Zinc in PDB 2z25: THR110VAL Dihydroorotase From E. Coli

All present enzymatic activity of THR110VAL Dihydroorotase From E. Coli:
3.5.2.3;

The structure of THR110VAL Dihydroorotase From E. Coli, PDB code: 2z25 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 (°)	51.447, 78.968, 180.534, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 18.5

The binding sites of Zinc atom in the THR110VAL Dihydroorotase From E. Coli (pdb code 2z25). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the THR110VAL Dihydroorotase From E. Coli, PDB code: 2z25:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the THR110VAL 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 THR110VAL Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:20.7 occ:1.00 NE2 A:HIS18 2.1 27.1 1.0 O A:HOH1551 2.1 18.6 1.0 NE2 A:HIS16 2.1 25.1 1.0 OQ1 A:KCX102 2.2 29.9 1.0 OD1 A:ASP250 2.2 28.8 1.0 CD2 A:HIS18 3.0 27.8 1.0 CE1 A:HIS18 3.1 29.1 1.0 CX A:KCX102 3.1 34.1 1.0 CD2 A:HIS16 3.1 24.4 1.0 CG A:ASP250 3.1 29.2 1.0 CE1 A:HIS16 3.2 30.4 1.0 OQ2 A:KCX102 3.4 28.0 1.0 ZN A:ZN401 3.5 22.7 1.0 OD2 A:ASP250 3.5 28.4 1.0 NZ A:KCX102 4.1 26.3 1.0 ND1 A:HIS18 4.2 24.8 1.0 CG A:HIS18 4.2 24.3 1.0 CG A:HIS16 4.2 27.0 1.0 ND1 A:HIS16 4.2 26.6 1.0 CD2 A:HIS177 4.3 28.4 1.0 CB A:ASP250 4.3 28.0 1.0 C4 A:DOR1410 4.3 42.9 1.0 C6 A:DOR1410 4.4 26.6 1.0 NE2 A:HIS177 4.4 28.7 1.0 C5 A:DOR1410 4.4 26.1 1.0 CG A:MET42 4.4 24.8 1.0 O4 A:DOR1410 4.5 30.6 1.0 OH A:TYR104 4.6 30.3 1.0 N3 A:DOR1410 4.7 34.2 1.0 CA A:ASP250 4.7 27.3 1.0

Zinc binding site 2 out of 4 in the THR110VAL 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 THR110VAL Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:22.7 occ:1.00 OQ2 A:KCX102 2.0 28.0 1.0 NE2 A:HIS177 2.1 28.7 1.0 ND1 A:HIS139 2.1 31.1 1.0 O A:HOH1551 2.2 18.6 1.0 O4 A:DOR1410 2.9 30.6 1.0 CE1 A:HIS139 3.0 28.6 1.0 CX A:KCX102 3.0 34.1 1.0 CE1 A:HIS177 3.0 25.9 1.0 CD2 A:HIS177 3.1 28.4 1.0 CG A:HIS139 3.2 25.7 1.0 OQ1 A:KCX102 3.2 29.9 1.0 ZN A:ZN400 3.5 20.7 1.0 C4 A:DOR1410 3.6 42.9 1.0 CB A:HIS139 3.6 29.9 1.0 CE1 A:HIS16 4.1 30.4 1.0 NE2 A:HIS139 4.1 29.9 1.0 ND1 A:HIS177 4.1 24.7 1.0 NZ A:KCX102 4.1 26.3 1.0 N3 A:DOR1410 4.2 34.2 1.0 CG A:HIS177 4.2 25.3 1.0 NE2 A:HIS16 4.2 25.1 1.0 CD2 A:HIS139 4.2 25.2 1.0 CE2 A:TYR104 4.3 28.4 1.0 OD2 A:ASP250 4.4 28.4 1.0 O A:LEU222 4.6 30.4 1.0 CE A:KCX102 4.6 27.6 1.0 C5 A:DOR1410 4.6 26.1 1.0 CA A:HIS139 4.6 26.4 1.0 OD1 A:ASP250 4.8 28.8 1.0 CD2 A:TYR104 4.8 31.8 1.0 CG A:ASP250 4.9 29.2 1.0

