Zinc in PDB 7uof: Dihydroorotase From M. Jannaschii

All present enzymatic activity of Dihydroorotase From M. Jannaschii:
3.5.2.3;

The structure of Dihydroorotase From M. Jannaschii, PDB code: 7uof was solved by J.Vitali, J.C.Nix, H.E.Newman, M.J.Colaneri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.18 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.267, 111.267, 101.233, 90, 90, 120
R / Rfree (%)	17.8 / 21.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the Dihydroorotase From M. Jannaschii (pdb code 7uof). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Dihydroorotase From M. Jannaschii, PDB code: 7uof:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:22.0 occ:1.00 O A:HOH692 1.9 22.9 1.0 NE2 A:HIS56 2.0 20.8 1.0 NE2 A:HIS58 2.0 23.4 1.0 OQ2 A:KCX137 2.2 20.6 1.0 OD1 A:ASP302 2.2 19.7 1.0 CE1 A:HIS58 2.9 26.4 1.0 CE1 A:HIS56 3.0 22.0 1.0 CD2 A:HIS56 3.0 19.2 1.0 CX A:KCX137 3.1 24.4 1.0 CG A:ASP302 3.1 20.6 1.0 CD2 A:HIS58 3.1 23.5 1.0 ZN A:ZN502 3.3 22.8 1.0 OQ1 A:KCX137 3.3 21.3 1.0 OD2 A:ASP302 3.5 24.8 1.0 ND1 A:HIS56 4.1 19.6 1.0 ND1 A:HIS58 4.1 24.0 1.0 CG A:HIS56 4.1 20.5 1.0 NZ A:KCX137 4.2 23.1 1.0 CG A:HIS58 4.2 26.6 1.0 CB A:ASP302 4.4 19.0 1.0 CG A:MET87 4.4 21.2 1.0 NE2 A:HIS227 4.5 23.5 1.0 CD2 A:HIS227 4.5 22.3 1.0 CA A:ASP302 4.7 18.2 1.0

Zinc binding site 2 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:22.8 occ:1.00 OQ1 A:KCX137 1.9 21.3 1.0 NE2 A:HIS227 2.1 23.5 1.0 ND1 A:HIS168 2.1 21.8 1.0 O A:HOH692 2.1 22.9 1.0 CX A:KCX137 2.9 24.4 1.0 CE1 A:HIS168 3.0 20.8 1.0 CE1 A:HIS227 3.0 21.9 1.0 CD2 A:HIS227 3.1 22.3 1.0 CG A:HIS168 3.1 21.6 1.0 OQ2 A:KCX137 3.2 20.6 1.0 ZN A:ZN501 3.3 22.0 1.0 CB A:HIS168 3.5 19.3 1.0 CE1 A:HIS56 3.8 22.0 1.0 NE2 A:HIS56 4.0 20.8 1.0 NZ A:KCX137 4.1 23.1 1.0 NE2 A:HIS168 4.1 23.8 1.0 ND1 A:HIS227 4.2 21.8 1.0 OD2 A:ASP302 4.2 24.8 1.0 CG A:HIS227 4.2 22.5 1.0 CD2 A:HIS168 4.2 20.6 1.0 CE2 A:PHE139 4.3 26.6 1.0 CA A:HIS168 4.5 22.2 1.0 OD1 A:ASP302 4.6 19.7 1.0 CE A:KCX137 4.7 22.3 1.0 CG A:ASP302 4.7 20.6 1.0 O A:ASN275 4.8 25.0 1.0 CB A:CYS226 4.8 19.7 1.0 CD2 A:PHE139 5.0 26.7 1.0

Zinc binding site 3 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:41.6 occ:0.72 O A:HOH601 1.9 30.9 1.0 OE2 A:GLU380 2.0 50.6 1.0 CD A:GLU380 2.5 48.8 1.0 OE1 A:GLU380 2.6 49.5 1.0 CG A:GLU380 4.0 40.7 1.0 O A:HOH610 4.2 42.2 1.0 OE2 A:GLU401 4.7 49.6 1.0 CD A:GLU401 4.7 48.5 1.0 OE1 A:GLU401 4.9 52.9 1.0 CB A:GLU380 5.0 33.3 1.0

Zinc binding site 4 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:23.5 occ:0.89 NZ A:LYS231 2.0 28.5 1.0 OD2 A:ASP283 2.0 22.8 1.0 OE1 A:GLU280 2.0 29.4 1.0 OE1 A:GLU196 2.2 29.1 1.0 OE2 A:GLU196 2.2 28.5 1.0 CD A:GLU196 2.5 24.3 1.0 CG A:ASP283 2.7 23.6 1.0 OD1 A:ASP283 2.7 24.0 1.0 CD A:GLU280 3.0 30.7 1.0 CE A:LYS231 3.2 27.3 1.0 CG A:GLU280 3.6 30.3 1.0 CB A:GLU280 3.9 25.0 1.0 O A:HOH645 3.9 25.4 1.0 CD A:LYS231 3.9 29.3 1.0 CG A:GLU196 4.0 22.8 1.0 OE2 A:GLU280 4.1 34.8 1.0 CB A:ASP283 4.1 20.0 1.0 CG A:LYS231 4.3 26.0 1.0 N A:GLU280 4.3 24.6 1.0 N A:ASP283 4.6 22.9 1.0 CA A:GLU280 4.7 24.6 1.0 O A:HOH679 4.8 29.6 1.0 CA A:ASP283 4.9 22.2 1.0 CB A:GLU196 4.9 22.8 1.0 CB A:ARG279 4.9 20.7 1.0

