Zinc in PDB 7c42: The Crystal Structure of Trypanosoma Brucei Rnase D

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D, PDB code: 7c42 was solved by Y.Q.Gao, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.50 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.929, 77.451, 101.544, 90, 90, 90
R / Rfree (%)	17.6 / 21.5

The binding sites of Zinc atom in the The Crystal Structure of Trypanosoma Brucei Rnase D (pdb code 7c42). 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 Trypanosoma Brucei Rnase D, PDB code: 7c42:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Crystal Structure of Trypanosoma Brucei Rnase D


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 Trypanosoma Brucei Rnase D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:22.2 occ:1.00 NE2 A:HIS328 2.1 20.1 1.0 SG A:CYS333 2.2 17.5 1.0 SG A:CYS320 2.3 18.4 1.0 SG A:CYS323 2.3 22.7 1.0 CB A:CYS333 3.0 21.1 1.0 CD2 A:HIS328 3.1 21.0 1.0 CE1 A:HIS328 3.1 26.2 1.0 CB A:CYS320 3.2 21.1 1.0 CB A:CYS323 3.4 25.4 1.0 N A:CYS323 3.9 21.5 1.0 CA A:CYS333 4.0 20.5 1.0 CA A:CYS323 4.2 25.1 1.0 ND1 A:HIS328 4.2 25.5 1.0 CG A:HIS328 4.2 20.5 1.0 CA A:CYS320 4.6 23.0 1.0 C A:CYS323 4.8 27.4 1.0 CB A:PHE322 4.8 18.5 1.0 C A:PHE322 4.9 21.4 1.0 CD A:LYS335 4.9 41.8 1.0 C A:CYS333 4.9 22.6 1.0 N A:GLY324 5.0 26.9 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of Trypanosoma Brucei Rnase D


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 Trypanosoma Brucei Rnase D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:18.6 occ:1.00 NE2 A:HIS305 2.1 15.1 1.0 SG A:CYS300 2.2 16.9 1.0 SG A:CYS310 2.3 20.4 1.0 SG A:CYS297 2.4 17.1 1.0 CE1 A:HIS305 3.0 18.2 1.0 CB A:CYS297 3.1 16.3 1.0 CB A:CYS310 3.2 19.4 1.0 CD2 A:HIS305 3.2 19.9 1.0 CB A:CYS300 3.2 19.0 1.0 N A:CYS300 3.7 15.2 1.0 O A:HOH692 3.8 33.3 1.0 CA A:CYS310 4.0 22.4 1.0 CA A:CYS300 4.0 17.2 1.0 ND1 A:HIS305 4.1 17.1 1.0 CG A:HIS305 4.3 17.8 1.0 CA A:CYS297 4.6 15.1 1.0 C A:CYS300 4.8 16.5 1.0 CB A:PHE299 4.8 14.0 1.0 C A:PHE299 4.8 18.4 1.0 O A:THR306 4.9 17.3 1.0 N A:GLY301 4.9 19.9 1.0 C A:CYS310 5.0 25.3 1.0

Y.Gao, H.Liu, C.Zhang, S.Su, Y.Chen, X.Chen, Y.Li, Z.Shao, Y.Zhang, Q.Shao, J.Li, Z.Huang, J.Ma, J.Gan. Structural Basis For Guide Rna Trimming By Rnase D Ribonuclease in Trypanosoma Brucei. Nucleic Acids Res. V. 49 568 2021.
ISSN: ESSN 1362-4962
PubMed: 33332555
DOI: 10.1093/NAR/GKAA1197