Zinc in PDB 2z28: THR109VAL Dihydroorotase From E. Coli

All present enzymatic activity of THR109VAL Dihydroorotase From E. Coli:
3.5.2.3;

The structure of THR109VAL Dihydroorotase From E. Coli, PDB code: 2z28 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 (°)	51.378, 78.413, 179.970, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18.9

The binding sites of Zinc atom in the THR109VAL Dihydroorotase From E. Coli (pdb code 2z28). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the THR109VAL Dihydroorotase From E. Coli, PDB code: 2z28:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the THR109VAL 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 THR109VAL Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:22.2 occ:1.00 OD1 A:ASP250 2.1 26.9 1.0 NE2 A:HIS18 2.1 27.5 1.0 O A:HOH1704 2.1 21.7 1.0 NE2 A:HIS16 2.1 27.0 1.0 OQ1 A:KCX102 2.2 30.0 1.0 CD2 A:HIS18 3.0 30.7 1.0 CG A:ASP250 3.0 27.2 1.0 CD2 A:HIS16 3.0 27.5 1.0 CX A:KCX102 3.1 32.9 1.0 CE1 A:HIS18 3.1 30.5 1.0 CE1 A:HIS16 3.1 30.6 1.0 OQ2 A:KCX102 3.4 29.5 1.0 OD2 A:ASP250 3.5 30.6 1.0 ZN A:ZN401 3.5 25.8 1.0 NZ A:KCX102 4.1 28.1 1.0 CG A:HIS18 4.2 27.5 1.0 ND1 A:HIS16 4.2 27.1 1.0 ND1 A:HIS18 4.2 24.2 1.0 CG A:HIS16 4.2 28.4 1.0 CB A:ASP250 4.2 29.2 1.0 C4 A:DOR1410 4.3 38.3 1.0 CD2 A:HIS177 4.3 31.8 1.0 C5 A:DOR1410 4.3 28.4 1.0 C6 A:DOR1410 4.4 22.8 1.0 O4 A:DOR1410 4.4 34.1 1.0 NE2 A:HIS177 4.4 29.6 1.0 CG A:MET42 4.4 24.1 1.0 N3 A:DOR1410 4.6 29.0 1.0 CA A:ASP250 4.7 27.7 1.0 OH A:TYR104 4.7 28.5 1.0

Zinc binding site 2 out of 4 in the THR109VAL 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 THR109VAL Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:25.8 occ:1.00 OQ2 A:KCX102 2.0 29.5 1.0 NE2 A:HIS177 2.1 29.6 1.0 ND1 A:HIS139 2.1 29.8 1.0 O A:HOH1704 2.2 21.7 1.0 O4 A:DOR1410 2.7 34.1 1.0 CE1 A:HIS139 3.0 30.9 1.0 CX A:KCX102 3.0 32.9 1.0 CE1 A:HIS177 3.1 27.9 1.0 CD2 A:HIS177 3.1 31.8 1.0 CG A:HIS139 3.2 27.2 1.0 OQ1 A:KCX102 3.3 30.0 1.0 ZN A:ZN400 3.5 22.2 1.0 C4 A:DOR1410 3.6 38.3 1.0 CB A:HIS139 3.6 31.4 1.0 CE1 A:HIS16 4.1 30.6 1.0 NE2 A:HIS139 4.1 31.9 1.0 NZ A:KCX102 4.2 28.1 1.0 ND1 A:HIS177 4.2 26.6 1.0 CG A:HIS177 4.2 25.9 1.0 CD2 A:HIS139 4.2 30.0 1.0 N3 A:DOR1410 4.2 29.0 1.0 NE2 A:HIS16 4.2 27.0 1.0 CE2 A:TYR104 4.3 29.2 1.0 OD2 A:ASP250 4.5 30.6 1.0 C5 A:DOR1410 4.5 28.4 1.0 O A:LEU222 4.6 32.1 1.0 CA A:HIS139 4.6 24.1 1.0 CE A:KCX102 4.6 27.9 1.0 O A:HOH1663 4.7 47.9 1.0 OD1 A:ASP250 4.8 26.9 1.0 CD2 A:TYR104 4.8 31.1 1.0 CG A:ASP250 4.9 27.2 1.0

