Zinc in PDB 4lcq: The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Ncbi

The structure of The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Ncbi, PDB code: 4lcq was solved by Y.C.Hsieh, M.C.Chen, C.C.Hsu, S.I.Chan, Y.S.Yang, C.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.81
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	161.204, 161.204, 93.803, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20

The binding sites of Zinc atom in the The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Ncbi (pdb code 4lcq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Ncbi, PDB code: 4lcq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Ncbi


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 Di-Zn Dihydropyrimidinase in Complex with Ncbi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:26.3 occ:1.00 OQ1 A:KCX155 2.0 14.4 0.5 OD1 A:ASP322 2.1 22.0 1.0 NE2 A:HIS63 2.1 20.5 1.0 NE2 A:HIS65 2.1 22.1 1.0 O42 A:URQ603 2.1 32.9 1.0 CG A:ASP322 3.0 23.8 1.0 C4 A:URQ603 3.0 44.7 1.0 CD2 A:HIS63 3.0 17.7 1.0 CE1 A:HIS65 3.0 19.2 1.0 CE1 A:HIS63 3.0 19.6 1.0 CD2 A:HIS65 3.1 18.6 1.0 CX A:KCX155 3.1 15.1 0.5 OD2 A:ASP322 3.5 24.9 1.0 OQ2 A:KCX155 3.6 12.3 0.5 C5 A:URQ603 3.7 40.5 1.0 ZN A:ZN602 3.7 26.9 1.0 O41 A:URQ603 4.0 32.5 1.0 CD2 A:HIS244 4.1 18.5 1.0 NZ A:KCX155 4.1 18.5 1.0 CB A:ASP322 4.2 19.7 1.0 ND1 A:HIS63 4.2 19.5 1.0 ND1 A:HIS65 4.2 18.3 1.0 CG A:HIS63 4.2 20.2 1.0 CG A:HIS65 4.2 19.5 1.0 C6 A:URQ603 4.4 45.4 1.0 NE2 A:HIS244 4.4 18.6 1.0 CA A:ASP322 4.5 19.8 1.0 C7 A:URQ603 4.5 43.0 1.0 CE2 A:PHE97 4.6 19.4 1.0 CD2 A:PHE97 4.6 19.0 1.0 N3 A:URQ603 4.7 55.8 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Ncbi


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 Di-Zn Dihydropyrimidinase in Complex with Ncbi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:26.9 occ:1.00 OQ2 A:KCX155 2.0 12.3 0.5 NE2 A:HIS244 2.1 18.6 1.0 O42 A:URQ603 2.1 32.9 1.0 ND1 A:HIS188 2.2 20.8 1.0 O41 A:URQ603 2.3 32.5 1.0 C4 A:URQ603 2.6 44.7 1.0 CE1 A:HIS188 2.9 21.1 1.0 CX A:KCX155 3.0 15.1 0.5 CD2 A:HIS244 3.0 18.5 1.0 CE1 A:HIS244 3.2 18.8 1.0 CG A:HIS188 3.2 19.3 1.0 OQ1 A:KCX155 3.3 14.4 0.5 ZN A:ZN601 3.7 26.3 1.0 CB A:HIS188 3.7 19.6 1.0 N3 A:URQ603 3.8 55.8 1.0 O A:GLY294 4.0 24.0 1.0 CE1 A:PHE157 4.0 24.3 1.0 NE2 A:HIS188 4.1 21.5 1.0 NZ A:KCX155 4.1 18.5 1.0 C5 A:URQ603 4.1 40.5 1.0 CG A:HIS244 4.2 18.5 1.0 ND1 A:HIS244 4.3 18.6 1.0 CD2 A:HIS188 4.3 20.5 1.0 CG2 A:VAL243 4.5 18.1 1.0 OH A:TYR160 4.5 31.7 1.0 CE A:KCX155 4.6 18.1 1.0 OD2 A:ASP322 4.7 24.9 1.0 CA A:HIS188 4.7 18.4 1.0 CD1 A:PHE157 4.7 22.6 1.0 CE1 A:HIS63 4.8 19.6 1.0 CE2 A:TYR160 4.8 29.9 1.0 NE2 A:HIS63 4.8 20.5 1.0 C7 A:URQ603 4.9 43.0 1.0 OD1 A:ASP322 4.9 22.0 1.0 CZ A:PHE157 4.9 20.4 1.0 C A:GLY294 5.0 21.8 1.0

Y.C.Hsieh, M.C.Chen, C.C.Hsu, S.I.Chan, Y.S.Yang, C.J.Chen. Crystal Structures of Vertebrate Dihydropyrimidinase and Complexes From Tetraodon Nigroviridis with Lysine Carbamylation: Metal and Structural Requirements For Post-Translational Modification and Function. J.Biol.Chem. V. 288 30645 2013.
ISSN: ISSN 0021-9258
PubMed: 24005677
DOI: 10.1074/JBC.M113.496778