Zinc in PDB 5e5c: Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1

All present enzymatic activity of Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1:
3.5.2.2;

The structure of Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1, PDB code: 5e5c was solved by C.C.Huang, Y.H.Huang, Y.C.Hsieh, C.T.Tzeng, C.J.Chen, C.Y.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.11 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.134, 112.134, 161.050, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 21.5

The binding sites of Zinc atom in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 (pdb code 5e5c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1, PDB code: 5e5c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1


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 Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:47.9 occ:1.00 OQ2 A:KCX150 1.8 38.2 1.0 ND1 A:HIS183 2.3 22.1 1.0 CE1 A:HIS239 2.4 22.5 1.0 CX A:KCX150 2.9 30.2 1.0 ZN A:ZN502 2.9 32.2 1.0 OQ1 A:KCX150 2.9 33.4 1.0 CE1 A:HIS183 3.1 21.9 1.0 NE2 A:HIS239 3.1 25.1 1.0 ND1 A:HIS239 3.4 26.8 1.0 CG A:HIS183 3.4 19.4 1.0 CB A:HIS183 3.9 18.1 1.0 CE1 A:HIS59 4.0 18.2 1.0 NE2 A:HIS59 4.0 19.0 1.0 CE1 A:PHE152 4.1 20.3 1.0 O A:SER289 4.1 27.2 1.0 NZ A:KCX150 4.1 23.7 1.0 CG2 A:VAL238 4.3 17.3 1.0 NE2 A:HIS183 4.3 21.6 1.0 CD2 A:HIS239 4.4 21.7 1.0 OD1 A:ASP316 4.5 24.6 1.0 CD2 A:HIS183 4.5 22.9 1.0 CG A:HIS239 4.5 23.1 1.0 CE A:KCX150 4.7 20.5 1.0 CD1 A:PHE152 4.7 19.2 1.0 CG A:ASP316 4.9 27.0 1.0 CA A:HIS183 4.9 16.4 1.0 OD2 A:ASP316 4.9 35.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1


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 Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:32.2 occ:1.00 OQ1 A:KCX150 2.0 33.4 1.0 NE2 A:HIS59 2.2 19.0 1.0 OD1 A:ASP316 2.3 24.6 1.0 NE2 A:HIS61 2.3 18.8 1.0 ZN A:ZN501 2.9 47.9 1.0 CX A:KCX150 3.1 30.2 1.0 CE1 A:HIS59 3.1 18.2 1.0 CD2 A:HIS59 3.2 16.4 1.0 CD2 A:HIS61 3.2 16.9 1.0 CE1 A:HIS61 3.3 19.1 1.0 CG A:ASP316 3.3 27.0 1.0 OQ2 A:KCX150 3.3 38.2 1.0 OD2 A:ASP316 3.9 35.6 1.0 CE1 A:HIS239 4.1 22.5 1.0 ND1 A:HIS59 4.2 20.3 1.0 NZ A:KCX150 4.3 23.7 1.0 CG A:HIS59 4.3 16.4 1.0 CB A:ASP316 4.3 22.3 1.0 ND1 A:HIS239 4.4 26.8 1.0 ND1 A:HIS61 4.4 20.0 1.0 CG A:HIS61 4.4 17.9 1.0 CA A:ASP316 4.7 19.1 1.0 CE1 A:PHE93 4.8 16.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1


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 Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:49.0 occ:1.00 OQ2 C:KCX150 1.9 43.2 1.0 CD2 C:HIS183 2.2 24.6 1.0 CE1 C:HIS239 2.4 34.2 1.0 NE2 C:HIS239 2.9 37.9 1.0 CX C:KCX150 3.0 37.1 1.0 ZN C:ZN502 3.1 40.3 1.0 CG C:HIS183 3.1 23.6 1.0 NE2 C:HIS183 3.1 24.8 1.0 OQ1 C:KCX150 3.2 40.3 1.0 ND1 C:HIS239 3.6 33.5 1.0 CB C:HIS183 3.6 21.8 1.0 CE1 C:HIS59 4.0 24.4 1.0 CG2 C:VAL238 4.1 19.6 1.0 NE2 C:HIS59 4.1 26.3 1.0 NZ C:KCX150 4.1 27.6 1.0 CD2 C:HIS239 4.2 36.2 1.0 O C:SER289 4.2 28.2 1.0 ND1 C:HIS183 4.2 30.5 1.0 CE1 C:HIS183 4.2 25.5 1.0 CE2 C:PHE152 4.3 28.4 1.0 CG C:HIS239 4.5 30.4 1.0 OD1 C:ASP316 4.5 29.4 1.0 CE C:KCX150 4.6 25.8 1.0 CA C:HIS183 4.6 22.9 1.0 CD2 C:PHE152 4.8 26.3 1.0 OD2 C:ASP316 4.9 43.3 1.0 CG C:ASP316 4.9 32.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1


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 Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:40.3 occ:1.00 NE2 C:HIS59 2.1 26.3 1.0 OQ1 C:KCX150 2.2 40.3 1.0 OD1 C:ASP316 2.2 29.4 1.0 NE2 C:HIS61 2.3 32.2 1.0 CE1 C:HIS59 3.0 24.4 1.0 ZN C:ZN501 3.1 49.0 1.0 CX C:KCX150 3.1 37.1 1.0 CD2 C:HIS61 3.1 30.6 1.0 CD2 C:HIS59 3.1 23.5 1.0 CG C:ASP316 3.2 32.2 1.0 OQ2 C:KCX150 3.3 43.2 1.0 CE1 C:HIS61 3.4 30.2 1.0 OD2 C:ASP316 3.8 43.3 1.0 CE1 C:HIS239 4.0 34.2 1.0 ND1 C:HIS59 4.2 26.4 1.0 CG C:HIS59 4.3 23.7 1.0 NZ C:KCX150 4.3 27.6 1.0 CG C:HIS61 4.3 31.8 1.0 CB C:ASP316 4.3 32.1 1.0 ND1 C:HIS239 4.4 33.5 1.0 ND1 C:HIS61 4.4 31.4 1.0 CA C:ASP316 4.7 29.0 1.0 CE1 C:PHE93 4.8 27.8 1.0

C.T.Tzeng, Y.H.Huang, C.Y.Huang. Crystal Structure of Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1: Insights Into the Molecular Basis of Formation of A Dimer Biochem.Biophys.Res.Commun. V. 478 1449 2016.
ISSN: ESSN 1090-2104
PubMed: 27576201
DOI: 10.1016/J.BBRC.2016.08.144