Zinc in PDB 2eg6: The Crystal Structure of the Ligand-Free Dihydroorotase From E. Coli

All present enzymatic activity of The Crystal Structure of the Ligand-Free Dihydroorotase From E. Coli:
3.5.2.3;

The structure of The Crystal Structure of the Ligand-Free Dihydroorotase From E. Coli, PDB code: 2eg6 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)	17.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.426, 79.674, 180.987, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.4

The binding sites of Zinc atom in the The Crystal Structure of the Ligand-Free Dihydroorotase From E. Coli (pdb code 2eg6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of the Ligand-Free Dihydroorotase From E. Coli, PDB code: 2eg6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Crystal Structure of the Ligand-Free 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 The Crystal Structure of the Ligand-Free Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:27.6 occ:1.00 O A:HOH740 2.0 30.5 1.0 NE2 A:HIS18 2.1 37.8 1.0 NE2 A:HIS16 2.1 39.6 1.0 OD1 A:ASP250 2.2 39.2 1.0 OQ2 A:KCX102 2.2 40.7 1.0 CE1 A:HIS18 3.0 39.7 1.0 CD2 A:HIS18 3.1 39.4 1.0 CX A:KCX102 3.1 40.5 1.0 CD2 A:HIS16 3.1 38.0 1.0 CG A:ASP250 3.1 39.4 1.0 CE1 A:HIS16 3.1 41.5 1.0 O A:HOH692 3.3 44.6 1.0 ZN A:ZN401 3.4 30.8 1.0 OQ1 A:KCX102 3.5 39.6 1.0 OD2 A:ASP250 3.6 39.4 1.0 ND1 A:HIS18 4.2 37.7 1.0 NZ A:KCX102 4.2 38.4 1.0 CG A:HIS18 4.2 36.0 1.0 ND1 A:HIS16 4.2 36.1 1.0 CD2 A:HIS177 4.2 40.3 1.0 CG A:HIS16 4.3 38.7 1.0 CB A:ASP250 4.3 35.3 1.0 NE2 A:HIS177 4.3 39.1 1.0 CG A:MET42 4.4 35.6 1.0 O A:HOH440 4.6 34.1 1.0 OH A:TYR104 4.6 41.5 1.0 CA A:ASP250 4.7 34.9 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of the Ligand-Free 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 The Crystal Structure of the Ligand-Free Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:30.8 occ:1.00 NE2 A:HIS177 2.0 39.1 1.0 O A:HOH740 2.0 30.5 1.0 OQ1 A:KCX102 2.0 39.6 1.0 ND1 A:HIS139 2.1 38.8 1.0 CE1 A:HIS139 2.9 39.8 1.0 CE1 A:HIS177 2.9 39.2 1.0 CX A:KCX102 3.0 40.5 1.0 CD2 A:HIS177 3.1 40.3 1.0 O A:HOH692 3.1 44.6 1.0 CG A:HIS139 3.2 38.8 1.0 OQ2 A:KCX102 3.3 40.7 1.0 ZN A:ZN400 3.4 27.6 1.0 CB A:HIS139 3.7 38.9 1.0 CE1 A:HIS16 4.0 41.5 1.0 NE2 A:HIS139 4.1 36.5 1.0 ND1 A:HIS177 4.1 36.4 1.0 NZ A:KCX102 4.2 38.4 1.0 CG A:HIS177 4.2 37.4 1.0 NE2 A:HIS16 4.2 39.6 1.0 CD2 A:HIS139 4.2 37.2 1.0 CE2 A:TYR104 4.3 39.7 1.0 OD2 A:ASP250 4.6 39.4 1.0 CE A:KCX102 4.6 38.4 1.0 CA A:HIS139 4.6 37.5 1.0 O A:LEU222 4.7 42.2 1.0 OD1 A:ASP250 4.8 39.2 1.0 CD2 A:TYR104 4.9 40.4 1.0 CG A:ASP250 5.0 39.4 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of the Ligand-Free 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 The Crystal Structure of the Ligand-Free Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:35.0 occ:1.00 NE2 B:HIS18 2.0 36.4 1.0 OD1 B:ASP250 2.1 36.0 1.0 O B:HOH649 2.1 37.1 1.0 OQ2 B:KCX102 2.1 38.5 1.0 NE2 B:HIS16 2.2 36.6 1.0 CE1 B:HIS18 3.0 38.4 1.0 CG B:ASP250 3.0 38.3 1.0 CD2 B:HIS18 3.1 36.1 1.0 CX B:KCX102 3.1 43.7 1.0 CD2 B:HIS16 3.1 36.3 1.0 CE1 B:HIS16 3.1 32.5 1.0 O B:HOH579 3.3 55.0 1.0 ZN B:ZN401 3.5 37.7 1.0 OQ1 B:KCX102 3.5 36.0 1.0 OD2 B:ASP250 3.5 39.5 1.0 ND1 B:HIS18 4.1 40.5 1.0 NZ B:KCX102 4.1 38.2 1.0 CG B:HIS18 4.2 33.9 1.0 CG B:HIS16 4.2 34.6 1.0 ND1 B:HIS16 4.2 36.8 1.0 CD2 B:HIS177 4.3 37.8 1.0 CB B:ASP250 4.3 35.5 1.0 NE2 B:HIS177 4.4 38.8 1.0 CG B:MET42 4.4 36.7 1.0 OH B:TYR104 4.6 40.6 1.0 CA B:ASP250 4.7 34.8 1.0 O B:HOH456 4.8 38.4 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of the Ligand-Free 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 The Crystal Structure of the Ligand-Free Dihydroorotase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:37.7 occ:1.00 O B:HOH649 2.0 37.1 1.0 OQ1 B:KCX102 2.0 36.0 1.0 NE2 B:HIS177 2.0 38.8 1.0 ND1 B:HIS139 2.2 36.9 1.0 CE1 B:HIS139 2.9 38.9 1.0 CX B:KCX102 2.9 43.7 1.0 CE1 B:HIS177 3.0 39.2 1.0 CD2 B:HIS177 3.0 37.8 1.0 O B:HOH579 3.1 55.0 1.0 OQ2 B:KCX102 3.2 38.5 1.0 CG B:HIS139 3.3 37.2 1.0 ZN B:ZN400 3.5 35.0 1.0 CB B:HIS139 3.8 34.8 1.0 CE1 B:HIS16 4.0 32.5 1.0 NE2 B:HIS139 4.1 37.4 1.0 NZ B:KCX102 4.1 38.2 1.0 ND1 B:HIS177 4.1 33.5 1.0 CG B:HIS177 4.2 33.4 1.0 NE2 B:HIS16 4.2 36.6 1.0 CD2 B:HIS139 4.3 39.0 1.0 CE2 B:TYR104 4.4 34.8 1.0 OD2 B:ASP250 4.5 39.5 1.0 CE B:KCX102 4.5 35.8 1.0 CA B:HIS139 4.6 36.4 1.0 O B:HOH651 4.6 51.6 1.0 O B:LEU222 4.6 43.3 1.0 OD1 B:ASP250 4.7 36.0 1.0 CG B:ASP250 4.9 38.3 1.0 CD2 B:TYR104 4.9 32.6 1.0

M.Lee, C.W.Chan, S.C.Graham, R.I.Christopherson, J.M.Guss, M.J.Maher. Structures of Ligand-Free and Inhibitor Complexes of Dihydroorotase From Escherichia Coli: Implications For Loop Movement in Inhibitor Design J.Mol.Biol. V. 370 812 2007.
ISSN: ISSN 0022-2836
PubMed: 17550785
DOI: 10.1016/J.JMB.2007.05.019