0 CA A:HIS182 4.4 8.3 1.0 OH A:TYR312 4.4 10.6 1.0 N A:GLY310 4.5 8.4 1.0 CE1 A:HIS142 4.5 11.5 1.0 O A:HOH2317 4.5 31.1 1.0 C A:ASP180 4.7 8.2 1.0 CA A:ASP180 4.8 8.0 1.0 NE2 A:HIS143 4.8 9.8 1.0 C A:VAL181 4.9 7.4 1.0 C A:GLY310 4.9 8.4 1.0 CZ A:TYR312 4.9 8.9 1.0 N A:GLY311 4.9 9.0 1.0 CA A:VAL181 5.0 7.4 1.0

Zinc binding site 2 out of 4 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn370 b:8.9 occ:0.40 OD2 B:ASP268 2.0 7.9 1.0 OAT B:C65377 2.0 12.0 0.6 OD1 B:ASP180 2.1 8.2 1.0 OAS B:C65377 2.1 14.9 0.6 ND1 B:HIS182 2.2 8.1 1.0 OD2 B:ASP180 2.5 9.2 1.0 NAR B:C65377 2.5 18.2 0.6 CAQ B:C65377 2.5 19.6 0.6 CG B:ASP180 2.6 8.1 1.0 CG B:ASP268 3.0 7.6 1.0 CE1 B:HIS182 3.1 8.8 1.0 CG B:HIS182 3.2 7.7 1.0 OD1 B:ASP268 3.4 7.3 1.0 CB B:HIS182 3.6 8.2 1.0 CAP B:C65377 3.8 23.6 0.6 NE2 B:HIS142 4.0 10.7 1.0 N B:HIS182 4.0 6.8 1.0 CB B:ASP180 4.1 7.8 1.0 CA B:GLY310 4.2 8.0 1.0 NE2 B:HIS182 4.2 8.6 1.0 CB B:ASP268 4.3 7.0 1.0 CD2 B:HIS182 4.3 8.5 1.0 CE2 B:TYR312 4.3 10.9 1.0 CE1 B:HIS142 4.4 10.0 1.0 OH B:TYR312 4.4 16.0 1.0 CG1 B:VAL181 4.4 7.0 1.0 N B:VAL181 4.4 7.1 1.0 CA B:HIS182 4.5 7.6 1.0 O B:HOH2241 4.5 34.7 1.0 N B:GLY310 4.5 7.9 1.0 CAO B:C65377 4.6 22.6 0.6 NE2 B:HIS143 4.8 12.1 1.0 CA B:ASP180 4.8 7.4 1.0 C B:ASP180 4.9 7.0 1.0 CZ B:TYR312 4.9 12.0 1.0 C B:GLY310 4.9 7.9 1.0 N B:GLY311 4.9 8.3 1.0 C B:VAL181 5.0 6.7 1.0

Zinc binding site 3 out of 4 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn370 b:11.1 occ:0.50 OD2 C:ASP268 2.0 10.2 1.0 OD1 C:ASP180 2.0 8.9 1.0 OAS C:C65373 2.1 14.2 0.6 OAT C:C65373 2.1 9.8 0.6 ND1 C:HIS182 2.2 10.8 1.0 OD2 C:ASP180 2.4 10.4 1.0 CG C:ASP180 2.6 9.6 1.0 NAR C:C65373 2.7 17.8 0.6 CAQ C:C65373 2.7 16.9 0.6 CG C:ASP268 3.0 9.3 1.0 CE1 C:HIS182 3.1 11.0 1.0 CG C:HIS182 3.3 9.8 1.0 OD1 C:ASP268 3.5 9.5 1.0 CB C:HIS182 3.6 9.4 1.0 N C:HIS182 4.0 7.9 1.0 NE2 C:HIS142 4.0 12.6 1.0 CAP C:C65373 4.1 20.0 0.6 CB C:ASP180 4.1 10.1 1.0 CA C:GLY310 4.1 9.4 1.0 NE2 C:HIS182 4.2 10.9 1.0 CB C:ASP268 4.3 8.9 1.0 CD2 C:HIS182 4.3 10.1 1.0 CG1 C:VAL181 4.4 8.8 1.0 CE2 C:TYR312 4.4 11.3 1.0 N C:VAL181 4.4 8.4 1.0 CE1 C:HIS142 4.4 12.2 1.0 N C:GLY310 4.4 9.0 1.0 OH C:TYR312 4.4 16.8 1.0 CA C:HIS182 4.5 8.8 1.0 O C:HOH2286 4.5 41.9 1.0 CA C:ASP180 4.8 9.5 1.0 C C:ASP180 4.8 9.1 1.0 C C:GLY310 4.9 9.6 1.0 N C:GLY311 4.9 9.7 1.0 CZ C:TYR312 4.9 12.3 1.0 NE2 C:HIS143 4.9 14.8 1.0 C C:VAL181 5.0 8.0 1.0

Zinc binding site 4 out of 4 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn370 b:14.1 occ:0.50 OD2 D:ASP268 2.0 10.9 1.0 OD1 D:ASP180 2.1 9.2 1.0 OAS D:C65373 2.1 12.9 0.5 ND1 D:HIS182 2.2 9.7 1.0 OAT D:C65373 2.2 10.1 0.5 OD2 D:ASP180 2.4 11.8 1.0 CG D:ASP180 2.5 9.9 1.0 CAQ D:C65373 2.6 16.6 0.5 NAR D:C65373 2.7 16.6 0.5 CE1 D:HIS182 3.0 10.6 1.0 CG D:ASP268 3.0 9.9 1.0 CG D:HIS182 3.3 9.2 1.0 OD1 D:ASP268 3.4 9.9 1.0 CB D:HIS182 3.7 9.1 1.0 CAP D:C65373 3.9 18.7 0.5 NE2 D:HIS142 4.0 12.6 1.0 CB D:ASP180 4.0 10.0 1.0 N D:HIS182 4.1 8.4 1.0 CA D:GLY310 4.2 9.7 1.0 NE2 D:HIS182 4.2 10.1 1.0 CB D:ASP268 4.3 9.5 1.0 CD2 D:HIS182 4.3 9.8 1.0 CE2 D:TYR312 4.4 9.5 1.0 O D:HOH2207 4.4 45.7 1.0 OH D:TYR312 4.4 16.1 1.0 N D:VAL181 4.4 7.8 1.0 CE1 D:HIS142 4.4 11.6 1.0 CG1 D:VAL181 4.4 8.7 1.0 N D:GLY310 4.5 9.7 1.0 CA D:HIS182 4.5 8.8 1.0 CAO D:C65373 4.7 13.7 0.5 NE2 D:HIS143 4.8 12.7 1.0 CA D:ASP180 4.8 9.5 1.0 C D:ASP180 4.8 8.3 1.0 CZ D:TYR312 4.9 13.1 1.0 C D:GLY310 4.9 10.5 1.0 N D:GLY311 5.0 11.1 1.0

C.E.Weston, A.Kramer, F.Colin, O.Yildiz, M.G.Baud, F.J.Meyer-Almes, M.J.Fuchter. Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors. Acs Infect Dis V. 3 152 2017.
ISSN: ESSN 2373-8227
PubMed: 27756124
DOI: 10.1021/ACSINFECDIS.6B00148