Magnesium in PDB 7tuv: Crystal Structure of the Exoribonucleolytic Module of T. Brucei RRP44

The structure of Crystal Structure of the Exoribonucleolytic Module of T. Brucei RRP44, PDB code: 7tuv was solved by G.Cesaro, B.G.Guimaraes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.63 / 2.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.296, 91.113, 148.305, 90, 90, 90
R / Rfree (%)	19.4 / 26.5

The binding sites of Magnesium atom in the Crystal Structure of the Exoribonucleolytic Module of T. Brucei RRP44 (pdb code 7tuv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Exoribonucleolytic Module of T. Brucei RRP44, PDB code: 7tuv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Exoribonucleolytic Module of T. Brucei RRP44


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Exoribonucleolytic Module of T. Brucei RRP44 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:72.8 occ:1.00 O3' B:U5 2.1 60.9 1.0 OD1 A:ASP503 2.4 44.7 1.0 N A:ASP511 3.2 36.2 1.0 CG A:ASP503 3.3 44.0 1.0 OD2 A:ASP503 3.4 45.3 1.0 C3' B:U5 3.5 60.8 1.0 N A:ASP512 3.7 37.6 1.0 OD2 A:ASP512 3.7 46.6 1.0 MG A:MG1003 3.8 59.7 1.0 CB A:ASP511 3.9 40.1 1.0 CA A:ILE510 4.0 36.8 1.0 CA A:ASP511 4.0 37.2 1.0 C A:ILE510 4.0 35.9 1.0 CG A:ASP512 4.1 45.0 1.0 O2' B:U5 4.1 62.1 1.0 O2P A:U5P1001 4.1 108.8 0.8 O A:ASP509 4.2 39.0 1.0 CG2 A:ILE510 4.2 36.6 1.0 O A:ASP512 4.3 38.0 1.0 C4' B:U5 4.3 59.7 1.0 OD1 A:ASP512 4.3 46.5 1.0 C2' B:U5 4.3 61.7 1.0 C A:ASP511 4.3 37.6 1.0 O5' A:U5P1001 4.5 108.0 0.8 O A:HOH1102 4.6 25.7 1.0 CB A:ASP503 4.7 41.4 1.0 CA A:ASP512 4.7 37.7 1.0 CB A:ILE510 4.7 36.5 1.0 C5' A:U5P1001 4.7 107.2 0.8 P A:U5P1001 4.8 108.6 0.8 C5' B:U5 4.8 57.4 1.0 CB A:ASP512 4.9 39.6 1.0 O1P A:U5P1001 4.9 108.7 0.8 C A:ASP512 4.9 37.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Exoribonucleolytic Module of T. Brucei RRP44


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Exoribonucleolytic Module of T. Brucei RRP44 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:59.7 occ:1.00 CB A:ASP511 2.7 40.1 1.0 OD2 A:ASP511 2.7 50.1 1.0 O2P A:U5P1001 2.8 108.8 0.8 CG A:ASP511 2.9 46.4 1.0 O A:HOH1102 2.9 25.7 1.0 OG A:SER804 3.0 35.9 1.0 O1P A:U5P1001 3.3 108.7 0.8 O3' B:U5 3.3 60.9 1.0 NE A:ARG807 3.3 44.0 1.0 CB A:SER804 3.6 33.1 1.0 P A:U5P1001 3.6 108.6 0.8 C3' B:U5 3.7 60.8 1.0 NH2 A:ARG807 3.8 44.4 1.0 MG A:MG1002 3.8 72.8 1.0 OD1 A:ASP511 3.9 47.6 1.0 CZ A:ARG807 4.0 46.0 1.0 CA A:ASP511 4.1 37.2 1.0 O5' B:U5 4.2 55.2 1.0 CA A:SER804 4.2 31.2 1.0 O A:THR803 4.2 33.0 1.0 CD A:ARG807 4.2 39.5 1.0 OD2 A:ASP512 4.2 46.6 1.0 C5' B:U5 4.3 57.4 1.0 N A:ASP511 4.3 36.2 1.0 CG A:ARG807 4.4 33.7 1.0 C4' B:U5 4.6 59.7 1.0 O5' A:U5P1001 4.7 108.0 0.8 O3P A:U5P1001 4.8 108.7 0.8 OP1 B:U5 4.8 52.0 1.0 C A:ASP511 4.9 37.6 1.0 C A:THR803 4.9 32.3 1.0 N A:SER804 5.0 31.7 1.0

G.Cesaro, H.T.Da Soler, E.P.Guerra-Slompo, A.Haouz, P.Legrand, N.I.T.Zanchin, B.G.Guimaraes. Trypanosoma Brucei RRP44: A Versatile Enzyme For Processing Structured and Non-Structured Rna Substrates. Nucleic Acids Res. 2022.
ISSN: ESSN 1362-4962
PubMed: 36583334
DOI: 10.1093/NAR/GKAC1199