Sodium in PDB 2p7d: A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution

The structure of A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution, PDB code: 2p7d was solved by A.T.Torelli, J.Krucinska, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.10 / 2.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.900, 93.900, 134.400, 90.00, 90.00, 120.00
R / Rfree (%)	22.9 / 23.7

The structure of A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Sodium atom in the A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution (pdb code 2p7d). 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 A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution, PDB code: 2p7d:

Sodium binding site 1 out of 1 in the A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.4 occ:1.00 O2' A:A5 2.5 87.2 1.0 C2' A:A5 2.7 83.4 1.0 O3' A:A5 2.9 91.5 1.0 C3' A:A5 2.9 82.8 1.0 N1 B:G8 3.6 94.5 0.5 O6 B:G8 3.7 81.0 0.5 O6 B:G8 4.0 95.7 0.5 N6 B:A7 4.1 96.8 1.0 C1' A:A5 4.3 77.7 1.0 C6 B:G8 4.3 94.9 0.5 C4' A:A5 4.4 81.3 1.0 N2 B:G8 4.4 90.2 0.5 O5' P:G6 4.5 87.1 1.0 C2 B:G8 4.5 93.8 0.5 O5' A:A5 4.6 74.3 1.0 N9 A:A5 4.7 75.0 1.0 C6 B:G8 4.8 81.1 0.5 O4' A:A5 4.9 76.4 1.0

A.T.Torelli, J.Krucinska, J.E.Wedekind. A Comparison of Vanadate to A 2'-5' Linkage at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization Rna V. 13 1052 2007.
ISSN: ISSN 1355-8382
PubMed: 17488874
DOI: 10.1261/RNA.510807