Sodium in PDB 1vby: Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound

The structure of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound, PDB code: 1vby was solved by A.Ke, K.Zhou, F.Ding, J.H.D.Cate, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.16 / 2.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	108.589, 108.589, 190.519, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 28.4

The structure of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound (pdb code 1vby). 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 Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound, PDB code: 1vby:

Sodium binding site 1 out of 1 in the Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U Mutaion, and MN2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:55.3 occ:1.00 O2' B:C141 4.1 73.7 1.0 N7 B:G158 4.3 55.1 1.0 O6 B:G159 4.5 61.9 1.0 N7 B:G159 4.6 59.8 1.0 C2' B:C141 4.6 73.7 1.0 O6 B:G158 4.9 60.6 1.0 C5 B:G158 5.0 55.8 1.0

A.Ke, K.Zhou, F.Ding, J.H.D.Cate, J.A.Doudna. A Conformational Switch Controls Hepatitis Delta Virus Ribozyme Catalysis Nature V. 429 201 2004.
ISSN: ISSN 0028-0836
PubMed: 15141216
DOI: 10.1038/NATURE02522