Zinc in PDB 2z2a: THR109GLY Dihydroorotase From E. Coli

All present enzymatic activity of THR109GLY Dihydroorotase From E. Coli:
3.5.2.3;

The structure of THR109GLY Dihydroorotase From E. Coli, PDB code: 2z2a 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 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.435, 78.193, 179.961, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 19.6

The binding sites of Zinc atom in the THR109GLY Dihydroorotase From E. Coli (pdb code 2z2a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the THR109GLY Dihydroorotase From E. Coli, PDB code: 2z2a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the THR109GLY 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 THR109GLY Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:22.5 occ:1.00 OD1 A:ASP250 2.0 30.0 1.0 O A:HOH1411 2.1 22.0 1.0 NE2 A:HIS18 2.1 32.9 1.0 NE2 A:HIS16 2.1 29.6 1.0 OQ1 A:KCX102 2.1 31.3 1.0 CX A:KCX102 3.0 31.8 1.0 CG A:ASP250 3.0 31.2 1.0 CD2 A:HIS18 3.1 30.0 1.0 CD2 A:HIS16 3.1 28.8 1.0 CE1 A:HIS16 3.1 32.8 1.0 CE1 A:HIS18 3.1 33.5 1.0 OQ2 A:KCX102 3.4 31.6 1.0 OD2 A:ASP250 3.5 32.6 1.0 ZN A:ZN401 3.5 24.5 1.0 NZ A:KCX102 4.1 29.1 1.0 ND1 A:HIS18 4.2 28.4 1.0 ND1 A:HIS16 4.2 29.2 1.0 CG A:HIS18 4.2 28.6 1.0 CG A:HIS16 4.2 31.3 1.0 CB A:ASP250 4.3 32.0 1.0 CD2 A:HIS177 4.3 31.6 1.0 C6 A:DOR1410 4.3 21.1 1.0 C4 A:DOR1410 4.3 52.6 1.0 C5 A:DOR1410 4.4 22.6 1.0 CG A:MET42 4.4 28.5 1.0 NE2 A:HIS177 4.4 31.3 1.0 O4 A:DOR1410 4.5 33.1 1.0 CA A:ASP250 4.7 29.4 1.0 OH A:TYR104 4.7 31.5 1.0 N3 A:DOR1410 4.7 30.9 1.0

Zinc binding site 2 out of 4 in the THR109GLY 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 THR109GLY Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:24.5 occ:1.00 NE2 A:HIS177 2.1 31.3 1.0 OQ2 A:KCX102 2.1 31.6 1.0 O A:HOH1411 2.2 22.0 1.0 ND1 A:HIS139 2.2 29.3 1.0 O4 A:DOR1410 2.8 33.1 1.0 CE1 A:HIS139 3.0 32.0 1.0 CX A:KCX102 3.0 31.8 1.0 CE1 A:HIS177 3.0 28.2 1.0 CD2 A:HIS177 3.0 31.6 1.0 CG A:HIS139 3.2 31.7 1.0 OQ1 A:KCX102 3.3 31.3 1.0 ZN A:ZN400 3.5 22.5 1.0 C4 A:DOR1410 3.6 52.6 1.0 CB A:HIS139 3.6 32.7 1.0 CE1 A:HIS16 4.1 32.8 1.0 ND1 A:HIS177 4.1 29.6 1.0 NE2 A:HIS139 4.2 30.7 1.0 NZ A:KCX102 4.2 29.1 1.0 CG A:HIS177 4.2 32.7 1.0 N3 A:DOR1410 4.2 30.9 1.0 NE2 A:HIS16 4.3 29.6 1.0 CD2 A:HIS139 4.3 31.3 1.0 CE2 A:TYR104 4.4 29.5 1.0 OD2 A:ASP250 4.4 32.6 1.0 O A:LEU222 4.5 33.7 1.0 C5 A:DOR1410 4.6 22.6 1.0 CA A:HIS139 4.6 28.2 1.0 CE A:KCX102 4.6 33.6 1.0 O A:HOH1680 4.6 45.8 1.0 OD1 A:ASP250 4.7 30.0 1.0 CD2 A:TYR104 4.9 34.5 1.0 CG A:ASP250 4.9 31.2 1.0

