Zinc in PDB 4hk6: Crystal Structure of Cordyceps Militaris Idcase in Complex with 5- Nitro-Uracil

All present enzymatic activity of Crystal Structure of Cordyceps Militaris Idcase in Complex with 5- Nitro-Uracil:
4.1.1.66;

The structure of Crystal Structure of Cordyceps Militaris Idcase in Complex with 5- Nitro-Uracil, PDB code: 4hk6 was solved by S.Xu, J.Zhu, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.10 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.259, 145.284, 77.506, 90.00, 95.84, 90.00
R / Rfree (%)	15.3 / 20.2

The binding sites of Zinc atom in the Crystal Structure of Cordyceps Militaris Idcase in Complex with 5- Nitro-Uracil (pdb code 4hk6). 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 in Complex with 5- Nitro-Uracil, PDB code: 4hk6:
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 in Complex with 5- Nitro-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 in Complex with 5- Nitro-Uracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:25.2 occ:1.00 NE2 A:HIS195 2.2 12.9 1.0 O4 A:5NU402 2.2 18.8 1.0 OD1 A:ASP323 2.3 20.1 1.0 NE2 A:HIS12 2.3 13.5 1.0 O52 A:5NU402 2.3 23.6 1.0 NE2 A:HIS14 2.4 13.6 1.0 CG A:ASP323 3.0 19.7 1.0 CD2 A:HIS14 3.1 14.3 1.0 CE1 A:HIS195 3.2 14.1 1.0 N51 A:5NU402 3.2 24.6 1.0 OD2 A:ASP323 3.2 23.2 1.0 CD2 A:HIS12 3.2 13.0 1.0 C4 A:5NU402 3.3 20.7 1.0 CD2 A:HIS195 3.3 13.1 1.0 CE1 A:HIS12 3.3 12.9 1.0 CE1 A:HIS14 3.5 14.2 1.0 C5 A:5NU402 3.7 21.9 1.0 O53 A:5NU402 4.1 29.5 1.0 ND1 A:HIS195 4.3 14.8 1.0 NE2 A:HIS251 4.4 16.2 1.0 CG A:HIS14 4.4 14.3 1.0 CG A:HIS195 4.4 14.1 1.0 CB A:ASP323 4.4 16.7 1.0 CG A:HIS12 4.4 13.3 1.0 ND1 A:HIS12 4.5 14.0 1.0 N3 A:5NU402 4.5 21.4 1.0 ND1 A:HIS14 4.5 14.7 1.0 CD2 A:PHE326 4.8 19.0 1.0 CA A:ASP323 4.8 14.6 1.0 CE1 A:HIS251 4.8 16.3 1.0 CE2 A:PHE326 5.0 18.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase in Complex with 5- Nitro-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 in Complex with 5- Nitro-Uracil within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:23.0 occ:1.00 NE2 B:HIS195 2.2 13.5 1.0 O52 B:5NU402 2.2 23.8 1.0 NE2 B:HIS12 2.3 14.0 1.0 OD1 B:ASP323 2.3 17.1 1.0 O4 B:5NU402 2.3 18.6 1.0 NE2 B:HIS14 2.3 11.1 1.0 CG B:ASP323 3.0 19.1 1.0 CD2 B:HIS12 3.1 12.4 1.0 CD2 B:HIS14 3.1 11.1 1.0 OD2 B:ASP323 3.2 21.9 1.0 CE1 B:HIS195 3.2 13.6 1.0 CD2 B:HIS195 3.3 12.6 1.0 CE1 B:HIS12 3.3 13.1 1.0 N51 B:5NU402 3.3 24.8 1.0 C4 B:5NU402 3.3 20.8 1.0 CE1 B:HIS14 3.4 12.2 1.0 C5 B:5NU402 3.8 22.1 1.0 ND1 B:HIS195 4.3 12.8 1.0 CG B:HIS12 4.4 12.3 1.0 O53 B:5NU402 4.4 28.3 1.0 CG B:HIS14 4.4 12.6 1.0 CB B:ASP323 4.4 16.4 1.0 NE2 B:HIS251 4.4 16.1 1.0 ND1 B:HIS12 4.4 12.3 1.0 CG B:HIS195 4.4 13.1 1.0 ND1 B:HIS14 4.5 13.2 1.0 N3 B:5NU402 4.5 19.6 1.0 CA B:ASP323 4.7 14.8 1.0 CD2 B:PHE326 4.7 17.5 1.0 CE1 B:HIS251 4.8 16.2 1.0 CE2 B:PHE326 5.0 16.