Zinc in PDB 7c43: The Crystal Structure of Trypanosoma Brucei Rnase D : Amp Complex

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D : Amp Complex, PDB code: 7c43 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)	61.21 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.73, 77.73, 99.301, 90, 90, 90
R / Rfree (%)	20 / 24.2

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D : Amp 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 : Amp Complex (pdb code 7c43). 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 : Amp Complex, PDB code: 7c43:
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 : Amp 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 : Amp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:22.8 occ:1.00 SG A:CYS300 2.1 20.4 1.0 SG A:CYS310 2.2 26.4 1.0 NE2 A:HIS305 2.3 23.6 1.0 SG A:CYS297 2.4 17.3 1.0 CB A:CYS297 3.1 19.0 1.0 CD2 A:HIS305 3.2 22.4 1.0 CB A:CYS300 3.2 21.5 1.0 CB A:CYS310 3.2 30.3 1.0 CE1 A:HIS305 3.4 23.2 1.0 N A:CYS300 3.7 21.2 1.0 CA A:CYS300 4.0 21.9 1.0 CA A:CYS310 4.1 32.2 1.0 CG A:HIS305 4.4 22.1 1.0 ND1 A:HIS305 4.4 22.9 1.0 CA A:CYS297 4.6 19.6 1.0 CB A:PHE299 4.7 20.1 1.0 C A:CYS300 4.7 22.3 1.0 C A:PHE299 4.7 20.7 1.0 N A:GLY301 4.9 23.9 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of Trypanosoma Brucei Rnase D : Amp 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 : Amp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:26.6 occ:1.00 SG A:CYS333 2.2 22.2 1.0 NE2 A:HIS328 2.3 33.4 1.0 SG A:CYS323 2.3 25.2 1.0 SG A:CYS320 2.4 23.5 1.0 CD2 A:HIS328 3.0 33.9 1.0 CB A:CYS320 3.0 27.1 1.0 CB A:CYS333 3.2 25.7 1.0 CB A:CYS323 3.2 27.6 1.0 CE1 A:HIS328 3.4 34.6 1.0 N A:CYS323 3.7 26.6 1.0 CA A:CYS323 4.0 26.6 1.0 CA A:CYS333 4.2 26.4 1.0 CG A:HIS328 4.2 35.6 1.0 ND1 A:HIS328 4.4 35.5 1.0 CA A:CYS320 4.5 28.5 1.0 C A:CYS323 4.7 28.8 1.0 CB A:PHE322 4.8 28.4 1.0 C A:PHE322 4.9 27.5 1.0 N A:GLY324 4.9 30.8 1.0 O A:THR329 4.9 29.7 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