Zinc in PDB 7c45: The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12, PDB code: 7c45 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)	36.84 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.449, 65.843, 99.914, 90, 90, 90
R / Rfree (%)	19.3 / 22.1

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12 (pdb code 7c45). 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 Complex with Rna U12, PDB code: 7c45:
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 Complex with Rna U12


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 Complex with Rna U12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:16.7 occ:1.00 NE2 A:HIS305 2.2 16.3 1.0 SG A:CYS297 2.3 16.7 1.0 SG A:CYS310 2.3 16.9 1.0 SG A:CYS300 2.4 16.9 1.0 CB A:CYS297 3.1 18.4 1.0 CB A:CYS310 3.1 16.7 1.0 CD2 A:HIS305 3.1 16.1 1.0 CE1 A:HIS305 3.1 16.3 1.0 CB A:CYS300 3.3 17.3 1.0 N A:CYS300 3.8 17.4 1.0 CA A:CYS310 3.9 16.6 1.0 CA A:CYS300 4.1 17.5 1.0 ND1 A:HIS305 4.2 16.1 1.0 CG A:HIS305 4.3 16.0 1.0 O D:HOH215 4.3 30.8 1.0 O A:HOH676 4.4 26.9 1.0 O4 D:U6 4.5 16.4 1.0 CA A:CYS297 4.5 16.6 1.0 CB A:PHE299 4.6 17.4 1.0 C A:CYS300 4.8 17.5 1.0 C A:PHE299 4.8 17.6 1.0 N A:GLY301 4.8 17.4 1.0 C A:CYS310 4.8 16.8 1.0 O A:THR306 4.9 16.2 1.0 N A:CYS310 5.0 16.5 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12


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 Complex with Rna U12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:19.7 occ:1.00 NE2 A:HIS328 2.1 19.3 1.0 SG A:CYS323 2.3 20.6 1.0 SG A:CYS333 2.3 19.8 1.0 SG A:CYS320 2.4 19.1 1.0 CE1 A:HIS328 3.0 19.6 1.0 CB A:CYS333 3.0 19.0 1.0 CD2 A:HIS328 3.1 18.8 1.0 CB A:CYS320 3.1 19.1 1.0 CB A:CYS323 3.3 21.3 1.0 N A:CYS323 3.7 20.6 1.0 CA A:CYS333 3.9 18.8 1.0 CA A:CYS323 4.1 21.1 1.0 ND1 A:HIS328 4.1 19.2 1.0 CG A:HIS328 4.2 18.7 1.0 O A:HOH664 4.4 39.8 1.0 O4 D:U4 4.5 19.6 1.0 CB A:PHE322 4.5 19.9 1.0 O D:HOH203 4.5 24.5 1.0 CA A:CYS320 4.6 18.8 1.0 C A:CYS323 4.7 21.2 1.0 N A:GLY324 4.8 20.7 1.0 C A:PHE322 4.8 21.3 1.0 C A:CYS333 4.8 19.2 1.0 CG A:LYS335 4.9 21.8 1.0 O A:THR329 4.9 17.8 1.0 CD2 A:PHE322 5.0 21.1 1.0 N A:CYS333 5.0 18.2 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