Sodium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Lariat-Capping Ribozyme (Circular Permutation Form) (pdb code 6gyv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Lariat-Capping Ribozyme (Circular Permutation Form), PDB code: 6gyv:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lariat-Capping Ribozyme (Circular Permutation Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:37.0 occ:1.00 O1 A:MES201 2.8 35.0 1.0 C6 A:MES201 2.8 36.4 1.0 O A:HOH345 3.2 30.7 1.0 O3' A:A167 3.5 40.2 1.0 O2' A:C142 3.6 38.0 1.0 N4 A:C1 3.6 28.7 1.0 C5 A:U3 3.7 27.3 1.0 O2 A:C142 3.7 32.5 1.0 OP2 A:U168 3.8 38.0 1.0 O2' A:A167 3.8 31.6 1.0 C2 A:MES201 4.0 36.9 1.0 P A:U168 4.1 39.9 1.0 O4 A:U3 4.1 30.5 1.0 C4 A:U3 4.1 28.4 1.0 C5 A:MES201 4.3 31.6 1.0 C2' A:C142 4.4 32.9 1.0 OP1 A:U168 4.4 42.5 1.0 O2 A:C172 4.4 31.6 0.9 C6 A:U3 4.5 29.9 1.0 C3' A:A167 4.6 38.6 1.0 C1' A:C142 4.7 33.0 1.0 C2' A:A167 4.8 37.5 1.0 C2 A:C142 4.9 29.9 1.0 C4 A:C1 5.0 31.6 1.0 C3 A:MES201 5.0 36.7 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. V. 111 7659 2014U.S.A..
ISSN: ESSN 1091-6490
PubMed: 24821772
DOI: 10.1073/PNAS.1322248111