Zinc in PDB 7c47: The Crystal Structure of Trypanosoma Brucei Rnase D : Cmp Complex

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D : Cmp Complex, PDB code: 7c47 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)	30.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.333, 77.35, 102.336, 90, 90, 90
R / Rfree (%)	22.1 / 25

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

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the The Crystal Structure of Trypanosoma Brucei Rnase D : Cmp Complex (pdb code 7c47). 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 : Cmp Complex, PDB code: 7c47:
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 : Cmp Complex


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 : Cmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.4 occ:1.00 SG A:CYS300 2.2 19.1 1.0 SG A:CYS310 2.2 25.5 1.0 SG A:CYS297 2.3 20.9 1.0 NE2 A:HIS305 2.4 26.3 1.0 CB A:CYS297 3.1 21.5 1.0 CB A:CYS310 3.2 27.4 1.0 CD2 A:HIS305 3.3 26.4 1.0 CB A:CYS300 3.3 20.5 1.0 CE1 A:HIS305 3.4 26.2 1.0 N A:CYS300 3.8 21.3 1.0 CA A:CYS310 4.1 28.9 1.0 CA A:CYS300 4.1 21.0 1.0 O2 A:C404 4.2 48.8 1.0 CG A:HIS305 4.4 26.6 1.0 ND1 A:HIS305 4.4 26.8 1.0 C2 A:C404 4.5 47.5 1.0 CA A:CYS297 4.6 22.0 1.0 CB A:PHE299 4.6 21.9 1.0 N3 A:C404 4.8 46.3 1.0 C A:CYS300 4.8 21.4 1.0 C A:PHE299 4.9 21.7 1.0 N A:GLY301 4.9 22.0 1.0 O A:THR306 5.0 25.5 1.0

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


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 : Cmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:27.9 occ:1.00 SG A:CYS323 2.2 29.7 1.0 SG A:CYS333 2.2 24.7 1.0 SG A:CYS320 2.3 26.8 1.0 NE2 A:HIS328 2.7 33.1 1.0 CB A:CYS333 3.1 26.3 1.0 CB A:CYS320 3.1 27.7 1.0 CB A:CYS323 3.2 30.4 1.0 CD2 A:HIS328 3.4 33.3 1.0 CE1 A:HIS328 3.7 33.4 1.0 N A:CYS323 3.8 29.9 1.0 CA A:CYS323 4.0 30.6 1.0 CA A:CYS333 4.1 27.2 1.0 CG A:HIS328 4.6 32.5 1.0 CA A:CYS320 4.6 28.2 1.0 ND1 A:HIS328 4.7 33.4 1.0 C A:CYS323 4.7 31.4 1.0 CB A:PHE322 4.9 26.8 1.0 C A:PHE322 4.9 28.4 1.0 N A:GLY324 5.0 31.9 1.0 O A:THR329 5.0 27.5 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