Calcium 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:

Zinc

(Zn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12, PDB code: 7c45:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca403 b:18.9 occ:1.00 OD2 A:ASP80 2.2 15.6 1.0 OP1 D:U12 2.2 25.6 1.0 OE2 A:GLU82 2.3 19.4 1.0 OD2 A:ASP230 2.4 25.0 1.0 O A:HOH666 2.5 36.5 1.0 O A:HOH606 2.9 18.3 1.0 CG A:ASP80 3.0 14.3 1.0 OD1 A:ASP80 3.1 14.2 1.0 CG A:ASP230 3.4 23.1 1.0 CD A:GLU82 3.4 19.9 1.0 P D:U12 3.6 23.2 1.0 O A:HOH518 3.8 45.2 1.0 CB A:ASP230 3.8 17.4 1.0 CA D:CA101 3.9 20.1 1.0 OE1 A:GLU82 3.9 16.2 1.0 O A:HOH517 4.0 26.4 1.0 NE2 A:GLN100 4.2 14.8 1.0 OP2 D:U12 4.2 20.2 1.0 O A:HOH637 4.3 35.3 1.0 OD1 A:ASP230 4.4 24.0 1.0 CB A:ASP80 4.4 14.3 1.0 O5' D:U12 4.4 21.1 1.0 O A:HOH577 4.4 14.9 1.0 O A:ILE81 4.6 14.3 1.0 C5' D:U12 4.6 23.5 1.0 O3' D:U11 4.6 19.8 1.0 CG A:GLU82 4.7 16.4 1.0 O A:HOH619 4.8 15.4 1.0 O A:ALA227 4.9 15.4 1.0

Calcium 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 Calcium with other atoms in the Ca 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 D:Ca101 b:20.1 occ:1.00 O3' D:U11 2.2 19.8 1.0 O A:HOH513 2.4 14.1 1.0 OD1 A:ASP80 2.4 14.2 1.0 O A:HOH619 2.4 15.4 1.0 OP1 D:U12 2.5 25.6 1.0 O A:HOH515 2.5 15.5 1.0 P D:U12 2.9 23.2 1.0 C3' D:U11 3.4 14.3 1.0 CG A:ASP80 3.5 14.3 1.0 O2' D:U11 3.5 22.9 1.0 C5' D:U12 3.9 23.5 1.0 O5' D:U12 3.9 21.1 1.0 CA A:CA403 3.9 18.9 1.0 C4' D:U11 3.9 21.3 1.0 C2' D:U11 4.0 26.2 1.0 OD2 A:ASP80 4.0 15.6 1.0 OD2 A:ASP145 4.1 23.2 1.0 OP2 D:U12 4.2 20.2 1.0 O A:HOH548 4.3 13.9 1.0 O A:ILE81 4.3 14.3 1.0 O A:PHE140 4.4 13.8 1.0 OD1 A:ASP145 4.4 18.1 1.0 OD2 A:ASP230 4.4 25.0 1.0 N A:ILE81 4.6 14.1 1.0 C5' D:U11 4.6 18.7 1.0 CB A:ASP80 4.6 14.3 1.0 CG A:ASP145 4.7 17.6 1.0 O D:HOH218 4.8 18.5 1.0 CA A:ASP80 4.8 14.1 1.0 O A:HOH517 4.9 26.4 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