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 4duy 4DUY (3.39Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u13c List of all 302 Mg2+ binding sites in the PDB structure 4duy 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 8 of 16 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4duy A1698 other RNA-inner types 5   0.10   0.58   0.71 no 4duy A1701 Mg2+ not bound by RNA 1   0.16  0   0.76 no 4duy A1687 Mg2+ not bound by RNA 1   0.16  0   0.66 no 4duy A1708 Mg2+ not bound by RNA 1   0.16  0   0.90 no 4duy A1655 Mg2+ not bound by RNA 1   0.16  0   0.97 no 4duy A1815 Mg2+ not bound by RNA 1   0.16  0   0.75 no 4duy A1661 poly-nuclear Mg2+ site 1   0.16  0   0.78 no 4duy A1640 Oph 2   0.17   0.09   0.51 no 4duy A1705 Oph 2   0.18   0.24   0.87 no 4duy A1706 poly-nuclear Mg2+ site 2   0.19   0.07   0.55 no 4duy D303 Mg2+ bound by non-RNA 3   0.19   0.19   0.77 no 4duy A1703 Oph·Ob 3   0.20   0.11   0.96 no 4duy A1680 cis-2Oph 3   0.20   0.14   0.67 no 4duy A1684 cis-2Oph 3   0.20   0.18   0.60 no 4duy A1646 other RNA-inner types 4   0.21   0.21   0.58 no 4duy A1615 mer-3Oph 4   0.21   0.36   0.56 no 4duy A1647 fac-3Oph 4   0.25   0.29   0.90 no 4duy A1768 Bout 2   0.31   0.30   0.57 no 4duy A1674 Mg2+ not bound by RNA 2   0.31   0.31   0.53 no 4duy A1832 2Bout 2   0.31   0.30   0.47 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>