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 3cxc 3CXC (3Å) -- RIBOSOME : The structure of an enhanced oxazolidinone inhibitor bound to the 50s ribosomal subunit of h. marismortui List of all 117 Mg2+ binding sites in the PDB structure 3cxc 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 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3cxc X8109 Mg2+ not bound by RNA 6   0.40   0.76   0.82 no 3cxc 08026 fac-3Oph 6   0.73   0.76   0.75 yes 3cxc 08116 poly-nuclear Mg2+ site 6   0.50   0.78   0.81 no 3cxc 28078 Mg2+ bound by non-RNA 6   0.50   0.78   0.96 yes 3cxc 08113 Nb 6   0.41   0.78   0.97 no 3cxc 08083 Oph·2Pout 6   0.62   0.79   0.99 yes 3cxc 08104 cis-2Oph 4   0.20   0.79   0.85 no 3cxc 08064 other RNA-inner types 5   0.17   0.79   0.67 no 3cxc 08029 cis-2Oph 6   0.73   0.80   0.97 yes 3cxc 08115 2Pout 5   0.36   0.80   0.75 no 3cxc 08098 Nb 6   0.39   0.81   0.83 no 3cxc 08034 cis-2Oph 6   0.82   0.81   0.81 yes 3cxc 08014 cis-2Oph 6   0.75   0.81   0.86 yes 3cxc 08056 Mg2+ bound by non-RNA 6   0.83   0.82   0.94 yes 3cxc B8055 2Pout 6   0.62   0.82   1.00 yes 3cxc 08022 Oph·Pout 5   0.37   0.82   0.54 no 3cxc 08053 Ob 6   0.35   0.82   0.94 no 3cxc 08072 4Pout 5   0.50   0.83   0.92 yes 3cxc 08054 cis-2Oph 6   0.93   0.83   0.94 yes 3cxc J8069 Mg2+ bound by non-RNA 6   0.69   0.83   0.72 yes

^# 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>