Zinc in PDB 7e3u: Crystal Structure of the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au

All present enzymatic activity of Crystal Structure of the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au:
3.5.2.2;

The structure of Crystal Structure of the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au, PDB code: 7e3u was solved by Y.C.Yang, R.H.Luo, Y.H.Huang, C.Y.Huang, E.S.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.01 / 2.16
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.667, 112.667, 161.432, 90, 90, 120
R / Rfree (%)	18.6 / 23

The binding sites of Zinc atom in the Crystal Structure of the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au (pdb code 7e3u). 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 the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au, PDB code: 7e3u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au


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 the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:54.7 occ:1.00 OQ2 A:KCX150 2.1 40.2 1.0 NE2 A:HIS239 2.3 30.1 1.0 ND1 A:HIS183 2.4 28.1 1.0 O4 A:WBU501 3.0 49.0 1.0 CX A:KCX150 3.0 35.3 1.0 ZN A:ZN503 3.0 40.3 1.0 OQ1 A:KCX150 3.1 37.8 1.0 CE1 A:HIS239 3.2 30.5 1.0 CE1 A:HIS183 3.2 29.3 1.0 CD2 A:HIS239 3.3 29.6 1.0 C4 A:WBU501 3.3 50.8 1.0 CG A:HIS183 3.5 25.4 1.0 H3 A:WBU501 3.6 60.1 1.0 N3 A:WBU501 3.7 50.2 1.0 CB A:HIS183 3.8 22.4 1.0 CE1 A:HIS59 4.0 29.1 1.0 NE2 A:HIS59 4.0 25.7 1.0 O A:SER289 4.0 35.6 1.0 C5 A:WBU501 4.1 49.7 1.0 CE1 A:PHE152 4.2 30.4 1.0 H011 A:WBU501 4.2 61.2 1.0 CG2 A:VAL238 4.2 23.6 1.0 NZ A:KCX150 4.3 25.6 1.0 ND1 A:HIS239 4.4 29.3 1.0 NE2 A:HIS183 4.4 26.5 1.0 CG A:HIS239 4.4 30.8 1.0 N01 A:WBU501 4.5 51.1 1.0 CD2 A:HIS183 4.5 31.2 1.0 OD1 A:ASP316 4.6 32.0 1.0 C2 A:WBU501 4.6 47.2 1.0 OD2 A:ASP316 4.7 38.3 1.0 CD1 A:PHE152 4.7 25.5 1.0 CG A:ASP316 4.8 32.1 1.0 CE A:KCX150 4.8 26.4 1.0 CA A:HIS183 4.9 23.6 1.0 C6 A:WBU501 5.0 47.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au


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 the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:40.3 occ:1.00 OQ1 A:KCX150 2.2 37.8 1.0 NE2 A:HIS59 2.2 25.7 1.0 OD1 A:ASP316 2.3 32.0 1.0 NE2 A:HIS61 2.3 29.3 1.0 ZN A:ZN502 3.0 54.7 1.0 CD2 A:HIS61 3.1 24.1 1.0 C5 A:WBU501 3.2 49.7 1.0 N01 A:WBU501 3.2 51.1 1.0 CD2 A:HIS59 3.2 23.0 1.0 CX A:KCX150 3.2 35.3 1.0 CE1 A:HIS59 3.2 29.1 1.0 CG A:ASP316 3.2 32.1 1.0 CE1 A:HIS61 3.3 29.5 1.0 H011 A:WBU501 3.4 61.2 1.0 H012 A:WBU501 3.5 61.2 1.0 OQ2 A:KCX150 3.5 40.2 1.0 C4 A:WBU501 3.6 50.8 1.0 C6 A:WBU501 3.6 47.2 1.0 OD2 A:ASP316 3.8 38.3 1.0 O4 A:WBU501 3.9 49.0 1.0 H6 A:WBU501 3.9 56.6 1.0 N3 A:WBU501 4.3 50.2 1.0 N1 A:WBU501 4.3 44.4 1.0 ND1 A:HIS59 4.3 29.7 1.0 CG A:HIS61 4.3 27.3 1.0 CB A:ASP316 4.3 27.3 1.0 CG A:HIS59 4.3 20.9 1.0 NE2 A:HIS239 4.3 30.1 1.0 NZ A:KCX150 4.3 25.6 1.0 ND1 A:HIS61 4.4 27.8 1.0 CD2 A:HIS239 4.4 29.6 1.0 C2 A:WBU501 4.6 47.2 1.0 CA A:ASP316 4.7 22.6 1.0 CE1 A:PHE93 4.8 24.8 1.0 H3 A:WBU501 4.9 60.1 1.0 H1 A:WBU501 5.0 53.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au


