Manganese 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:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese 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 Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn513 b:34.2 occ:1.00 O A:HOH1038 2.4 55.6 1.0 ND2 A:ASN317 3.3 37.7 1.0 O A:HOH1042 3.6 24.9 1.0 CB A:ASN317 3.6 33.5 1.0 O A:HOH728 3.6 27.1 1.0 O A:HOH1076 3.7 48.4 1.0 CB A:ALA425 3.8 28.7 1.0 CG A:ASN317 4.0 38.2 1.0 CA A:VAL314 4.3 25.6 1.0 CG2 A:THR449 4.3 31.6 1.0 CG2 A:VAL314 4.4 20.7 1.0 O A:ASN313 4.4 26.7 1.0 OD1 A:ASN313 4.5 33.0 1.0 CG A:ARG424 4.5 37.1 1.0 O A:HOH841 4.6 34.5 1.0 CD A:ARG424 4.7 38.2 1.0 O A:HOH1054 4.8 53.0 1.0 CB A:VAL314 4.8 25.5 1.0 O A:VAL314 4.9 26.6 1.0 N A:VAL314 4.9 24.0 1.0 C A:ASN313 4.9 27.0 1.0 O A:HOH909 5.0 56.4 1.0 CA A:ASN317 5.0 29.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn511 b:31.9 occ:1.00 O B:HOH1064 3.0 53.3 1.0 O B:HOH1039 3.4 46.1 1.0 ND2 B:ASN317 3.4 40.4 1.0 O B:HOH1016 3.5 28.6 1.0 O B:HOH719 3.6 29.3 1.0 CB B:ASN317 3.7 27.1 1.0 CB B:ALA425 3.8 25.5 1.0 CG B:ASN317 4.0 40.4 1.0 CA B:VAL314 4.3 22.4 1.0 CG2 B:THR449 4.3 28.6 1.0 CG B:ARG424 4.4 34.7 1.0 ND2 B:ASN313 4.5 27.9 1.0 O B:ASN313 4.6 27.9 1.0 CG2 B:VAL314 4.6 25.7 1.0 CD B:ARG424 4.6 33.2 1.0 O B:HOH806 4.7 34.2 1.0 O B:VAL314 4.9 23.7 1.0 N B:VAL314 4.9 26.1 1.0 CB B:VAL314 4.9 25.4 1.0 O B:HOH808 5.0 34.1 1.0 C B:ASN313 5.0 30.3 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