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 4dhb 4DHB (3.2Å) -- RIBOSOME : Crystal structure of yaej bound to the 70s ribosome List of all 238 Mg2+ binding sites in the PDB structure 4dhb 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 12 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dhb A1713 Mg2+ not bound by RNA 0  0  0   0.75 no 4dhb A1617 Oph 1   0.03  0   0.76 no 4dhb A1830 Mg2+ not bound by RNA 3   0.36   0.67   0.76 no 4dhb A1625 Ob 1   0.01  0   0.76 no 4dhb A1616 Mg2+ bound by non-RNA 5   0.10   0.78   0.76 no 4dhb A1606 trans-2Oph 2   0.03   0.81   0.77 no 4dhb A1811 2Pout 6   0.70   0.97   0.77 yes 4dhb A1672 Oph 1   0.02  0   0.77 no 4dhb A1698 Oph 1   0.04  0   0.78 no 4dhb A1828 3Bout 4   0.48   0.98   0.78 no 4dhb A1805 Pout 4   0.49   0.97   0.78 no 4dhb A1774 Oph 4   0.38   0.71   0.78 no 4dhb A1763 3Pout 4   0.37   0.71   0.78 no 4dhb A1734 Bout 2   0.25   0.42   0.78 no 4dhb A1694 Oph 1   0.03  0   0.78 no 4dhb V103 poly-nuclear Mg2+ site 1   0.02  0   0.78 no 4dhb A1607 other RNA-inner types 4   0.08   0.62   0.78 no 4dhb A1668 Mg2+ not bound by RNA 0  0  0   0.79 no 4dhb V101 cis-2Oph 2   0.08   0.17   0.79 no 4dhb A1722 cis-2Oph 2   0.06   0.15   0.79 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>