Magnesium in PDB 5k7c: The Native Structure of Native Pistol Ribozyme

The structure of The Native Structure of Native Pistol Ribozyme, PDB code: 5k7c was solved by A.Ren, D.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.70 / 2.73
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.196, 56.196, 89.311, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 25

The binding sites of Magnesium atom in the The Native Structure of Native Pistol Ribozyme (pdb code 5k7c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Native Structure of Native Pistol Ribozyme, PDB code: 5k7c:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the The Native Structure of Native Pistol Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Native Structure of Native Pistol Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:0.8 occ:1.00 OP2 A:G42 2.3 96.7 1.0 OP2 A:C41 2.6 95.6 1.0 P A:G42 3.6 97.4 1.0 P A:C41 4.0 96.5 1.0 OP1 A:G42 4.1 99.9 1.0 O3' A:C41 4.6 95.9 1.0 O5' A:G42 4.6 95.2 1.0 OP1 A:C41 4.7 0.1 1.0 O3' A:G40 4.7 95.1 1.0

Magnesium binding site 2 out of 3 in the The Native Structure of Native Pistol Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Native Structure of Native Pistol Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:78.3 occ:1.00 N7 A:G33 2.1 75.9 1.0 C8 A:G33 3.0 75.0 1.0 C5 A:G33 3.1 74.7 1.0 O6 A:G33 3.5 74.4 1.0 C6 A:G33 3.6 74.3 1.0 OP2 A:C35 3.9 77.1 1.0 N9 A:G33 4.1 73.5 1.0 C4 A:G33 4.2 73.6 1.0 O4 A:U6 4.2 82.7 1.0 O2' A:A32 4.4 93.9 1.0 OP2 B:U54 4.4 85.4 1.0 OP2 A:G33 4.8 86.7 1.0 C4 A:U6 4.9 82.5 1.0 OP1 A:C35 4.9 77.9 1.0 N1 A:G33 5.0 74.2 1.0 P A:C35 5.0 77.3 1.0 O3' A:A32 5.0 89.3 1.0 O5' B:U54 5.0 88.8 1.0

Magnesium binding site 3 out of 3 in the The Native Structure of Native Pistol Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Native Structure of Native Pistol Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:0.6 occ:1.00 O6 A:G40 3.9 91.4 1.0 OP2 A:A38 4.1 87.3 1.0 N7 A:A39 4.3 99.4 1.0 N7 A:A38 4.3 87.4 1.0 C8 A:A39 4.7 0.3 1.0 C8 A:A38 4.7 89.1 1.0 C6 A:G40 4.8 90.8 1.0 OP2 A:U37 4.9 77.9 1.0

A.Ren, N.Vusurovic, J.Gebetsberger, P.Gao, M.Juen, C.Kreutz, R.Micura, D.J.Patel. Pistol Ribozyme Adopts A Pseudoknot Fold Facilitating Site-Specific in-Line Cleavage. Nat.Chem.Biol. V. 12 702 2016.
ISSN: ESSN 1552-4469
PubMed: 27398999
DOI: 10.1038/NCHEMBIO.2125