Zinc in PDB 2z24: THR110SER Dihydroorotase From E. Coli

All present enzymatic activity of THR110SER Dihydroorotase From E. Coli:
3.5.2.3;

The structure of THR110SER Dihydroorotase From E. Coli, PDB code: 2z24 was solved by M.Lee, M.J.Maher, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.447, 78.790, 180.221, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 19.8

The binding sites of Zinc atom in the THR110SER Dihydroorotase From E. Coli (pdb code 2z24). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the THR110SER Dihydroorotase From E. Coli, PDB code: 2z24:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the THR110SER Dihydroorotase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of THR110SER Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:23.0 occ:1.00 NE2 A:HIS18 2.0 30.9 1.0 O A:HOH1411 2.1 20.1 1.0 NE2 A:HIS16 2.2 28.5 1.0 OD1 A:ASP250 2.2 29.3 1.0 OQ1 A:KCX102 2.2 32.9 1.0 CD2 A:HIS18 3.0 32.5 1.0 CE1 A:HIS18 3.1 32.3 1.0 CX A:KCX102 3.1 39.0 1.0 CD2 A:HIS16 3.1 26.6 1.0 CG A:ASP250 3.1 34.0 1.0 CE1 A:HIS16 3.1 30.4 1.0 OQ2 A:KCX102 3.4 28.6 1.0 ZN A:ZN401 3.5 26.3 1.0 OD2 A:ASP250 3.5 29.7 1.0 NZ A:KCX102 4.1 27.9 1.0 ND1 A:HIS18 4.2 25.1 1.0 CG A:HIS18 4.2 25.7 1.0 C4 A:DOR1410 4.2 42.1 1.0 ND1 A:HIS16 4.2 28.5 1.0 CG A:HIS16 4.2 28.9 1.0 CD2 A:HIS177 4.3 29.8 1.0 CB A:ASP250 4.3 31.1 1.0 C6 A:DOR1410 4.3 26.5 1.0 O4 A:DOR1410 4.3 31.4 1.0 C5 A:DOR1410 4.3 24.5 1.0 NE2 A:HIS177 4.4 29.4 1.0 CG A:MET42 4.5 28.2 1.0 N3 A:DOR1410 4.6 36.5 1.0 CA A:ASP250 4.6 26.9 1.0 OH A:TYR104 4.7 32.0 1.0

Zinc binding site 2 out of 4 in the THR110SER Dihydroorotase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of THR110SER Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:26.3 occ:1.00 OQ2 A:KCX102 2.0 28.6 1.0 NE2 A:HIS177 2.1 29.4 1.0 O A:HOH1411 2.2 20.1 1.0 ND1 A:HIS139 2.2 28.8 1.0 O4 A:DOR1410 2.7 31.4 1.0 CX A:KCX102 3.0 39.0 1.0 CE1 A:HIS139 3.0 35.7 1.0 CE1 A:HIS177 3.0 29.6 1.0 CD2 A:HIS177 3.1 29.8 1.0 CG A:HIS139 3.2 28.6 1.0 OQ1 A:KCX102 3.3 32.9 1.0 ZN A:ZN400 3.5 23.0 1.0 C4 A:DOR1410 3.5 42.1 1.0 CB A:HIS139 3.6 31.9 1.0 N3 A:DOR1410 4.1 36.5 1.0 CE1 A:HIS16 4.1 30.4 1.0 NE2 A:HIS139 4.1 29.2 1.0 ND1 A:HIS177 4.1 30.3 1.0 NZ A:KCX102 4.1 27.9 1.0 CG A:HIS177 4.2 32.9 1.0 CD2 A:HIS139 4.3 32.2 1.0 NE2 A:HIS16 4.3 28.5 1.0 CE2 A:TYR104 4.3 32.8 1.0 OD2 A:ASP250 4.4 29.7 1.0 O A:LEU222 4.5 32.9 1.0 C5 A:DOR1410 4.5 24.5 1.0 CE A:KCX102 4.6 30.2 1.0 CA A:HIS139 4.6 29.8 1.0 OD1 A:ASP250 4.8 29.3 1.0 O A:HOH1695 4.8 44.9 1.0 CD2 A:TYR104 4.8 30.1 1.0 CG A:ASP250 4.9 34.0 1.0