Zinc binding site 5 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:25.4 occ:0.81 OD2 A:ASP68 2.0 31.1 1.0 CG A:ASP68 2.7 27.2 1.0 OD1 A:ASP68 2.8 24.3 1.0 NZ A:LYS391 3.9 32.0 1.0 CE A:LYS391 4.0 31.9 1.0 CB A:LEU70 4.0 25.5 1.0 CB A:ASP68 4.2 25.5 1.0 O A:HOH818 4.3 42.7 1.0 N A:SER71 4.4 23.0 1.0 CD2 A:LEU70 4.5 30.9 1.0 O A:HOH775 4.6 39.5 1.0 CG A:LEU70 4.6 30.1 1.0 CB A:SER71 4.8 23.7 1.0 CA A:LEU70 5.0 27.0 1.0 OG A:SER71 5.0 24.4 1.0

Zinc binding site 6 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:31.2 occ:0.68 OE2 A:GLU243 1.9 40.6 1.0 NZ A:LYS211 2.0 34.3 1.0 O A:HOH602 2.1 42.3 1.0 CE A:LYS211 2.6 37.5 1.0 CD A:GLU243 2.6 40.0 1.0 OE1 A:GLU243 2.7 42.5 1.0 CD A:LYS211 4.0 38.1 1.0 CG A:GLU243 4.1 38.3 1.0 CG2 A:VAL240 4.6 30.8 1.0 CB A:GLU243 4.8 37.1 1.0 CB A:VAL240 4.9 28.8 1.0 CA A:VAL240 4.9 26.9 1.0

Zinc binding site 7 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:33.9 occ:0.73 N A:MET1 2.0 36.3 1.0 O A:HOH616 2.1 35.8 1.0 OE2 A:GLU23 2.2 45.3 1.0 O A:HOH733 2.3 35.5 1.0 OE1 A:GLU23 2.3 46.5 1.0 CD A:GLU23 2.6 46.2 1.0 CA A:MET1 3.0 38.6 1.0 CB A:MET1 3.2 36.1 1.0 O A:ILE21 3.6 40.5 1.0 OD2 A:ASP38 3.8 44.7 1.0 OD1 A:ASP38 4.0 45.1 1.0 O A:HOH608 4.0 53.2 1.0 CG A:GLU23 4.1 42.0 1.0 CG A:ASP38 4.3 43.8 1.0 C A:MET1 4.3 35.9 1.0 O A:ASP22 4.6 41.3 1.0 O A:MET1 4.7 35.2 1.0 CG A:MET1 4.7 38.5 1.0 C A:ASP22 4.7 41.6 1.0 C A:ILE21 4.8 37.6 1.0 CA A:GLU23 4.8 42.7 1.0 N A:GLU23 4.9 40.6 1.0 CB A:GLU23 5.0 45.6 1.0

Zinc binding site 8 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:32.6 occ:0.51 OE2 A:GLU309 2.0 41.6 1.0 NZ A:LYS313 2.2 41.9 1.0 CE A:LYS313 2.7 35.6 1.0 CD A:GLU309 3.0 42.0 1.0 ZN A:ZN509 3.0 32.1 0.5 OE1 A:GLU309 3.3 42.6 1.0 OD1 A:ASP310 3.9 38.0 1.0 CD A:LYS313 4.2 31.1 1.0 CG A:GLU309 4.3 38.6 1.0 O A:HOH661 4.5 42.9 1.0 O A:HOH668 4.9 50.7 1.0

Zinc binding site 9 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:32.1 occ:0.48 O A:HOH661 1.8 42.9 1.0 OE1 A:GLU309 2.0 42.6 1.0 OD1 A:ASP310 2.0 38.0 1.0 O A:HOH668 2.3 50.7 1.0 CG A:ASP310 2.8 32.8 1.0 CD A:GLU309 3.0 42.0 1.0 ZN A:ZN508 3.0 32.6 0.5 OD2 A:ASP310 3.0 36.0 1.0 NZ A:LYS313 3.2 41.9 1.0 OE2 A:GLU309 3.3 41.6 1.0 CB A:ASP310 4.2 31.8 1.0 CE A:LYS313 4.2 35.6 1.0 CG A:GLU309 4.4 38.6 1.0 N A:ASP310 4.5 25.7 1.0 CA A:ASP310 4.6 28.8 1.0 CB A:GLU309 4.7 31.4 1.0 CD1 A:LEU307 4.9 37.9 1.0 C A:GLU309 5.0 29.5 1.0

Zinc binding site 10 out of 11 in the Dihydroorotase From M. Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Dihydroorotase From M. Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn510 b:57.9 occ:0.50 OD2 A:ASP37 2.1 61.6 1.0 CG A:ASP37 2.9 61.9 1.0 OD1 A:ASP37 3.2 68.8 1.0 CB A:ASP37 4.3 63.9 1.0 O A:HOH700 4.3 52.7 1.0 O A:ASP37 4.8 54.0 1.0

J.Vitali, J.C.Nix, H.E.Newman, M.J.Colaneri. Crystal Structure of Methanococcus Jannaschii Dihydroorotase. Proteins V. 91 91 2023.
ISSN: ESSN 1097-0134
PubMed: 35978488
DOI: 10.1002/PROT.26412