Manganese 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:

Zinc

(Zn)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the The Crystal Structure of Trypanosoma Brucei Rnase D : Ump Complex, PDB code: 7c4b:
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 : Ump 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 : Ump Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:106.1 occ:1.00 OD1 A:ASP80 2.2 48.0 1.0 OD2 A:ASP145 3.2 66.0 1.0 CG A:ASP80 3.4 45.3 1.0 O A:HOH514 3.7 36.9 1.0 OD1 A:ASP145 3.8 62.3 1.0 CG A:ASP145 3.9 59.8 1.0 OD2 A:ASP80 3.9 52.9 1.0 MN A:MN404 4.0 80.6 1.0 O A:PHE140 4.2 39.9 1.0 O A:ASP141 4.5 37.8 1.0 CB A:ASP80 4.6 35.1 1.0 N A:ILE81 4.6 40.8 1.0 O A:ILE81 4.7 54.9 1.0 O A:HOH510 4.7 41.6 1.0 CA A:ASP80 4.7 40.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn404 b:80.6 occ:1.00 OD2 A:ASP80 2.0 52.9 1.0 OD2 A:ASP230 2.5 57.7 1.0 CG A:ASP80 3.0 45.3 1.0 OE2 A:GLU82 3.1 72.4 1.0 OD1 A:ASP80 3.3 48.0 1.0 CG A:ASP230 3.5 49.8 1.0 CB A:ASP230 3.8 42.9 1.0 MN A:MN403 4.0 106.1 1.0 CD A:GLU82 4.2 49.5 1.0 O A:ILE81 4.3 54.9 1.0 CB A:ASP80 4.3 35.1 1.0 NE2 A:GLN100 4.4 39.9 1.0 OD1 A:ASP230 4.6 61.2 1.0 O A:HOH512 4.7 40.9 1.0 OE1 A:GLU82 4.7 58.0 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