Magnesium in PDB 1sj3: Hepatitis Delta Virus Gemonic Ribozyme Precursor, with MG2+ Bound

The structure of Hepatitis Delta Virus Gemonic Ribozyme Precursor, with MG2+ Bound, PDB code: 1sj3 was solved by A.Ke, K.Zhou, F.Ding, J.H.Cate, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.39 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	108.731, 108.731, 191.726, 90.00, 90.00, 120.00
R / Rfree (%)	25.5 / 28.2

The binding sites of Magnesium atom in the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with MG2+ Bound (pdb code 1sj3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with MG2+ Bound, PDB code: 1sj3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with MG2+ Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hepatitis Delta Virus Gemonic Ribozyme Precursor, with MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg201 b:66.0 occ:0.50 O4 R:U163 2.2 74.2 1.0 OP1 R:U123 2.9 88.8 1.0 C4 R:U163 3.4 73.4 1.0 O2 R:U120 3.7 68.6 1.0 OP2 R:G101 3.7 95.1 1.0 OP2 R:C122 3.8 73.4 1.0 C5' R:C122 4.1 75.3 1.0 C5 R:U163 4.2 73.4 1.0 O5' R:G101 4.3 92.4 1.0 P R:U123 4.3 89.6 1.0 N3 R:U163 4.3 72.9 1.0 P R:G101 4.6 94.2 1.0 O5' R:U123 4.7 92.0 1.0 P R:C122 4.7 72.4 1.0 C2 R:U120 4.9 67.6 1.0 O5' R:C122 5.0 73.4 1.0

Magnesium binding site 2 out of 2 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with MG2+ Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hepatitis Delta Virus Gemonic Ribozyme Precursor, with MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg202 b:66.5 occ:0.80 O2' R:C141 3.9 77.3 1.0 C2' R:C141 4.4 77.8 1.0 O6 R:G159 4.6 49.7 1.0 N7 R:G158 4.7 49.3 1.0 N7 R:G159 4.8 50.7 1.0 OP2 R:A142 4.9 81.6 1.0

A.Ke, K.Zhou, F.Ding, J.H.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