Sodium in PDB 1vc5: Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in Edta Solution

The structure of Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in Edta Solution, PDB code: 1vc5 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)	20.00 / 3.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	109.488, 109.488, 187.580, 90.00, 90.00, 120.00
R / Rfree (%)	30.5 / 32.7

The binding sites of Sodium atom in the Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in Edta Solution (pdb code 1vc5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in Edta Solution, PDB code: 1vc5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in Edta Solution


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 Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in Edta Solution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:67.3 occ:1.00 O6 B:G159 4.0 71.5 1.0 O2' B:C141 4.1 0.1 1.0 N7 B:G158 4.7 0.4 1.0 N7 B:G159 4.7 0.7 1.0 C2' B:C141 4.7 0.1 1.0 OP2 B:A142 4.8 0.7 1.0 C6 B:G159 4.9 94.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in Edta Solution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in Edta Solution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:0.0 occ:1.00 O2' B:G102 3.3 0.2 1.0 O4' B:C103 3.9 0.5 1.0 C4' B:C103 4.3 0.3 1.0 C2' B:G102 4.5 0.2 1.0 C1' B:C103 4.6 0.6 1.0 C5' B:C103 4.8 0.6 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