Zinc in PDB 7c4b: The Crystal Structure of Trypanosoma Brucei Rnase D : Ump Complex

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D : Ump Complex, PDB code: 7c4b 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)	29.71 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.432, 77.956, 101.703, 90, 90, 90
R / Rfree (%)	23.1 / 26.7

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D : Ump 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 : Ump Complex (pdb code 7c4b). 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 : Ump Complex, PDB code: 7c4b:
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 : Ump 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 : Ump Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:41.3 occ:1.00 NE2 A:HIS305 2.2 37.8 1.0 SG A:CYS300 2.2 36.1 1.0 SG A:CYS310 2.3 42.6 1.0 SG A:CYS297 2.3 40.1 1.0 CB A:CYS310 3.1 36.1 1.0 CB A:CYS297 3.1 42.2 1.0 CD2 A:HIS305 3.2 40.9 1.0 CE1 A:HIS305 3.2 39.1 1.0 CB A:CYS300 3.3 47.8 1.0 N A:CYS300 3.7 40.8 1.0 CA A:CYS310 3.9 45.7 1.0 CA A:CYS300 4.1 36.2 1.0 CG A:HIS305 4.3 41.1 1.0 ND1 A:HIS305 4.3 42.3 1.0 O4 A:U405 4.5 52.4 1.0 CA A:CYS297 4.6 42.6 1.0 CB A:PHE299 4.6 41.0 1.0 O A:THR306 4.8 39.5 1.0 C A:CYS300 4.8 39.3 1.0 C A:PHE299 4.8 44.4 1.0 N A:GLY301 4.8 36.3 1.0 C A:CYS310 4.9 52.7 1.0 N A:CYS310 4.9 36.5 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of Trypanosoma Brucei Rnase D : Ump 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 : Ump Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:51.7 occ:1.00 SG A:CYS320 2.3 40.5 1.0 SG A:CYS323 2.3 57.3 1.0 SG A:CYS333 2.3 42.2 1.0 NE2 A:HIS328 2.4 50.4 1.0 CB A:CYS333 3.0 45.2 1.0 CB A:CYS320 3.1 48.4 1.0 CD2 A:HIS328 3.2 50.8 1.0 CB A:CYS323 3.2 50.2 1.0 CE1 A:HIS328 3.5 54.5 1.0 N A:CYS323 3.9 48.3 1.0 CA A:CYS333 4.0 49.0 1.0 CA A:CYS323 4.1 58.4 1.0 CG A:HIS328 4.4 64.2 1.0 ND1 A:HIS328 4.5 55.4 1.0 CA A:CYS320 4.6 50.5 1.0 C A:CYS323 4.7 51.5 1.0 C A:PHE322 4.9 46.6 1.0 CB A:PHE322 4.9 48.7 1.0 C A:CYS333 4.9 46.8 1.0 O A:THR329 4.9 47.3 1.0 N A:GLY324 5.0 49.2 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