Magnesium in PDB 4p9r: Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)

The structure of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative), PDB code: 4p9r was solved by M.Meyer, H.Nielsen, V.Olieric, P.Roblin, S.D.Johansen, E.Westhof, B.Masquida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.95 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.440, 86.260, 109.780, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.6

The structure of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) also contains other interesting chemical elements:

Iridium

(Ir)

10 atoms

The binding sites of Magnesium atom in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) (pdb code 4p9r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative), PDB code: 4p9r:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg611 b:49.0 occ:1.00 O A:HOH729 1.8 40.7 1.0 O A:HOH731 1.8 46.0 1.0 O A:HOH728 1.8 43.9 1.0 O A:HOH727 1.8 45.4 1.0 O A:HOH730 1.8 45.3 1.0 OP1 A:G325 2.2 45.3 1.0 P A:G325 3.5 41.6 1.0 O6 A:G290 3.9 44.4 1.0 OP2 A:G325 4.0 49.1 1.0 O2' A:C324 4.1 41.3 1.0 O3' A:C324 4.1 44.2 1.0 N7 A:G289 4.2 46.5 1.0 O6 A:G289 4.2 43.6 1.0 C8 A:G325 4.3 45.0 1.0 N7 A:G325 4.4 44.6 1.0 C2' A:C324 4.4 43.5 1.0 O5' A:G325 4.7 45.0 1.0 C3' A:C324 4.8 42.1 1.0 C6 A:G289 4.8 48.4 1.0 C5 A:G289 4.8 48.3 1.0 C6 A:G290 4.9 46.7 1.0 N7 A:G290 4.9 48.5 1.0

Magnesium binding site 2 out of 3 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg612 b:42.4 occ:1.00 O A:HOH734 1.8 36.4 1.0 O A:HOH736 1.8 43.9 1.0 O A:HOH737 1.8 46.5 1.0 O A:HOH733 1.8 40.2 1.0 O A:HOH732 1.8 37.4 1.0 O A:HOH735 1.8 40.2 1.0 O4 A:U315 4.1 45.8 1.0 N3 A:C324 4.1 44.8 1.0 O6 A:G323 4.2 44.9 1.0 O2 A:C324 4.2 46.4 1.0 O6 A:G325 4.3 41.7 1.0 N7 A:G314 4.4 45.3 1.0 O6 A:G314 4.6 43.9 1.0 C2 A:C324 4.6 43.9 1.0 N4 A:C313 4.7 41.0 1.0 C5 A:C313 4.9 42.1 1.0 C4 A:C313 4.9 42.0 1.0

Magnesium binding site 3 out of 3 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg613 b:27.8 occ:1.00 O A:HOH702 1.8 38.0 1.0 O A:HOH710 1.8 48.4 1.0 O A:HOH707 1.8 36.2 1.0 O A:HOH738 1.8 37.6 1.0 O2' A:C272 4.1 37.6 1.0 O2 A:U547 4.8 35.9 1.0 O A:HOH704 4.9 33.9 1.0 O2 A:C272 5.0 38.2 1.0 O4' A:G548 5.0 43.7 1.0

M.Meyer, H.Nielsen, V.Olieric, P.Roblin, S.D.Johansen, E.Westhof, B.Masquida. Speciation of A Group I Intron Into A Lariat Capping Ribozyme. Proc.Natl.Acad.Sci.Usa V. 111 7659 2014.
ISSN: ESSN 1091-6490
PubMed: 24821772
DOI: 10.1073/PNAS.1322248111