Magnesium in PDB 7ld5: Polynucleotide Phosphorylase

All present enzymatic activity of Polynucleotide Phosphorylase:
2.7.7.8;

The binding sites of Magnesium atom in the Polynucleotide Phosphorylase (pdb code 7ld5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Polynucleotide Phosphorylase, PDB code: 7ld5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Polynucleotide Phosphorylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Polynucleotide Phosphorylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:10.1 occ:1.00 OD2 A:ASP526 2.7 44.5 1.0 CB A:ASP532 3.2 10.4 1.0 OD2 A:ASP532 3.4 10.4 1.0 CG A:ASP532 3.5 10.4 1.0 CG A:ASP526 3.9 44.5 1.0 CD1 A:ILE521 4.0 20.4 1.0 OD1 A:ASP532 4.3 10.4 1.0 CA A:ASP532 4.4 10.4 1.0 CB A:SER469 4.5 24.7 1.0 OD1 A:ASP526 4.6 44.5 1.0 C A:ASP532 4.7 10.4 1.0 MG A:MG802 4.7 4.3 1.0 CG1 A:ILE521 4.8 20.4 1.0 CD A:LYS534 4.9 2.7 1.0 OG A:SER469 4.9 24.7 1.0 CG A:LYS534 4.9 2.7 1.0 N A:PHE533 5.0 6.6 1.0 O A:MET498 5.0 10.6 1.0

Magnesium binding site 2 out of 6 in the Polynucleotide Phosphorylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Polynucleotide Phosphorylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:4.3 occ:1.00 OD2 A:ASP532 2.7 10.4 1.0 OE1 A:GLN546 3.4 2.0 1.0 CG A:GLN546 3.6 2.0 1.0 O A:ASP532 3.8 10.4 1.0 CD A:GLN546 3.9 2.0 1.0 CG A:ASP532 4.0 10.4 1.0 CE A:LYS534 4.0 2.7 1.0 OD1 A:ASP548 4.1 5.9 1.0 CG A:ASP548 4.2 5.9 1.0 CG A:LYS534 4.4 2.7 1.0 C A:ASP532 4.5 10.4 1.0 OD2 A:ASP548 4.5 5.9 1.0 N A:ASP548 4.6 5.9 1.0 CB A:ASP548 4.6 5.9 1.0 O A:GLN546 4.6 2.0 1.0 MG A:MG801 4.7 10.1 1.0 C A:GLN546 4.7 2.0 1.0 N A:LEU547 4.7 2.8 1.0 CD A:LYS534 4.7 2.7 1.0 CB A:GLN546 4.7 2.0 1.0 OD1 A:ASP532 4.7 10.4 1.0 CA A:LEU547 4.9 2.8 1.0 CA A:PHE533 4.9 6.6 1.0 C A:LEU547 4.9 2.8 1.0 CB A:ASP532 4.9 10.4 1.0 NZ A:LYS534 4.9 2.7 1.0 NH2 A:ARG109 5.0 3.3 1.0

Magnesium binding site 3 out of 6 in the Polynucleotide Phosphorylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Polynucleotide Phosphorylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:14.4 occ:1.00 OD2 B:ASP526 2.6 47.7 1.0 CB B:ASP532 3.3 13.1 1.0 OD2 B:ASP532 3.4 13.1 1.0 CG B:ASP532 3.5 13.1 1.0 CG B:ASP526 3.9 47.7 1.0 CD1 B:ILE521 3.9 20.6 1.0 OD1 B:ASP532 4.3 13.1 1.0 CA B:ASP532 4.5 13.1 1.0 OD1 B:ASP526 4.5 47.7 1.0 CB B:SER469 4.5 26.1 1.0 C B:ASP532 4.7 13.1 1.0 MG B:MG802 4.8 3.2 1.0 CG1 B:ILE521 4.8 20.6 1.0 OG B:SER469 4.9 26.1 1.0 CB B:ASP526 4.9 47.7 1.0 CD B:LYS534 5.0 3.0 1.0 O B:MET498 5.0 11.4 1.0

