MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 3i56 3I56 (2.9Å) -- RIBOSOME/ANTIBIOTIC : Co-crystal structure of triacetyloleandomcyin bound to the large ribosomal subunit List of all 93 Mg2+ binding sites in the PDB structure 3i56 in the full dataset (switch to benchmark dataset) Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv #", "Qs #", "Qe #", "Site type" or "Mg2+ ID" Page 3 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3i56 08079 Oph·Ob 5   0.17   0.48   0.63 no 3i56 08055 Oph·Ob 6   0.17   0.79   0.81 no 3i56 08087 Oph·Nb 6   0.23   0.80   0.47 no 3i56 08031 Oph·2Or 6   0.19   0.88   0.78 no 3i56 08084 cis-2Oph 5   0.30   0.65   0.92 no 3i56 08010 cis-2Oph 6   0.27   0.69   0.10 no 3i56 08011 cis-2Oph 5   0.28   0.47   0.11 no 3i56 98040 cis-2Oph 6   0.17   0.51   0.55 no 3i56 08062 cis-2Oph 6   0.21   0.59   0.48 no 3i56 08082 cis-2Oph 3   0.05   0.79   0.96 no 3i56 08058 cis-2Oph 6   0.34   0.65   0.03 no 3i56 08073 cis-2Oph 4   0.11   0.42   0.73 no 3i56 08048 cis-2Oph 5   0.25   0.46   0.49 no 3i56 08039 cis-2Oph 4   0.09   0.42   0.98 no 3i56 08023 cis-2Oph 6   0.30   0.63   0.20 no 3i56 08081 cis-2Oph 3   0.08   0.45   0.34 no 3i56 08009 cis-2Oph 6   0.32   0.69   0.28 no 3i56 08016 cis-2Oph 6   0.22   0.58   0.10 no 3i56 08022 cis-2Oph 6   0.23   0.49   0.53 no 3i56 08002 trans-2Oph·Ob 6   0.34   0.61   0.54 no

^# Validation parameters Q_v, Q_s, Q_e are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Q_v measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg²⁺ (+2)
Q_s measures the geometrical symmetry of the ligands distribution around the Mg²⁺ required for octahedral geometry
Q_e measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg²⁺ compared to those of all atoms in its environment

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>