Magnesium in PDB 6j7y: Human Mitochondrial Oligoribonuclease in Complex with Dna

The structure of Human Mitochondrial Oligoribonuclease in Complex with Dna, PDB code: 6j7y 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)	28.34 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	87.282, 125.293, 85.478, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.4

The binding sites of Magnesium atom in the Human Mitochondrial Oligoribonuclease in Complex with Dna (pdb code 6j7y). 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 Dna, PDB code: 6j7y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Mitochondrial Oligoribonuclease in Complex with 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 Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:62.8 occ:0.81 OP1 C:DT2 2.1 65.0 0.3 OD2 B:ASP199 2.5 54.7 1.0 OE2 B:GLU49 2.5 47.5 1.0 OD2 B:ASP47 3.1 46.4 1.0 CD B:GLU49 3.3 50.9 1.0 P C:DT2 3.4 69.5 0.6 CG B:ASP199 3.5 52.5 1.0 OE1 B:GLU49 3.6 60.3 1.0 OD1 B:ASP47 3.8 48.9 1.0 CG B:ASP47 3.9 44.0 1.0 O B:LEU48 3.9 37.2 1.0 O5' C:DT2 3.9 71.0 0.5 CB B:ASP199 4.0 33.9 1.0 CD2 B:HIS194 4.1 99.1 1.0 C5' C:DT2 4.1 72.8 1.0 OP2 C:DT2 4.2 74.0 0.6 MG B:MG302 4.2 64.2 0.7 O B:HOH441 4.5 65.1 0.9 O3' C:DT1 4.6 71.2 0.6 OD1 B:ASP199 4.6 50.4 1.0 CG B:GLU49 4.7 43.3 1.0 C B:HIS194 4.8 62.5 1.0 CA B:HIS194 4.8 76.8 1.0 CG B:HIS194 4.8 98.2 1.0 NE2 B:HIS194 4.9 98.5 1.0 C B:LEU48 4.9 40.4 1.0

Magnesium binding site 2 out of 2 in the Human Mitochondrial Oligoribonuclease in Complex with 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 Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:64.2 occ:0.73 O B:HOH441 2.6 65.1 0.9 OG B:SER143 3.2 64.4 1.0 OP1 C:DT2 3.2 65.0 0.3 O3' C:DT1 3.5 71.2 0.6 OD1 B:ASP47 3.6 48.9 1.0 CB B:SER143 3.7 68.0 1.0 CB B:ASN142 3.7 45.2 1.0 N B:SER143 3.8 42.1 1.0 P C:DT2 3.9 69.5 0.6 O5' C:DT1 4.1 77.5 1.0 MG B:MG301 4.2 62.8 0.8 C5' C:DT1 4.3 78.1 0.5 C4' C:DT1 4.3 74.6 1.0 CA B:SER143 4.4 63.4 1.0 CG B:ASP47 4.4 44.0 1.0 OP2 C:DT2 4.4 74.0 0.6 C B:ASN142 4.5 46.2 1.0 C3' C:DT1 4.5 71.9 0.0 CA B:ASN142 4.6 43.9 1.0 OD2 B:ASP47 4.8 46.4 1.0 CG B:ASN142 4.9 53.5 1.0 N B:ASN142 4.9 26.6 1.0 CB B:ASP199 5.0 33.9 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