Magnesium in PDB 6j80: Human Mitochondrial Oligoribonuclease in Complex with Poly-Dt Dna

The structure of Human Mitochondrial Oligoribonuclease in Complex with Poly-Dt Dna, PDB code: 6j80 was solved by L.Y.Chu, S.Agrawal, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.12 / 1.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.079, 88.403, 45.939, 90.00, 105.36, 90.00
R / Rfree (%)	19.3 / 21.3

The binding sites of Magnesium atom in the Human Mitochondrial Oligoribonuclease in Complex with Poly-Dt Dna (pdb code 6j80). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Mitochondrial Oligoribonuclease in Complex with Poly-Dt Dna, PDB code: 6j80:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Mitochondrial Oligoribonuclease in Complex with Poly-Dt Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Mitochondrial Oligoribonuclease in Complex with Poly-Dt Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:33.3 occ:0.71 OE2 B:GLU49 2.5 20.4 1.0 OP1 C:DT10 2.7 24.5 0.9 O B:HOH462 2.8 32.8 1.0 CD B:GLU49 3.3 22.6 1.0 OE1 B:GLU49 3.3 24.7 1.0 CA B:HIS194 3.6 29.5 1.0 P C:DT10 3.6 24.2 0.8 CD2 B:HIS194 3.7 35.1 1.0 C B:HIS194 3.7 23.5 1.0 OD2 B:ASP47 3.8 23.6 1.0 OP2 C:DT10 3.9 25.0 1.0 CB B:ALA199 4.0 18.9 1.0 CB B:HIS194 4.0 35.0 1.0 N B:ARG195 4.0 20.5 1.0 O5' C:DT10 4.2 26.4 1.0 CG B:HIS194 4.2 40.1 1.0 O B:HIS194 4.2 22.9 1.0 O B:ARG195 4.4 18.4 1.0 O B:SER193 4.5 28.5 1.0 O C:HOH102 4.6 34.9 0.6 C B:ARG195 4.6 21.3 1.0 MG B:MG303 4.6 28.3 0.6 C5' C:DT10 4.7 22.5 1.0 CG B:GLU49 4.7 18.6 1.0 CG B:ASP47 4.7 23.1 1.0 CA B:ARG195 4.8 20.2 1.0 N B:HIS194 4.8 29.1 1.0 NE2 B:HIS194 4.8 40.4 1.0 O B:LEU48 4.9 19.6 1.0 OD1 B:ASP47 5.0 25.2 1.0

Magnesium binding site 2 out of 2 in the Human Mitochondrial Oligoribonuclease in Complex with Poly-Dt Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Mitochondrial Oligoribonuclease in Complex with Poly-Dt Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:28.3 occ:0.58 O C:HOH107 2.8 35.7 1.0 OP1 C:DT10 3.0 24.5 0.9 OD1 B:ASP47 3.1 25.2 1.0 O B:HOH429 3.3 36.2 1.0 O B:HOH486 3.4 26.5 1.0 O3' C:DT9 3.6 29.9 0.8 P C:DT10 3.8 24.2 0.8 O B:HOH448 3.9 22.6 0.9 CG B:ASP47 3.9 23.1 1.0 O B:ASN142 4.0 21.6 1.0 CB B:ALA199 4.0 18.9 1.0 O C:HOH102 4.1 34.9 0.6 CB B:ASN142 4.1 19.8 1.0 OD2 B:ASP47 4.2 23.6 1.0 C5' C:DT9 4.3 27.3 0.6 OP2 C:DT10 4.4 25.0 1.0 C4' C:DT9 4.5 30.1 1.0 O B:HOH433 4.5 23.2 1.0 C3' C:DT9 4.6 29.7 0.8 MG B:MG302 4.6 33.3 0.7 C B:ASN142 4.8 20.1 1.0 O B:HOH406 4.8 29.3 1.0 CA B:ASN142 4.9 16.7 1.0 N B:ASN142 4.9 15.5 1.0

L.Y.Chu, S.Agrawal, Y.P.Chen, W.Z.Yang, H.S.Yuan. Structural Insights Into Nanorna Degradation By Human REXO2. Rna V. 25 737 2019.
ISSN: ESSN 1469-9001
PubMed: 30926754
DOI: 10.1261/RNA.070557.119