Zinc in PDB 4lcr: The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Ncba

The structure of The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Ncba, PDB code: 4lcr 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 / 2.00
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 (%)	17.2 / 20.3

The binding sites of Zinc atom in the The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Ncba (pdb code 4lcr). 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 Ncba, PDB code: 4lcr:
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 Ncba


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 Ncba within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:33.8 occ:1.00 OQ1 A:KCX155 2.0 17.8 0.5 NE2 A:HIS63 2.1 22.9 1.0 NE2 A:HIS65 2.2 26.0 1.0 OD1 A:ASP322 2.2 26.1 1.0 O42 A:URP601 2.9 65.6 1.0 CD2 A:HIS63 3.0 19.7 1.0 CG A:ASP322 3.1 26.2 1.0 CE1 A:HIS63 3.1 18.8 1.0 CX A:KCX155 3.1 19.7 0.5 CE1 A:HIS65 3.1 20.2 1.0 CD2 A:HIS65 3.2 19.2 1.0 OD2 A:ASP322 3.5 27.3 1.0 C6 A:URP601 3.6 54.4 1.0 OQ2 A:KCX155 3.7 20.1 0.5 ZN A:ZN603 3.7 39.6 1.0 C4 A:URP601 3.7 63.4 1.0 CD2 A:HIS244 4.0 16.2 1.0 C5 A:URP601 4.2 56.1 1.0 NZ A:KCX155 4.2 24.3 1.0 CB A:ASP322 4.2 19.6 1.0 ND1 A:HIS63 4.2 18.8 1.0 CG A:HIS63 4.2 19.0 1.0 ND1 A:HIS65 4.3 20.2 1.0 CG A:HIS65 4.3 20.6 1.0 N1 A:URP601 4.4 54.8 1.0 NE2 A:HIS244 4.4 17.2 1.0 CE2 A:PHE97 4.5 15.7 1.0 CA A:ASP322 4.6 19.7 1.0 O41 A:URP601 4.6 58.0 1.0 CD2 A:PHE97 4.6 18.8 1.0

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


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 Ncba within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:39.6 occ:1.00 OQ2 A:KCX155 1.9 20.1 0.5 NE2 A:HIS244 2.0 17.2 1.0 ND1 A:HIS188 2.3 25.8 1.0 O42 A:URP601 2.4 65.6 1.0 O41 A:URP601 2.7 58.0 1.0 CD2 A:HIS244 2.9 16.2 1.0 CX A:KCX155 2.9 19.7 0.5 C4 A:URP601 2.9 63.4 1.0 CE1 A:HIS188 3.0 23.7 1.0 CE1 A:HIS244 3.1 17.7 1.0 OQ1 A:KCX155 3.3 17.8 0.5 CG A:HIS188 3.3 21.8 1.0 ZN A:ZN602 3.7 33.8 1.0 CB A:HIS188 3.8 19.1 1.0 O A:GLY294 4.0 27.3 1.0 NZ A:KCX155 4.0 24.3 1.0 CG A:HIS244 4.1 17.9 1.0 ND1 A:HIS244 4.2 17.9 1.0 CE1 A:PHE157 4.2 26.9 1.0 NE2 A:HIS188 4.2 25.4 1.0 CG2 A:VAL243 4.3 16.3 1.0 CD2 A:HIS188 4.4 22.2 1.0 C5 A:URP601 4.4 56.1 1.0 CE A:KCX155 4.5 25.6 1.0 N3 A:URP601 4.5 57.9 1.0 CA A:HIS188 4.7 19.6 1.0 OD2 A:ASP322 4.7 27.3 1.0 OH A:TYR160 4.8 47.6 1.0 C6 A:URP601 4.8 54.4 1.0 CE1 A:HIS63 4.8 18.8 1.0 NE2 A:HIS63 4.8 22.9 1.0 CE2 A:TYR160 4.9 38.1 1.0 CD1 A:PHE157 4.9 23.0 1.0 C A:GLY294 5.0 28.1 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