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 the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:48.0 occ:1.00 OD1 B:ASP316 2.1 31.4 1.0 NE2 B:HIS59 2.2 35.6 1.0 NE2 B:HIS61 2.2 33.9 1.0 OQ1 B:KCX150 2.3 42.6 1.0 CD2 B:HIS61 3.0 34.4 1.0 CE1 B:HIS59 3.1 33.7 1.0 ZN B:ZN502 3.1 58.0 1.0 CD2 B:HIS59 3.2 33.4 1.0 CG B:ASP316 3.2 36.4 1.0 CX B:KCX150 3.2 39.8 1.0 CE1 B:HIS61 3.3 34.7 1.0 OQ2 B:KCX150 3.4 41.4 1.0 OD2 B:ASP316 3.8 42.0 1.0 NE2 B:HIS239 4.1 39.7 1.0 CG B:HIS61 4.2 39.8 1.0 ND1 B:HIS59 4.3 34.1 1.0 CB B:ASP316 4.3 33.2 1.0 CG B:HIS59 4.3 30.7 1.0 ND1 B:HIS61 4.3 39.3 1.0 CD2 B:HIS239 4.4 34.5 1.0 NZ B:KCX150 4.4 31.6 1.0 CA B:ASP316 4.6 35.6 1.0 CE2 B:PHE93 4.9 34.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au


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 the Pseudomonas Aeruginosa Dihydropyrimidinase Complexed with 5-Au within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:58.0 occ:1.00 OQ2 B:KCX150 2.1 41.4 1.0 ND1 B:HIS183 2.2 33.5 1.0 NE2 B:HIS239 2.4 39.7 1.0 CX B:KCX150 3.0 39.8 1.0 CE1 B:HIS239 3.1 36.1 1.0 CE1 B:HIS183 3.1 28.5 1.0 ZN B:ZN501 3.1 48.0 1.0 CG B:HIS183 3.3 33.4 1.0 OQ1 B:KCX150 3.3 42.6 1.0 CD2 B:HIS239 3.5 34.5 1.0 CB B:HIS183 3.6 26.2 1.0 CE1 B:HIS59 4.0 33.7 1.0 CG2 B:VAL238 4.1 25.8 1.0 O B:SER289 4.1 35.0 1.0 NE2 B:HIS59 4.1 35.6 1.0 CE1 B:PHE152 4.2 37.4 1.0 NZ B:KCX150 4.2 31.6 1.0 NE2 B:HIS183 4.3 32.8 1.0 ND1 B:HIS239 4.3 38.3 1.0 CD2 B:HIS183 4.4 36.8 1.0 OD1 B:ASP316 4.5 31.4 1.0 CG B:HIS239 4.6 32.9 1.0 CE B:KCX150 4.7 31.5 1.0 CD1 B:PHE152 4.7 31.2 1.0 CA B:HIS183 4.7 30.9 1.0 OD2 B:ASP316 4.8 42.0 1.0 CG B:ASP316 4.9 36.4 1.0

E.S.Lin, R.H.Luo, Y.C.Yang, C.Y.Huang. Molecular Insights Into How the Dimetal Center in Dihydropyrimidinase Can Bind the Thymine Antagonist 5-Aminouracil: A Different Binding Mode From the Anticancer Drug 5-Fluorouracil. Bioinorg Chem Appl V.2022 17745 2022.
ISSN: ISSN 1565-3633
PubMed: 35198016
DOI: 10.1155/2022/1817745