Zinc binding site 3 out of 4 in the THR109VAL 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 THR109VAL Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:27.0 occ:1.00 NE2 B:HIS18 2.1 26.3 1.0 OD1 B:ASP250 2.1 29.0 1.0 OQ1 B:KCX102 2.1 27.5 1.0 O4 B:NCD2410 2.1 27.4 1.0 NE2 B:HIS16 2.1 31.1 1.0 CG B:ASP250 3.0 30.8 1.0 CD2 B:HIS18 3.0 27.1 1.0 CX B:KCX102 3.0 30.9 1.0 CD2 B:HIS16 3.1 28.9 1.0 CE1 B:HIS18 3.1 33.6 1.0 C4 B:NCD2410 3.2 43.3 1.0 CE1 B:HIS16 3.2 32.5 1.0 OD2 B:ASP250 3.4 32.5 1.0 OQ2 B:KCX102 3.5 29.6 1.0 ZN B:ZN401 3.6 29.8 1.0 C5 B:NCD2410 3.9 29.0 1.0 NZ B:KCX102 4.1 26.8 1.0 O5 B:NCD2410 4.1 34.0 1.0 CG B:HIS18 4.2 25.9 1.0 ND1 B:HIS18 4.2 25.3 1.0 C6 B:NCD2410 4.2 26.4 1.0 CD2 B:HIS177 4.2 32.4 1.0 CB B:ASP250 4.2 27.4 1.0 CG B:HIS16 4.2 26.5 1.0 ND1 B:HIS16 4.2 27.9 1.0 NE2 B:HIS177 4.4 29.7 1.0 CG B:MET42 4.5 23.7 1.0 N3 B:NCD2410 4.5 35.6 1.0 OH B:TYR104 4.6 29.7 1.0 CA B:ASP250 4.7 26.1 1.0 O61 B:NCD2410 5.0 28.8 1.0

Zinc binding site 4 out of 4 in the THR109VAL 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 THR109VAL Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:29.8 occ:1.00 OQ2 B:KCX102 2.0 29.6 1.0 NE2 B:HIS177 2.1 29.7 1.0 ND1 B:HIS139 2.1 30.8 1.0 O5 B:NCD2410 2.3 34.0 1.0 O4 B:NCD2410 2.5 27.4 1.0 C4 B:NCD2410 2.7 43.3 1.0 CX B:KCX102 2.9 30.9 1.0 CE1 B:HIS139 3.0 31.9 1.0 CE1 B:HIS177 3.0 28.9 1.0 CD2 B:HIS177 3.1 32.4 1.0 CG B:HIS139 3.2 31.3 1.0 OQ1 B:KCX102 3.3 27.5 1.0 CB B:HIS139 3.6 31.4 1.0 ZN B:ZN400 3.6 27.0 1.0 NZ B:KCX102 4.1 26.8 1.0 NE2 B:HIS139 4.1 28.8 1.0 ND1 B:HIS177 4.1 30.6 1.0 CG B:HIS177 4.2 29.5 1.0 C5 B:NCD2410 4.2 29.0 1.0 CD2 B:HIS139 4.3 31.4 1.0 CE1 B:HIS16 4.3 32.5 1.0 CE2 B:TYR104 4.3 31.7 1.0 NE2 B:HIS16 4.4 31.1 1.0 N3 B:NCD2410 4.4 35.6 1.0 OD2 B:ASP250 4.5 32.5 1.0 CA B:HIS139 4.5 27.1 1.0 CE B:KCX102 4.6 29.7 1.0 CD2 B:TYR104 4.8 29.9 1.0 O B:LEU222 4.8 33.1 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