Zinc binding site 3 out of 4 in the THR110VAL 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 THR110VAL Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:24.5 occ:1.00 OD1 B:ASP250 2.1 27.7 1.0 OQ1 B:KCX102 2.1 30.0 1.0 NE2 B:HIS18 2.1 27.2 1.0 NE2 B:HIS16 2.1 26.4 1.0 O4 B:NCD2410 2.1 23.0 1.0 CD2 B:HIS18 3.0 24.1 1.0 CG B:ASP250 3.0 31.4 1.0 CX B:KCX102 3.1 29.0 1.0 CD2 B:HIS16 3.1 25.5 1.0 CE1 B:HIS16 3.1 30.7 1.0 CE1 B:HIS18 3.1 29.0 1.0 C4 B:NCD2410 3.1 30.8 1.0 OD2 B:ASP250 3.5 31.0 1.0 OQ2 B:KCX102 3.5 28.1 1.0 ZN B:ZN401 3.8 24.2 1.0 C5 B:NCD2410 3.9 24.2 1.0 C6 B:NCD2410 4.0 26.7 1.0 O5 B:NCD2410 4.1 28.6 1.0 NZ B:KCX102 4.1 27.6 1.0 CG B:HIS18 4.2 27.1 1.0 ND1 B:HIS16 4.2 25.9 1.0 CG B:HIS16 4.2 24.9 1.0 ND1 B:HIS18 4.2 25.6 1.0 CB B:ASP250 4.2 28.1 1.0 CD2 B:HIS177 4.3 30.0 1.0 CG B:MET42 4.4 28.8 1.0 N3 B:NCD2410 4.4 21.1 1.0 NE2 B:HIS177 4.4 26.6 1.0 OH B:TYR104 4.6 27.8 1.0 CA B:ASP250 4.6 25.4 1.0 O61 B:NCD2410 4.8 22.6 1.0 C61 B:NCD2410 4.9 31.8 1.0

Zinc binding site 4 out of 4 in the THR110VAL 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 THR110VAL Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:24.2 occ:1.00 OQ2 B:KCX102 2.0 28.1 1.0 NE2 B:HIS177 2.1 26.6 1.0 ND1 B:HIS139 2.1 26.6 1.0 O5 B:NCD2410 2.2 28.6 1.0 O4 B:NCD2410 2.5 23.0 1.0 C4 B:NCD2410 2.7 30.8 1.0 CE1 B:HIS177 3.0 24.9 1.0 CE1 B:HIS139 3.0 25.4 1.0 CX B:KCX102 3.0 29.0 1.0 CD2 B:HIS177 3.1 30.0 1.0 CG B:HIS139 3.2 28.2 1.0 OQ1 B:KCX102 3.4 30.0 1.0 CB B:HIS139 3.6 28.6 1.0 ZN B:ZN400 3.8 24.5 1.0 ND1 B:HIS177 4.1 29.9 1.0 NE2 B:HIS139 4.1 24.8 1.0 NZ B:KCX102 4.2 27.6 1.0 C5 B:NCD2410 4.2 24.2 1.0 CG B:HIS177 4.2 27.1 1.0 CD2 B:HIS139 4.3 30.7 1.0 CE1 B:HIS16 4.3 30.7 1.0 CE2 B:TYR104 4.4 29.3 1.0 N3 B:NCD2410 4.4 21.1 1.0 OG1 B:THR109 4.5 34.9 1.0 CA B:HIS139 4.5 27.3 1.0 CG2 B:THR109 4.5 39.1 1.0 NE2 B:HIS16 4.5 26.4 1.0 CE B:KCX102 4.6 26.0 1.0 OD2 B:ASP250 4.7 31.0 1.0 O B:LEU222 4.8 28.8 1.0 CD2 B:TYR104 4.9 27.6 1.0 CB B:THR109 4.9 37.0 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