Zinc in PDB 3dc8: Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti

All present enzymatic activity of Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti:
3.5.2.2;

The structure of Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti, PDB code: 3dc8 was solved by J.A.Gavira, S.Martinez-Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.60 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	124.887, 126.281, 196.104, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 17.6

The binding sites of Zinc atom in the Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti (pdb code 3dc8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti, PDB code: 3dc8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:2.0 occ:0.50 OQ1 A:KCX147 2.0 5.5 1.0 ND1 A:HIS180 2.0 2.0 1.0 O A:HOH925 2.2 12.3 1.0 NE2 A:HIS236 2.2 5.4 1.0 O A:HOH620 2.4 12.4 1.0 CE1 A:HIS180 2.9 2.0 1.0 CX A:KCX147 3.1 7.9 1.0 CD2 A:HIS236 3.1 4.3 1.0 CE1 A:HIS236 3.2 3.5 1.0 CG A:HIS180 3.2 2.5 1.0 OQ2 A:KCX147 3.4 5.9 1.0 ZN A:ZN502 3.5 2.0 0.5 CB A:HIS180 3.6 3.8 1.0 O A:HOH1037 3.7 18.1 1.0 O A:SER286 4.0 6.5 1.0 NE2 A:HIS180 4.1 4.5 1.0 CE2 A:PHE149 4.1 7.6 1.0 CD2 A:HIS180 4.2 2.2 1.0 NZ A:KCX147 4.3 5.1 1.0 ND1 A:HIS236 4.3 3.9 1.0 CG A:HIS236 4.3 4.9 1.0 OH A:TYR152 4.3 10.1 1.0 CG2 A:VAL235 4.4 4.1 1.0 OD2 A:ASP313 4.6 11.6 1.0 NE2 A:HIS56 4.6 3.8 1.0 CA A:HIS180 4.6 3.2 1.0 CE1 A:HIS56 4.6 3.6 1.0 CE2 A:TYR152 4.7 9.4 1.0 CD2 A:PHE149 4.7 7.1 1.0 CE A:KCX147 4.7 4.5 1.0 OD1 A:ASP313 4.9 5.7 1.0 CZ A:TYR152 5.0 9.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:2.0 occ:0.50 OQ2 A:KCX147 2.0 5.9 1.0 O A:HOH925 2.0 12.3 1.0 NE2 A:HIS58 2.1 7.6 1.0 NE2 A:HIS56 2.2 3.8 1.0 OD1 A:ASP313 2.2 5.7 1.0 O A:HOH1037 2.9 18.1 1.0 CX A:KCX147 3.0 7.9 1.0 CD2 A:HIS58 3.0 5.8 1.0 CD2 A:HIS56 3.0 3.0 1.0 CG A:ASP313 3.1 7.7 1.0 CE1 A:HIS58 3.1 6.2 1.0 CE1 A:HIS56 3.2 3.6 1.0 OQ1 A:KCX147 3.4 5.5 1.0 OD2 A:ASP313 3.5 11.6 1.0 ZN A:ZN501 3.5 2.0 0.5 O A:HOH620 3.6 12.4 1.0 NZ A:KCX147 4.1 5.1 1.0 CG A:HIS58 4.2 5.4 1.0 ND1 A:HIS58 4.2 5.0 1.0 CB A:ASP313 4.2 3.7 1.0 CG A:HIS56 4.2 4.5 1.0 ND1 A:HIS56 4.3 3.7 1.0 CD2 A:HIS236 4.4 4.3 1.0 O A:HOH919 4.5 13.6 1.0 NE2 A:HIS236 4.5 5.4 1.0 CE2 A:PHE90 4.6 5.3 1.0 CA A:ASP313 4.6 3.7 1.0 CD2 A:PHE90 4.9 6.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:2.0 occ:0.50 OQ2 B:KCX147 1.9 3.9 1.0 ND1 B:HIS180 2.1 2.0 1.0 NE2 B:HIS236 2.2 7.4 1.0 O B:HOH1042 2.3 7.8 1.0 O B:HOH1041 2.4 12.4 1.0 CE1 B:HIS180 3.0 4.5 1.0 CX B:KCX147 3.0 6.7 1.0 CD2 B:HIS236 3.1 5.9 1.0 CG B:HIS180 3.2 2.7 1.0 CE1 B:HIS236 3.2 4.9 1.0 OQ1 B:KCX147 3.3 6.3 1.0 ZN B:ZN502 3.5 2.0 0.5 CB B:HIS180 3.6 2.0 1.0 O B:SER286 4.1 8.4 1.0 NE2 B:HIS180 4.1 5.7 1.0 OH B:TYR152 4.2 9.5 1.0 NZ B:KCX147 4.2 5.1 1.0 CG B:HIS236 4.3 4.3 1.0 CD2 B:HIS180 4.3 2.4 1.0 ND1 B:HIS236 4.3 5.0 1.0 CG2 B:VAL235 4.4 3.7 1.0 CE2 B:PHE149 4.4 6.8 1.0 OD2 B:ASP313 4.5 10.9 1.0 NE2 B:HIS56 4.5 5.3 1.0 CA B:HIS180 4.6 3.3 1.0 CE1 B:HIS56 4.6 4.9 1.0 CE B:KCX147 4.7 5.4 1.0 CE2 B:TYR152 4.7 10.7 1.0 CD2 B:PHE149 4.8 6.0 1.0 CZ B:TYR152 5.0 10.2 1.0 OD1 B:ASP313 5.0 5.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Dihydropyrimidinase From Sinorhizobium Meliloti within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:2.0 occ:0.50 OQ1 B:KCX147 2.0 6.3 1.0 O B:HOH1042 2.0 7.8 1.0 NE2 B:HIS56 2.2 5.3 1.0 NE2 B:HIS58 2.2 7.7 1.0 OD1 B:ASP313 2.2 5.7 1.0 CX B:KCX147 3.0 6.7 1.0 CG B:ASP313 3.1 8.2 1.0 CD2 B:HIS56 3.1 5.3 1.0 CE1 B:HIS58 3.1 8.2 1.0 CD2 B:HIS58 3.2 7.0 1.0 CE1 B:HIS56 3.2 4.9 1.0 OQ2 B:KCX147 3.3 3.9 1.0 OD2 B:ASP313 3.5 10.9 1.0 ZN B:ZN501 3.5 2.0 0.5 O B:HOH1041 3.7 12.4 1.0 NZ B:KCX147 4.2 5.1 1.0 ND1 B:HIS58 4.2 7.8 1.0 CG B:HIS56 4.2 4.7 1.0 CB B:ASP313 4.2 3.7 1.0 ND1 B:HIS56 4.3 4.1 1.0 CG B:HIS58 4.3 4.0 1.0 CD2 B:HIS236 4.4 5.9 1.0 NE2 B:HIS236 4.6 7.4 1.0 CE2 B:PHE90 4.6 4.8 1.0 O B:HOH1144 4.6 22.1 1.0 CA B:ASP313 4.6 2.8 1.0 CD2 B:PHE90 4.8 6.4 1.0

S.Martinez-Rodriguez, A.I.Martinez-Gomez, J.M.Clemente-Jimenez, F.Rodriguez-Vico, J.M.Garcia-Ruiz, F.J.Las Heras-Vazquez, J.A.Gavira. Structure of Dihydropyrimidinase From Sinorhizobium Meliloti CECT4114: New Features in An Amidohydrolase Family Member J.Struct.Biol. V. 169 200 2010.
ISSN: ISSN 1047-8477
PubMed: 19895890
DOI: 10.1016/J.JSB.2009.10.013