Sodium in PDB 4p95: Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme)

The structure of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme), PDB code: 4p95 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)	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 (%)	18.8 / 23.6

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

Magnesium

(Mg)

3 atoms

The binding sites of Sodium atom in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme) (pdb code 4p95). 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 Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme), PDB code: 4p95:

Sodium binding site 1 out of 1 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:7.2 occ:1.00 O1 A:MES601 2.7 11.8 1.0 C6 A:MES601 2.7 9.7 1.0 O A:HOH778 3.1 6.2 1.0 O3' A:A553 3.5 13.5 1.0 C5 A:U3 3.7 1.6 1.0 O2' A:C334 3.7 15.2 1.0 O2' A:A553 3.7 5.2 1.0 N4 A:C1 3.7 2.1 1.0 O2 A:C334 3.8 5.1 1.0 C2 A:MES601 3.8 10.7 1.0 OP2 A:U554 3.8 12.3 1.0 P A:U554 4.0 12.5 1.0 C4 A:U3 4.1 2.5 1.0 O4 A:U3 4.2 3.2 1.0 C5 A:MES601 4.2 3.9 1.0 OP1 A:U554 4.3 21.4 1.0 C6 A:U3 4.4 3.0 1.0 C2' A:C334 4.4 7.1 1.0 O2 A:C558 4.4 5.9 0.1 O2 A:C558 4.4 5.8 0.9 C3' A:A553 4.5 13.0 1.0 C2' A:A553 4.6 11.8 1.0 C1' A:C334 4.9 5.4 1.0 C2 A:C334 4.9 3.5 1.0 C3 A:MES601 5.0 4.3 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