Magnesium in PDB 8q1x: Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation

The structure of Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation, PDB code: 8q1x was solved by Y.Roske, O.Daumke, M.Damme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.78 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.535, 115.452, 101.335, 90, 106.62, 90
R / Rfree (%)	17.4 / 19.9

The structure of Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation (pdb code 8q1x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation, PDB code: 8q1x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg516 b:20.1 occ:1.00 O A:HOH668 2.6 32.9 1.0 O A:PHE438 2.7 30.6 1.0 O A:HOH1044 3.1 29.3 1.0 N A:LEU308 3.5 22.4 1.0 N A:ASP307 3.6 24.2 1.0 C A:PHE438 3.7 30.9 1.0 CB A:ALA295 3.7 23.0 1.0 CB A:PRO306 3.8 22.5 1.0 CA A:PHE438 3.9 28.3 1.0 CB A:LEU308 3.9 24.4 1.0 CB A:PHE438 4.0 25.1 1.0 CB A:ASP307 4.1 22.6 1.0 CD A:PRO297 4.2 28.2 1.0 C A:PRO306 4.2 27.6 1.0 O A:SER294 4.2 27.0 1.0 CA A:ASP307 4.3 19.5 1.0 CA A:PRO306 4.3 23.3 1.0 CA A:ALA295 4.3 24.8 1.0 CA A:LEU308 4.3 27.3 1.0 C A:ASP307 4.4 25.7 1.0 CD1 A:PHE438 4.5 22.1 1.0 CG A:PRO297 4.5 30.8 1.0 CG A:PHE438 4.8 23.4 1.0 O A:HOH948 4.8 31.2 1.0 N A:PRO297 4.9 27.9 1.0 CA A:PRO296 4.9 27.7 1.0 OD1 A:OCS300 4.9 28.8 0.8 N A:THR439 4.9 23.4 1.0 O A:HOH1058 5.0 37.1 1.0

Magnesium binding site 2 out of 2 in the Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg514 b:15.3 occ:1.00 O B:HOH734 2.5 36.1 1.0 O B:PHE438 2.8 44.5 1.0 O B:HOH1028 3.1 26.8 1.0 N B:LEU308 3.5 24.3 1.0 N B:ASP307 3.7 24.9 1.0 C B:PHE438 3.7 29.0 1.0 CB B:ALA295 3.8 24.0 1.0 CA B:PHE438 3.8 24.2 1.0 CB B:PRO306 3.8 22.4 1.0 CB B:PHE438 3.9 21.4 1.0 CB B:LEU308 4.0 26.4 1.0 CB B:ASP307 4.1 31.0 1.0 CD B:PRO297 4.2 29.3 1.0 C B:PRO306 4.2 28.0 1.0 CA B:ALA295 4.3 26.7 1.0 CA B:ASP307 4.3 21.7 1.0 O B:SER294 4.3 26.9 1.0 CA B:PRO306 4.3 25.0 1.0 CD1 B:PHE438 4.4 24.5 1.0 CA B:LEU308 4.4 22.0 1.0 C B:ASP307 4.4 23.1 1.0 CG B:PRO297 4.5 33.4 1.0 CG B:PHE438 4.6 25.4 1.0 CA B:PRO296 4.8 25.8 1.0 N B:PRO297 4.8 32.1 1.0 O B:HOH1011 4.9 36.8 1.0 OD1 B:OCS300 4.9 30.7 0.7 N B:THR439 5.0 29.0 1.0 C B:PRO296 5.0 33.5 1.0

Y.Roske, C.Cappel, N.Cremer, P.Hoffmann, T.Koudelka, A.Tholey, U.Heinemann, O.Daumke, M.Damme. Structural Analysis of PLD3 Reveals Insights Into the Mechanism of Lysosomal 5' Exonuclease-Mediated Nucleic Acid Degradation. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37994783
DOI: 10.1093/NAR/GKAD1114