Manganese in PDB 8q1k: 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: 8q1k 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)	44.65 / 1.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.251, 115.304, 101.082, 90, 106.64, 90
R / Rfree (%)	15.4 / 18.6

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 8q1k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 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: 8q1k:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 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:Mn508 b:27.9 occ:1.00 O A:HOH679 2.4 34.0 1.0 O A:PHE438 3.0 36.3 1.0 O A:HOH1112 3.3 26.0 1.0 N A:LEU308 3.6 19.1 1.0 N A:ASP307 3.7 20.8 1.0 CB A:ALA295 3.8 20.7 1.0 CA A:PHE438 3.8 22.9 1.0 C A:PHE438 3.8 26.0 1.0 CB A:PRO306 3.9 22.4 1.0 CB A:PHE438 4.0 22.9 1.0 CB A:LEU308 4.1 21.4 1.0 O A:SER294 4.1 21.1 1.0 CA A:ALA295 4.2 20.7 1.0 CD A:PRO297 4.2 23.5 1.0 CB A:ASP307 4.3 20.1 1.0 C A:PRO306 4.3 18.7 1.0 CA A:PRO306 4.3 21.3 1.0 CD1 A:PHE438 4.3 21.5 1.0 CA A:ASP307 4.4 19.9 1.0 CG A:PRO297 4.4 24.8 1.0 CA A:LEU308 4.5 19.3 1.0 C A:ASP307 4.5 18.7 1.0 CG A:PHE438 4.7 20.9 1.0 N A:PRO297 4.7 22.8 1.0 O A:HOH995 4.7 32.6 1.0 CA A:PRO296 4.7 19.9 1.0 OD1 A:OCS300 4.9 35.5 0.9 C A:SER294 4.9 19.0 1.0 N A:ALA295 5.0 20.4 1.0 C A:PRO296 5.0 21.7 1.0

Manganese binding site 2 out of 4 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 A:Mn509 b:29.6 occ:1.00 O A:HOH1154 2.8 60.6 1.0 O A:HOH1121 3.3 49.3 1.0 ND2 A:ASN317 3.4 34.2 1.0 O A:HOH1122 3.5 26.8 1.0 CB A:ASN317 3.6 26.3 1.0 O A:HOH769 3.6 25.1 1.0 CB A:ALA425 3.8 27.7 1.0 CG A:ASN317 4.0 29.2 1.0 CA A:VAL314 4.3 21.2 1.0 CG2 A:THR449 4.3 27.0 1.0 CG A:ARG424 4.4 31.9 1.0 ND2 A:ASN313 4.5 25.0 1.0 O A:ASN313 4.5 22.7 1.0 CG2 A:VAL314 4.6 22.4 1.0 O A:HOH884 4.6 34.0 1.0 CD A:ARG424 4.7 36.6 1.0 O A:VAL314 4.8 23.0 1.0 N A:VAL314 4.9 19.8 1.0 O A:HOH939 4.9 31.8 1.0 CB A:VAL314 4.9 20.4 1.0 C A:ASN313 4.9 20.9 1.0 O A:HOH1035 5.0 70.1 1.0 CA A:ASN317 5.0 24.8 1.0 O A:HOH1000 5.0 58.7 1.0

Manganese binding site 3 out of 4 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 3 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:Mn509 b:27.2 occ:1.00 O B:HOH693 2.4 31.4 1.0 O B:PHE438 3.1 36.8 1.0 O B:HOH1059 3.3 24.7 1.0 N B:LEU308 3.6 16.7 1.0 N B:ASP307 3.7 18.1 1.0 CB B:ALA295 3.7 22.2 1.0 CA B:PHE438 3.8 21.7 1.0 C B:PHE438 3.8 25.1 1.0 CB B:PRO306 3.9 21.9 1.0 CB B:PHE438 4.0 22.1 1.0 CB B:LEU308 4.1 20.1 1.0 O B:SER294 4.1 20.5 1.0 CD B:PRO297 4.1 25.5 1.0 CA B:ALA295 4.2 20.5 1.0 CB B:ASP307 4.2 21.1 1.0 CD1 B:PHE438 4.3 21.9 1.0 C B:PRO306 4.3 18.7 1.0 CA B:PRO306 4.3 21.0 1.0 CG B:PRO297 4.4 25.9 1.0 CA B:ASP307 4.4 18.3 1.0 C B:ASP307 4.5 17.0 1.0 CA B:LEU308 4.5 18.2 1.0 N B:PRO297 4.6 24.0 1.0 CG B:PHE438 4.7 20.5 1.0 O B:HOH964 4.7 32.2 1.0 CA B:PRO296 4.7 21.9 1.0 OD1 B:OCS300 4.8 34.7 0.8 C B:SER294 4.9 20.4 1.0 C B:PRO296 4.9 21.1 1.0 N B:ALA295 4.9 21.3 1.0

Manganese binding site 4 out of 4 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 4 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:Mn510 b:29.2 occ:1.00 O B:HOH1130 3.1 60.2 1.0 O B:HOH1080 3.3 47.1 1.0 ND2 B:ASN317 3.4 29.8 1.0 O B:HOH1079 3.5 25.8 1.0 O B:HOH818 3.6 23.6 1.0 CB B:ASN317 3.6 23.5 1.0 CB B:ALA425 3.8 24.3 1.0 CG B:ASN317 4.0 28.1 1.0 CA B:VAL314 4.2 20.2 1.0 CG2 B:THR449 4.3 24.4 1.0 CG B:ARG424 4.5 30.5 1.0 ND2 B:ASN313 4.5 22.1 1.0 O B:ASN313 4.5 21.9 1.0 CG2 B:VAL314 4.5 21.5 1.0 O B:HOH854 4.7 29.9 1.0 CD B:ARG424 4.7 35.5 1.0 N B:VAL314 4.8 19.4 1.0 CB B:VAL314 4.8 20.4 1.0 O B:VAL314 4.8 22.0 1.0 O B:HOH895 4.9 33.5 1.0 C B:ASN313 4.9 17.8 1.0 CA B:ASN317 5.0 22.5 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