Zinc in PDB 4lal: Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil

The structure of Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil, PDB code: 4lal was solved by S.Xu, W.Li, J.Zhu, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.96 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.266, 54.301, 143.776, 90.00, 121.04, 90.00
R / Rfree (%)	17.5 / 22

The binding sites of Zinc atom in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil (pdb code 4lal). 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 Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil, PDB code: 4lal:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil


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 Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:37.7 occ:1.00 O53 A:5CU402 2.0 33.0 1.0 O4 A:5CU402 2.0 31.7 1.0 NE2 A:HIS195 2.3 23.4 1.0 NE2 A:HIS14 2.3 21.6 1.0 NE2 A:HIS12 2.5 22.5 1.0 C51 A:5CU402 3.0 37.8 1.0 C4 A:5CU402 3.0 37.8 1.0 CE1 A:HIS195 3.1 23.5 1.0 CD2 A:HIS14 3.2 22.0 1.0 CD2 A:HIS12 3.3 22.7 1.0 CD2 A:HIS195 3.3 23.5 1.0 CE1 A:HIS14 3.4 22.3 1.0 C5 A:5CU402 3.4 39.1 1.0 CE1 A:HIS12 3.6 23.2 1.0 O52 A:5CU402 4.1 33.5 1.0 N3 A:5CU402 4.2 37.5 1.0 ND1 A:HIS195 4.2 23.1 1.0 NE2 A:HIS251 4.3 24.3 1.0 CG A:HIS14 4.4 22.4 1.0 CG A:HIS195 4.4 22.9 1.0 ND1 A:HIS14 4.4 22.4 1.0 CG A:HIS12 4.5 22.9 1.0 CB A:ALA323 4.6 24.7 1.0 ND1 A:HIS12 4.6 23.7 1.0 CA A:ALA323 4.7 24.2 1.0 CD2 A:PHE326 4.7 20.5 1.0 CE1 A:HIS251 4.8 24.5 1.0 C6 A:5CU402 4.8 40.2 1.0 CE2 A:PHE326 4.9 20.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil


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 Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:38.8 occ:1.00 O52 B:5CU402 1.9 36.8 1.0 O4 B:5CU402 2.0 28.8 1.0 NE2 B:HIS195 2.2 21.8 1.0 NE2 B:HIS14 2.3 25.5 1.0 NE2 B:HIS12 2.5 20.9 1.0 C51 B:5CU402 3.0 39.0 1.0 C4 B:5CU402 3.0 37.8 1.0 CE1 B:HIS195 3.1 21.9 1.0 CD2 B:HIS14 3.1 25.0 1.0 CD2 B:HIS195 3.3 21.6 1.0 CD2 B:HIS12 3.3 21.2 1.0 C5 B:5CU402 3.4 39.2 1.0 CE1 B:HIS14 3.4 25.6 1.0 CE1 B:HIS12 3.6 21.6 1.0 O53 B:5CU402 4.0 35.1 1.0 N3 B:5CU402 4.2 37.9 1.0 ND1 B:HIS195 4.2 21.6 1.0 NE2 B:HIS251 4.3 27.2 1.0 CG B:HIS14 4.3 25.4 1.0 CG B:HIS195 4.4 21.2 1.0 ND1 B:HIS14 4.4 25.8 1.0 CG B:HIS12 4.5 21.9 1.0 ND1 B:HIS12 4.6 22.4 1.0 CB B:ALA323 4.6 27.0 1.0 CD2 B:PHE326 4.7 23.7 1.0 CA B:ALA323 4.7 26.1 1.0 C6 B:5CU402 4.8 39.5 1.0 CE1 B:HIS251 4.9 27.8 1.0 CE2 B:PHE326 5.0 23.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil


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 Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:36.5 occ:1.00 O53 C:5CU402 2.0 31.4 1.0 O4 C:5CU402 2.0 31.4 1.0 NE2 C:HIS195 2.3 21.7 1.0 NE2 C:HIS14 2.4 21.2 1.0 NE2 C:HIS12 2.4 23.7 1.0 C51 C:5CU402 3.0 37.5 1.0 C4 C:5CU402 3.0 39.9 1.0 CD2 C:HIS14 3.2 21.9 1.0 CD2 C:HIS12 3.2 23.3 1.0 CD2 C:HIS195 3.3 21.9 1.0 CE1 C:HIS195 3.3 22.6 1.0 C5 C:5CU402 3.4 39.6 1.0 CE1 C:HIS12 3.5 23.3 1.0 CE1 C:HIS14 3.5 21.3 1.0 O52 C:5CU402 4.1 34.9 1.0 N3 C:5CU402 4.2 39.7 1.0 NE2 C:HIS251 4.2 24.7 1.0 CG C:HIS14 4.4 22.4 1.0 ND1 C:HIS195 4.4 22.7 1.0 CG C:HIS195 4.4 22.1 1.0 CG C:HIS12 4.5 23.8 1.0 ND1 C:HIS14 4.5 22.4 1.0 ND1 C:HIS12 4.5 23.9 1.0 CB C:ALA323 4.6 25.6 1.0 CE1 C:HIS251 4.7 24.7 1.0 CA C:ALA323 4.7 25.3 1.0 CD2 C:PHE326 4.7 28.0 1.0 C6 C:5CU402 4.8 39.7 1.0 CE2 C:PHE326 5.0 28.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil


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 Cordyceps Militaris Idcase D323A Mutant in Complex with 5-Carboxyl-Uracil within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:42.3 occ:1.00 O4 D:5CU402 2.0 38.0 1.0 O52 D:5CU402 2.0 36.4 1.0 NE2 D:HIS195 2.2 26.7 1.0 NE2 D:HIS14 2.4 27.1 1.0 NE2 D:HIS12 2.4 26.0 1.0 C4 D:5CU402 3.0 42.4 1.0 C51 D:5CU402 3.0 40.0 1.0 CE1 D:HIS195 3.0 28.3 1.0 CD2 D:HIS14 3.1 26.6 1.0 CD2 D:HIS12 3.3 26.7 1.0 CD2 D:HIS195 3.3 27.1 1.0 C5 D:5CU402 3.4 42.1 1.0 CE1 D:HIS12 3.5 27.2 1.0 CE1 D:HIS14 3.5 26.7 1.0 O53 D:5CU402 4.1 35.5 1.0 N3 D:5CU402 4.2 41.6 1.0 ND1 D:HIS195 4.2 28.8 1.0 NE2 D:HIS251 4.3 28.4 1.0 CG D:HIS14 4.4 26.4 1.0 CG D:HIS195 4.4 27.5 1.0 ND1 D:HIS14 4.5 26.8 1.0 CG D:HIS12 4.5 27.9 1.0 ND1 D:HIS12 4.5 27.7 1.0 CB D:ALA323 4.6 32.6 1.0 CE1 D:HIS251 4.7 27.8 1.0 CA D:ALA323 4.7 31.3 1.0 CD2 D:PHE326 4.8 27.6 1.0 C6 D:5CU402 4.8 43.2 1.0 CE2 D:PHE326 5.0 27.8 1.0

S.Xu, W.Li, J.Zhu, R.Wang, Z.Li, G.L.Xu, J.Ding. Crystal Structures of Isoorotate Decarboxylases Reveal A Novel Catalytic Mechanism of 5-Carboxyl-Uracil Decarboxylation and Shed Light on the Search For Dna Decarboxylase. Cell Res. V. 23 1296 2013.
ISSN: ISSN 1001-0602
PubMed: 23917530
DOI: 10.1038/CR.2013.107