Magnesium in PDB 8vah: E.Coli Pnpase in Complex with Single 8-Oxog Rna

The binding sites of Magnesium atom in the E.Coli Pnpase in Complex with Single 8-Oxog Rna (pdb code 8vah). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the E.Coli Pnpase in Complex with Single 8-Oxog Rna, PDB code: 8vah:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the E.Coli Pnpase in Complex with Single 8-Oxog Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E.Coli Pnpase in Complex with Single 8-Oxog Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:101.0 occ:1.00 OD2 A:ASP486 2.9 110.9 1.0 OD2 A:ASP492 3.1 91.7 1.0 OP1 D:8GM5 3.3 20.0 1.0 CD1 A:ILE481 3.5 94.2 1.0 CG A:ASP486 3.5 110.9 1.0 CG1 A:ILE481 3.9 94.2 1.0 CB A:ASP486 4.1 110.9 1.0 OD1 A:ASP486 4.3 110.9 1.0 C5' D:8GM5 4.3 20.0 1.0 CG A:ASP492 4.3 91.7 1.0 NZ A:LYS494 4.4 75.3 1.0 P D:8GM5 4.7 20.0 1.0 O A:LEU482 4.8 99.8 1.0 O A:ILE481 4.8 94.2 1.0 CA A:ASP486 4.8 110.9 1.0 N A:SER437 4.9 78.8 1.0 OD1 A:ASP492 4.9 91.7 1.0 O5' D:8GM5 5.0 20.0 1.0

Magnesium binding site 2 out of 3 in the E.Coli Pnpase in Complex with Single 8-Oxog Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E.Coli Pnpase in Complex with Single 8-Oxog Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:93.1 occ:1.00 OD2 B:ASP486 3.3 105.4 1.0 CG2 B:ILE481 3.4 93.8 1.0 OP1 E:8GM5 3.8 20.0 1.0 CG B:ASP486 3.9 105.4 1.0 NZ B:LYS494 4.2 70.1 1.0 N B:SER437 4.3 81.1 1.0 OD1 B:ASP486 4.4 105.4 1.0 O B:ILE481 4.5 93.8 1.0 CB B:ASP486 4.6 105.4 1.0 O B:LEU482 4.6 96.2 1.0 CB B:ILE481 4.7 93.8 1.0 CB B:ALA465 4.8 79.3 1.0 C5' E:8GM5 4.8 20.0 1.0 CA B:GLY436 4.8 83.8 1.0 CA B:SER437 4.9 81.1 1.0 OD2 B:ASP492 5.0 93.2 1.0

Magnesium binding site 3 out of 3 in the E.Coli Pnpase in Complex with Single 8-Oxog Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E.Coli Pnpase in Complex with Single 8-Oxog Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:102.0 occ:1.00 OD2 C:ASP486 2.6 111.5 1.0 OD2 C:ASP492 2.7 88.3 1.0 OP1 F:8GM5 2.8 20.0 1.0 CG C:ASP486 3.0 111.5 1.0 CD1 C:ILE481 3.2 94.2 1.0 OD1 C:ASP486 3.4 111.5 1.0 CB C:ASP486 3.7 111.5 1.0 CG C:ASP492 3.8 88.3 1.0 CG1 C:ILE481 3.9 94.2 1.0 NZ C:LYS494 4.2 70.2 1.0 P F:8GM5 4.3 20.0 1.0 C5' F:8GM5 4.5 20.0 1.0 OD1 C:ASP492 4.6 88.3 1.0 CB C:ASP492 4.7 88.3 1.0 CA C:ASP486 4.7 111.5 1.0 N C:SER437 4.8 81.3 1.0 O C:LEU482 5.0 100.1 1.0 O5' F:8GM5 5.0 20.0 1.0

L.G.Miller, W.Kim, S.Schowe, K.Taylor, R.Han, V.Jain, R.Park, M.Sherman, J.Fang, H.Ramirez, A.Ellington, P.Tamamis, M.J.E.Resendiz, Y.J.Zhang, L.Contreras. Selective 8-Oxo-Rg Stalling Occurs in the Catalytic Core of Polynucleotide Phosphorylase (Pnpase) During Degradation. Proc.Natl.Acad.Sci.Usa V. 121 65121 2024.
ISSN: ESSN 1091-6490
PubMed: 39495922
DOI: 10.1073/PNAS.2317865121