Manganese 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:

Zinc

(Zn)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the The Crystal Structure of Trypanosoma Brucei Rnase D : Amp Complex, PDB code: 7c43:
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 : Amp 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 : Amp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:39.0 occ:1.00 O1P A:AMP405 2.2 31.6 1.0 OD2 A:ASP80 2.3 18.0 1.0 OD2 A:ASP230 2.4 27.3 1.0 OE1 A:GLU82 2.7 34.6 1.0 O2P A:AMP405 3.0 34.6 1.0 P A:AMP405 3.1 35.5 1.0 CG A:ASP230 3.3 26.2 1.0 CG A:ASP80 3.4 18.3 1.0 CD A:GLU82 3.7 28.5 1.0 O5' A:AMP405 3.8 36.8 1.0 CB A:ASP230 3.9 24.9 1.0 OD1 A:ASP80 3.9 17.7 1.0 MN A:MN404 3.9 37.8 1.0 OE1 A:GLN100 4.0 23.8 1.0 OE2 A:GLU82 4.1 29.9 1.0 OD1 A:ASP230 4.3 26.4 1.0 O A:ILE81 4.4 21.3 1.0 O3P A:AMP405 4.4 34.0 1.0 C5' A:AMP405 4.6 39.8 1.0 CB A:ASP80 4.7 18.7 1.0 O A:HOH505 4.8 45.7 1.0 CG A:GLU82 4.9 26.4 1.0 O A:ALA227 4.9 28.5 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn404 b:37.8 occ:1.00 O1P A:AMP405 2.1 31.6 1.0 O A:HOH501 2.1 37.4 1.0 OD1 A:ASP80 2.1 17.7 1.0 O A:HOH505 2.2 45.7 1.0 O3P A:AMP405 2.8 34.0 1.0 P A:AMP405 3.0 35.5 1.0 CG A:ASP80 3.1 18.3 1.0 OD2 A:ASP80 3.4 18.0 1.0 OD2 A:ASP145 3.7 36.2 1.0 MN A:MN403 3.9 39.0 1.0 O5' A:AMP405 4.0 36.8 1.0 C5' A:AMP405 4.0 39.8 1.0 O2P A:AMP405 4.1 34.6 1.0 OD1 A:ASP145 4.2 33.4 1.0 OD2 A:ASP230 4.2 27.3 1.0 O A:HOH517 4.3 24.1 1.0 O A:ILE81 4.3 21.3 1.0 CG A:ASP145 4.4 32.3 1.0 CB A:ASP80 4.5 18.7 1.0 N A:ILE81 4.6 20.5 1.0 O A:PHE140 4.6 20.1 1.0 CA A:ASP80 4.9 18.9 1.0 O A:HOH514 4.9 24.7 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