Magnesium in PDB 6gyv: Lariat-Capping Ribozyme (Circular Permutation Form)

The structure of Lariat-Capping Ribozyme (Circular Permutation Form), PDB code: 6gyv was solved by B.Masquida, M.Meyer, H.Nielsen, V.Olieric, P.Roblin, S.D.Johansen, E.Westhof, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.82 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.630, 85.710, 108.530, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.5

The structure of Lariat-Capping Ribozyme (Circular Permutation Form) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Lariat-Capping Ribozyme (Circular Permutation Form) (pdb code 6gyv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Lariat-Capping Ribozyme (Circular Permutation Form), PDB code: 6gyv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Lariat-Capping Ribozyme (Circular Permutation Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lariat-Capping Ribozyme (Circular Permutation Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:30.8 occ:1.00 OP1 A:G133 2.1 33.1 1.0 O A:HOH370 2.2 24.4 1.0 O A:HOH363 2.2 36.5 1.0 O A:HOH329 2.2 32.0 1.0 O A:HOH366 2.2 32.6 1.0 O A:HOH373 2.2 25.4 1.0 P A:G133 3.4 32.9 1.0 O3' A:C132 4.0 32.9 1.0 O6 A:G98 4.0 33.1 1.0 O6 A:G97 4.1 31.6 1.0 OP2 A:G133 4.1 45.0 1.0 O2' A:C132 4.1 28.3 1.0 C8 A:G133 4.1 35.0 1.0 N7 A:G97 4.2 32.7 1.0 N7 A:G133 4.2 33.2 1.0 C2' A:C132 4.3 33.4 1.0 O5' A:G133 4.6 35.3 1.0 C3' A:C132 4.6 32.9 1.0 C6 A:G97 4.7 35.9 1.0 C5 A:G97 4.8 34.9 1.0 N7 A:G98 5.0 33.5 1.0

Magnesium binding site 2 out of 2 in the Lariat-Capping Ribozyme (Circular Permutation Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lariat-Capping Ribozyme (Circular Permutation Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:28.6 occ:1.00 O A:HOH330 2.2 29.7 1.0 O A:HOH399 2.2 30.2 1.0 O A:HOH356 2.2 27.3 1.0 O A:HOH332 2.2 26.3 1.0 O A:HOH306 2.2 23.3 1.0 O A:HOH315 2.2 29.9 1.0 O A:HOH351 3.5 33.9 1.0 O4 A:U123 3.8 33.6 1.0 O6 A:G131 4.0 24.7 1.0 N3 A:C132 4.2 29.7 1.0 O2 A:C132 4.2 31.0 1.0 O A:HOH331 4.2 33.3 1.0 O6 A:G133 4.3 32.6 1.0 N7 A:G122 4.4 33.2 1.0 O6 A:G122 4.4 36.8 1.0 N4 A:C121 4.5 32.5 1.0 C2 A:C132 4.7 32.7 1.0 O A:HOH384 4.7 36.1 1.0 C5 A:C121 4.7 36.8 1.0 C4 A:C121 4.8 33.2 1.0 C4 A:U123 4.9 31.9 1.0 N6 A:A95 4.9 32.7 1.0 N4 A:C124 5.0 30.0 1.0 O A:HOH346 5.0 31.1 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. V. 111 7659 2014U.S.A..
ISSN: ESSN 1091-6490
PubMed: 24821772
DOI: 10.1073/PNAS.1322248111