Zinc binding site 3 out of 4 in the THR110SER Dihydroorotase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of THR110SER Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:26.7 occ:1.00 NE2 B:HIS18 2.0 26.8 1.0 NE2 B:HIS16 2.1 30.1 1.0 OD1 B:ASP250 2.1 29.8 1.0 OQ1 B:KCX102 2.1 31.7 1.0 O4 B:NCD2410 2.1 29.6 1.0 CD2 B:HIS18 3.0 28.0 1.0 CX B:KCX102 3.0 32.2 1.0 CE1 B:HIS18 3.0 35.5 1.0 CG B:ASP250 3.0 27.5 1.0 CE1 B:HIS16 3.1 27.9 1.0 CD2 B:HIS16 3.1 33.2 1.0 C4 B:NCD2410 3.2 64.3 1.0 OQ2 B:KCX102 3.4 32.6 1.0 OD2 B:ASP250 3.5 30.4 1.0 ZN B:ZN401 3.6 30.1 1.0 C5 B:NCD2410 3.9 33.0 1.0 NZ B:KCX102 4.1 29.5 1.0 ND1 B:HIS18 4.1 29.6 1.0 CG B:HIS18 4.1 29.5 1.0 C6 B:NCD2410 4.2 31.9 1.0 ND1 B:HIS16 4.2 26.9 1.0 CD2 B:HIS177 4.2 33.5 1.0 CB B:ASP250 4.2 28.0 1.0 CG B:HIS16 4.2 26.7 1.0 O5 B:NCD2410 4.2 37.4 1.0 NE2 B:HIS177 4.4 29.2 1.0 CG B:MET42 4.4 26.6 1.0 N3 B:NCD2410 4.5 40.9 1.0 OH B:TYR104 4.6 31.2 1.0 CA B:ASP250 4.7 24.9 1.0

Zinc binding site 4 out of 4 in the THR110SER Dihydroorotase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of THR110SER Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:30.1 occ:1.00 OQ2 B:KCX102 1.9 32.6 1.0 NE2 B:HIS177 2.0 29.2 1.0 ND1 B:HIS139 2.2 30.5 1.0 O4 B:NCD2410 2.3 29.6 1.0 O5 B:NCD2410 2.5 37.4 1.0 C4 B:NCD2410 2.8 64.3 1.0 CX B:KCX102 3.0 32.2 1.0 CE1 B:HIS177 3.0 23.9 1.0 CE1 B:HIS139 3.0 31.4 1.0 CD2 B:HIS177 3.1 33.5 1.0 CG B:HIS139 3.2 28.8 1.0 OQ1 B:KCX102 3.3 31.7 1.0 CB B:HIS139 3.6 28.9 1.0 ZN B:ZN400 3.6 26.7 1.0 NZ B:KCX102 4.1 29.5 1.0 ND1 B:HIS177 4.1 31.3 1.0 CE1 B:HIS16 4.2 27.9 1.0 NE2 B:HIS139 4.2 31.2 1.0 CG B:HIS177 4.2 28.7 1.0 C5 B:NCD2410 4.3 33.0 1.0 CD2 B:HIS139 4.3 33.1 1.0 N3 B:NCD2410 4.3 40.9 1.0 CE2 B:TYR104 4.3 38.6 1.0 NE2 B:HIS16 4.4 30.1 1.0 CA B:HIS139 4.5 26.1 1.0 OD2 B:ASP250 4.5 30.4 1.0 CE B:KCX102 4.6 34.1 1.0 O B:LEU222 4.7 33.5 1.0 CD2 B:TYR104 4.8 28.8 1.0 OD1 B:ASP250 4.9 29.8 1.0

M.Lee, M.J.Maher, R.I.Christopherson, J.M.Guss. Kinetic and Structural Analysis of Mutant Escherichia Coli Dihydroorotases: A Flexible Loop Stabilizes the Transition State Biochemistry V. 46 10538 2007.
ISSN: ISSN 0006-2960
PubMed: 17711307
DOI: 10.1021/BI701098E