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase in Complex with 5- Nitro-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 in Complex with 5- Nitro-Uracil within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:21.3 occ:1.00 OD1 C:ASP323 2.2 17.3 1.0 NE2 C:HIS195 2.2 12.1 1.0 O52 C:5NU402 2.3 24.0 1.0 O4 C:5NU402 2.3 14.9 1.0 NE2 C:HIS12 2.3 13.3 1.0 NE2 C:HIS14 2.4 10.2 1.0 CG C:ASP323 3.0 18.6 1.0 CD2 C:HIS14 3.1 10.4 1.0 CE1 C:HIS195 3.1 12.6 1.0 OD2 C:ASP323 3.2 22.3 1.0 CD2 C:HIS195 3.2 11.9 1.0 CD2 C:HIS12 3.2 12.1 1.0 N51 C:5NU402 3.3 22.9 1.0 C4 C:5NU402 3.3 17.4 1.0 CE1 C:HIS12 3.3 13.3 1.0 CE1 C:HIS14 3.5 11.4 1.0 C5 C:5NU402 3.8 19.2 1.0 ND1 C:HIS195 4.3 12.0 1.0 O53 C:5NU402 4.3 26.3 1.0 CG C:HIS14 4.4 11.6 1.0 CG C:HIS195 4.4 11.9 1.0 CB C:ASP323 4.4 15.1 1.0 CG C:HIS12 4.4 12.4 1.0 NE2 C:HIS251 4.4 16.0 1.0 ND1 C:HIS12 4.5 13.4 1.0 N3 C:5NU402 4.5 17.3 1.0 ND1 C:HIS14 4.5 12.7 1.0 CD2 C:PHE326 4.8 15.1 1.0 CA C:ASP323 4.8 13.4 1.0 CE1 C:HIS251 4.9 16.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Cordyceps Militaris Idcase in Complex with 5- Nitro-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 in Complex with 5- Nitro-Uracil within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:21.5 occ:1.00 OD1 D:ASP323 2.2 18.1 1.0 NE2 D:HIS195 2.2 12.8 1.0 NE2 D:HIS12 2.3 13.6 1.0 O52 D:5NU402 2.3 20.4 1.0 O4 D:5NU402 2.3 18.5 1.0 NE2 D:HIS14 2.4 10.5 1.0 CG D:ASP323 3.0 18.5 1.0 CD2 D:HIS12 3.2 12.2 1.0 CD2 D:HIS14 3.2 10.3 1.0 OD2 D:ASP323 3.2 21.4 1.0 CE1 D:HIS195 3.2 13.4 1.0 N51 D:5NU402 3.2 22.6 1.0 CD2 D:HIS195 3.2 12.2 1.0 C4 D:5NU402 3.3 19.2 1.0 CE1 D:HIS12 3.3 12.5 1.0 CE1 D:HIS14 3.4 12.0 1.0 C5 D:5NU402 3.7 20.3 1.0 O53 D:5NU402 4.2 28.5 1.0 ND1 D:HIS195 4.4 12.4 1.0 NE2 D:HIS251 4.4 14.1 1.0 CG D:HIS12 4.4 12.5 1.0 CG D:HIS14 4.4 11.8 1.0 CG D:HIS195 4.4 12.2 1.0 CB D:ASP323 4.4 14.7 1.0 ND1 D:HIS12 4.4 13.6 1.0 ND1 D:HIS14 4.5 13.0 1.0 N3 D:5NU402 4.5 18.7 1.0 CD2 D:PHE326 4.7 16.5 1.0 CA D:ASP323 4.8 13.1 1.0 CE1 D:HIS251 4.9 14.2 1.0 CE2 D:PHE326 5.0 16.2 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