Manganese 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:

Zinc

(Zn)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the The Crystal Structure of Trypanosoma Brucei Rnase D : Cmp Complex, PDB code: 7c47:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn405 b:88.1 occ:1.00 OD2 A:ASP80 2.3 33.1 1.0 OD2 A:ASP230 2.8 40.5 1.0 OE2 A:GLU82 3.0 34.1 1.0 CG A:ASP80 3.3 30.2 1.0 OD1 A:ASP80 3.6 31.9 1.0 CG A:ASP230 3.8 37.5 1.0 CD A:GLU82 4.0 32.3 1.0 CB A:ASP230 4.0 36.3 1.0 O A:ILE81 4.1 28.1 1.0 NE2 A:GLN100 4.2 29.5 1.0 OE1 A:GLU82 4.3 32.2 1.0 O A:HOH508 4.6 39.1 1.0 CB A:ASP80 4.6 28.5 1.0 MN A:MN406 4.8 85.1 1.0 OD1 A:ASP230 4.9 37.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn406 b:85.1 occ:1.00 OD1 A:ASP80 2.3 31.9 1.0 OD2 A:ASP145 2.7 27.4 1.0 CG A:ASP80 3.5 30.2 1.0 CG A:ASP145 3.5 26.1 1.0 OD1 A:ASP145 3.5 26.4 1.0 O A:HOH531 3.5 20.8 1.0 OD2 A:ASP80 4.1 33.1 1.0 O A:PHE140 4.2 20.7 1.0 O A:HOH516 4.2 27.6 1.0 O A:ASP141 4.3 20.6 1.0 N A:ILE81 4.5 26.9 1.0 CB A:ASP80 4.5 28.5 1.0 CA A:ASP80 4.6 26.9 1.0 MN A:MN405 4.8 88.1 1.0 O A:ILE81 4.8 28.1 1.0 CB A:ASP145 4.9 25.2 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