Zinc binding site 3 out of 4 in the THR109GLY 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 THR109GLY Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:26.1 occ:1.00 NE2 B:HIS18 2.0 28.4 1.0 O B:HOH2411 2.1 14.4 0.5 NE2 B:HIS16 2.1 35.3 1.0 OD1 B:ASP250 2.1 33.3 1.0 OQ1 B:KCX102 2.1 29.6 1.0 O4 B:NCD2410 2.1 38.0 0.5 CD2 B:HIS18 3.0 28.6 1.0 CG B:ASP250 3.0 32.7 1.0 CE1 B:HIS18 3.0 34.4 1.0 CX B:KCX102 3.1 33.9 1.0 CD2 B:HIS16 3.1 31.5 1.0 CE1 B:HIS16 3.1 30.7 1.0 C4 B:NCD2410 3.2 39.0 0.5 OD2 B:ASP250 3.4 34.8 1.0 OQ2 B:KCX102 3.5 31.2 1.0 ZN B:ZN401 3.6 27.7 1.0 C5 B:NCD2410 3.9 32.8 0.5 NZ B:KCX102 4.1 30.9 1.0 O5 B:NCD2410 4.1 24.6 0.5 ND1 B:HIS18 4.1 32.8 1.0 CG B:HIS18 4.1 27.1 1.0 ND1 B:HIS16 4.2 30.4 1.0 CD2 B:HIS177 4.2 32.7 1.0 CG B:HIS16 4.2 28.6 1.0 CB B:ASP250 4.2 29.1 1.0 C6 B:DOR1411 4.3 24.0 0.5 C6 B:NCD2410 4.3 30.3 0.5 C5 B:DOR1411 4.3 23.7 0.5 CG B:MET42 4.4 29.6 1.0 NE2 B:HIS177 4.4 28.0 1.0 C4 B:DOR1411 4.5 23.2 0.5 N3 B:NCD2410 4.6 32.3 0.5 OH B:TYR104 4.7 33.5 1.0 CA B:ASP250 4.7 29.6 1.0 N3 B:DOR1411 4.7 22.9 0.5

Zinc binding site 4 out of 4 in the THR109GLY 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 THR109GLY Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:27.7 occ:1.00 OQ2 B:KCX102 2.0 31.2 1.0 NE2 B:HIS177 2.0 28.0 1.0 ND1 B:HIS139 2.1 31.4 1.0 O B:HOH2411 2.3 14.4 0.5 O5 B:NCD2410 2.4 24.6 0.5 O4 B:NCD2410 2.5 38.0 0.5 C4 B:NCD2410 2.8 39.0 0.5 CX B:KCX102 3.0 33.9 1.0 CE1 B:HIS139 3.0 29.9 1.0 CE1 B:HIS177 3.0 30.5 1.0 CD2 B:HIS177 3.0 32.7 1.0 CG B:HIS139 3.2 29.9 1.0 OQ1 B:KCX102 3.3 29.6 1.0 O4 B:DOR1411 3.4 42.9 0.5 ZN B:ZN400 3.6 26.1 1.0 CB B:HIS139 3.6 30.9 1.0 C4 B:DOR1411 3.8 23.2 0.5 NE2 B:HIS139 4.1 29.9 1.0 NZ B:KCX102 4.1 30.9 1.0 ND1 B:HIS177 4.1 30.6 1.0 CG B:HIS177 4.2 30.4 1.0 CE1 B:HIS16 4.2 30.7 1.0 N3 B:DOR1411 4.2 22.9 0.5 CD2 B:HIS139 4.2 34.1 1.0 C5 B:NCD2410 4.3 32.8 0.5 NE2 B:HIS16 4.4 35.3 1.0 CE2 B:TYR104 4.4 33.1 1.0 OD2 B:ASP250 4.4 34.8 1.0 C5 B:DOR1411 4.5 23.7 0.5 CA B:HIS139 4.5 28.4 1.0 CE B:KCX102 4.6 31.9 1.0 O B:LEU222 4.6 34.8 1.0 N3 B:NCD2410 4.8 32.3 0.5 CD2 B:TYR104 4.9 27.4 1.0 OD1 B:ASP250 5.0 33.3 1.0 CG B:ASP250 5.0 32.7 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