Magnesium binding site 4 out of 6 in the Polynucleotide Phosphorylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Polynucleotide Phosphorylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:3.2 occ:1.00 OD2 B:ASP532 2.7 13.1 1.0 OE1 B:GLN546 3.4 2.1 1.0 CG B:GLN546 3.5 2.1 1.0 O B:ASP532 3.7 13.1 1.0 CD B:GLN546 3.9 2.1 1.0 CG B:ASP532 4.0 13.1 1.0 OD1 B:ASP548 4.1 5.8 1.0 CE B:LYS534 4.1 3.0 1.0 CG B:ASP548 4.2 5.8 1.0 CG B:LYS534 4.3 3.0 1.0 C B:ASP532 4.5 13.1 1.0 OD2 B:ASP548 4.5 5.8 1.0 N B:ASP548 4.5 5.8 1.0 CB B:ASP548 4.6 5.8 1.0 O B:GLN546 4.6 2.1 1.0 C B:GLN546 4.6 2.1 1.0 N B:LEU547 4.6 3.1 1.0 CB B:GLN546 4.7 2.1 1.0 CD B:LYS534 4.7 3.0 1.0 OD1 B:ASP532 4.7 13.1 1.0 MG B:MG801 4.8 14.4 1.0 CA B:LEU547 4.8 3.1 1.0 CA B:PHE533 4.9 8.0 1.0 C B:LEU547 4.9 3.1 1.0 CB B:ASP532 4.9 13.1 1.0 NH2 B:ARG109 5.0 3.3 1.0 NZ B:LYS534 5.0 3.0 1.0

Magnesium binding site 5 out of 6 in the Polynucleotide Phosphorylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Polynucleotide Phosphorylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:8.8 occ:1.00 OD2 C:ASP526 2.7 47.0 1.0 CB C:ASP532 3.2 12.5 1.0 OD2 C:ASP532 3.4 12.5 1.0 CG C:ASP532 3.5 12.5 1.0 CG C:ASP526 3.9 47.0 1.0 CD1 C:ILE521 4.0 20.0 1.0 OD1 C:ASP532 4.3 12.5 1.0 CA C:ASP532 4.4 12.5 1.0 CB C:SER469 4.5 25.1 1.0 OD1 C:ASP526 4.5 47.0 1.0 MG C:MG802 4.6 3.9 1.0 C C:ASP532 4.7 12.5 1.0 CD C:LYS534 4.9 3.0 1.0 CG1 C:ILE521 4.9 20.0 1.0 OG C:SER469 4.9 25.1 1.0 CG C:LYS534 4.9 3.0 1.0 N C:PHE533 5.0 8.4 1.0

Magnesium binding site 6 out of 6 in the Polynucleotide Phosphorylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Polynucleotide Phosphorylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg802 b:3.9 occ:1.00 OD2 C:ASP532 2.7 12.5 1.0 OE1 C:GLN546 3.4 1.8 1.0 CG C:GLN546 3.5 1.8 1.0 O C:ASP532 3.7 12.5 1.0 CD C:GLN546 3.9 1.8 1.0 CG C:ASP532 4.0 12.5 1.0 CE C:LYS534 4.0 3.0 1.0 OD1 C:ASP548 4.1 5.9 1.0 CG C:ASP548 4.2 5.9 1.0 CG C:LYS534 4.3 3.0 1.0 C C:ASP532 4.4 12.5 1.0 OD2 C:ASP548 4.5 5.9 1.0 O C:GLN546 4.5 1.8 1.0 N C:ASP548 4.5 5.9 1.0 C C:GLN546 4.6 1.8 1.0 N C:LEU547 4.6 2.7 1.0 CB C:ASP548 4.6 5.9 1.0 MG C:MG801 4.6 8.8 1.0 CB C:GLN546 4.7 1.8 1.0 CD C:LYS534 4.7 3.0 1.0 OD1 C:ASP532 4.8 12.5 1.0 CA C:LEU547 4.8 2.7 1.0 CA C:PHE533 4.8 8.4 1.0 C C:LEU547 4.9 2.7 1.0 CB C:ASP532 4.9 12.5 1.0 NZ C:LYS534 5.0 3.0 1.0 N C:PHE533 5.0 8.4 1.0 NH2 C:ARG109 5.0 3.3 1.0

M.C.Unciuleac, S.Ghosh, M.J.De La Cruz, Y.Goldgur, S.Shuman. Structure and Mechanism of Mycobacterium Smegmatis Polynucleotide Phosphorylase. Rna 2021.
ISSN: ESSN 1469-9001
PubMed: 34088850
DOI: 10.1261/RNA.078822.121