Zinc in PDB 4yrd: Crystal Structure of Capf with Inhibitor 3-Isopropenyl-Tropolone

The structure of Crystal Structure of Capf with Inhibitor 3-Isopropenyl-Tropolone, PDB code: 4yrd was solved by K.Nakano, T.Chigira, T.Miyafusa, S.Nagatoishi, J.M.M.Caaveiro, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.80 / 2.44
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.580, 194.620, 158.360, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 26.1

The binding sites of Zinc atom in the Crystal Structure of Capf with Inhibitor 3-Isopropenyl-Tropolone (pdb code 4yrd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Capf with Inhibitor 3-Isopropenyl-Tropolone, PDB code: 4yrd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Capf with Inhibitor 3-Isopropenyl-Tropolone


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 Capf with Inhibitor 3-Isopropenyl-Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:34.0 occ:1.00 OAD A:3IT402 1.9 30.2 1.0 OAC A:3IT402 2.2 33.2 1.0 OE1 A:GLU295 2.3 30.8 1.0 NE2 A:HIS288 2.4 27.6 1.0 NE2 A:HIS337 2.5 14.1 1.0 CAJ A:3IT402 2.9 34.9 1.0 CAL A:3IT402 2.9 32.3 1.0 CD2 A:HIS288 3.0 27.4 1.0 CD2 A:HIS337 3.3 13.8 1.0 CD A:GLU295 3.5 29.5 1.0 CE1 A:HIS337 3.5 14.6 1.0 CE1 A:HIS288 3.5 28.5 1.0 CAB A:3IT402 3.9 51.2 1.0 NE2 A:HIS290 3.9 21.1 1.0 OE2 A:GLU295 4.1 34.6 1.0 CAK A:3IT402 4.1 38.8 1.0 CG A:HIS288 4.2 27.0 1.0 CAH A:3IT402 4.3 28.3 1.0 CZ A:PHE297 4.4 15.4 1.0 ND1 A:HIS288 4.5 28.6 1.0 CAI A:3IT402 4.5 43.9 1.0 CG A:HIS337 4.5 13.9 1.0 CE1 A:HIS290 4.6 22.0 1.0 ND1 A:HIS337 4.6 14.6 1.0 CG A:GLU295 4.7 26.1 1.0 CG2 A:ILE331 5.0 14.8 1.0 CD2 A:HIS290 5.0 20.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Capf with Inhibitor 3-Isopropenyl-Tropolone


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 Capf with Inhibitor 3-Isopropenyl-Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:38.2 occ:1.00 OAD B:3IT402 1.9 33.3 1.0 OAC B:3IT402 2.2 38.2 1.0 NE2 B:HIS288 2.4 26.8 1.0 NE2 B:HIS337 2.4 16.1 1.0 OE2 B:GLU295 2.5 25.2 1.0 CAJ B:3IT402 2.8 37.3 1.0 CAL B:3IT402 2.9 36.0 1.0 CD2 B:HIS288 2.9 26.4 1.0 CD2 B:HIS337 3.3 15.7 1.0 CE1 B:HIS337 3.5 16.7 1.0 CE1 B:HIS288 3.5 27.9 1.0 CD B:GLU295 3.5 24.6 1.0 CAB B:3IT402 3.9 52.4 1.0 NE2 B:HIS290 3.9 21.4 1.0 OE1 B:GLU295 4.0 28.6 1.0 CAK B:3IT402 4.1 40.4 1.0 CG B:HIS288 4.2 26.8 1.0 CAH B:3IT402 4.2 30.7 1.0 ND1 B:HIS288 4.4 27.5 1.0 CAI B:3IT402 4.4 44.7 1.0 CZ B:PHE297 4.5 16.3 1.0 CG B:HIS337 4.5 16.0 1.0 CE1 B:HIS290 4.5 22.3 1.0 ND1 B:HIS337 4.6 16.7 1.0 CG B:GLU295 4.7 22.4 1.0 O B:HOH578 4.9 31.3 1.0 CG2 B:ILE331 5.0 14.2 1.0 CD2 B:HIS290 5.0 21.4 1.0

K.Nakano, T.Chigira, T.Miyafusa, S.Nagatoishi, J.M.Caaveiro, K.Tsumoto. Discovery and Characterization of Natural Tropolones As Inhibitors of the Antibacterial Target Capf From Staphylococcus Aureus. Sci Rep V. 5 15337 2015.
ISSN: ESSN 2045-2322
PubMed: 26471247
DOI: 10.1038/SREP15337