Magnesium in PDB 5k7d: The Structure of Native Pistol Ribozyme, Bound to Iridium

The structure of The Structure of Native Pistol Ribozyme, Bound to Iridium, PDB code: 5k7d 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)	49.00 / 2.68
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.573, 56.573, 88.297, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 24

The structure of The Structure of Native Pistol Ribozyme, Bound to Iridium also contains other interesting chemical elements:

Iridium

(Ir)

2 atoms

The binding sites of Magnesium atom in the The Structure of Native Pistol Ribozyme, Bound to Iridium (pdb code 5k7d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the The Structure of Native Pistol Ribozyme, Bound to Iridium, PDB code: 5k7d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the The Structure of Native Pistol Ribozyme, Bound to Iridium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Native Pistol Ribozyme, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:84.9 occ:1.00 OP2 A:G42 1.9 85.1 1.0 O A:HOH204 2.0 79.8 1.0 O A:HOH201 2.1 93.6 1.0 O A:HOH202 2.1 76.8 1.0 O A:HOH205 2.2 75.7 1.0 OP2 A:C41 2.3 88.9 1.0 P A:G42 3.4 85.5 1.0 P A:C41 3.6 85.8 1.0 O3' A:G40 4.0 83.9 1.0 O5' A:G42 4.0 82.1 1.0 O3' A:C41 4.3 81.3 1.0 OP1 A:G42 4.4 86.9 1.0 OP1 A:C41 4.4 91.8 1.0 C3' A:C41 4.4 82.0 1.0 C8 A:G42 4.7 81.1 1.0 O5' A:C41 4.8 86.0 1.0 N7 A:G42 4.8 81.7 1.0 O4 A:U43 4.8 82.5 1.0 O2' A:G40 4.9 86.7 1.0

Magnesium binding site 2 out of 5 in the The Structure of Native Pistol Ribozyme, Bound to Iridium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Native Pistol Ribozyme, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:81.4 occ:1.00 O A:HOH208 2.0 78.5 1.0 O A:HOH211 2.0 1.0 1.0 O A:HOH203 2.1 67.4 1.0 N7 A:G33 2.1 69.5 1.0 C8 A:G33 2.9 68.7 1.0 C5 A:G33 3.2 67.0 1.0 OP2 B:U54 3.8 78.6 1.0 O6 A:G33 3.8 63.9 1.0 C6 A:G33 3.9 64.2 1.0 O2' A:A32 4.0 73.9 1.0 OP2 A:C35 4.0 74.0 1.0 N9 A:G33 4.1 66.9 1.0 C4 A:G33 4.3 64.6 1.0 OP2 A:G33 4.3 77.1 1.0 O3' A:A32 4.5 75.8 1.0 P B:U54 4.6 80.1 1.0 O4 A:U6 4.6 79.9 1.0 O5' B:U54 4.7 82.2 1.0 C5' B:U54 4.8 81.8 1.0 OP1 B:U54 4.9 81.8 1.0 C2' A:A32 4.9 75.0 1.0 P A:G33 5.0 75.9 1.0

Magnesium binding site 3 out of 5 in the The Structure of Native Pistol Ribozyme, Bound to Iridium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Native Pistol Ribozyme, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:0.1 occ:1.00 O A:HOH209 2.0 79.5 1.0 O A:HOH212 2.1 84.8 1.0 OP2 A:U37 3.4 75.2 1.0 OP2 A:A38 3.7 86.0 1.0 N7 A:A38 4.1 78.2 1.0 O5' A:U37 4.5 79.6 1.0 C8 A:A38 4.5 80.3 1.0 P A:U37 4.5 80.4 1.0 C5 A:U37 4.7 80.5 1.0 C6 A:U37 4.8 81.0 1.0 N7 A:A39 5.0 79.4 1.0

Magnesium binding site 4 out of 5 in the The Structure of Native Pistol Ribozyme, Bound to Iridium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Native Pistol Ribozyme, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:93.0 occ:1.00 O A:HOH207 2.0 88.1 1.0 O A:HOH213 2.1 99.5 1.0 O A:HOH210 2.1 97.6 1.0 OP2 A:A23 3.4 0.0 1.0 N7 A:G24 4.7 80.4 1.0 P A:A23 4.8 0.8 1.0

Magnesium binding site 5 out of 5 in the The Structure of Native Pistol Ribozyme, Bound to Iridium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Native Pistol Ribozyme, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:0.2 occ:1.00 O B:HOH202 2.1 83.1 1.0 O B:HOH201 2.1 73.2 1.0 N6 B:IRI101 3.3 0.9 1.0 O6 B:DG53 3.6 85.5 1.0 N4 B:IRI101 3.8 0.1 1.0 O6 B:G52 4.0 85.8 1.0 N1 B:IRI101 4.3 0.8 1.0 IR B:IRI101 4.6 0.2 1.0 C6 B:DG53 4.8 80.7 1.0 N7 B:G52 4.8 86.2 1.0 C6 B:G52 5.0 84.7 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