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 4kvb 4KVB (4.2Å) -- RIBOSOME : Thermus thermophilus hb27 30s ribosomal subunit lacking ribosomal protein s17 List of all 144 Mg2+ binding sites in the PDB structure 4kvb 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 1 of 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4kvb A1697 Or 2   0.22   0.16   0.72 no 4kvb A1677 Or 2   0.21   0.14   0.74 no 4kvb A1737 Or 2   0.24   0.17   0.68 no 4kvb A1664 Ob 1   0.09  0   0.86 no 4kvb A1620 Ob 1   0.03  0   0.66 no 4kvb A1703 Ob 1   0.02  0   0.59 no 4kvb A1744 Ob 1   0.02  0   0.57 no 4kvb A1654 Ob 1   0.13  0   0.65 no 4kvb A1742 Ob 1   0.02  0   0.77 no 4kvb A1745 Ob 1   0.12  0   0.92 no 4kvb A1666 Ob 1   0.03  0   0.68 no 4kvb A1672 Ob 1   0.02  0   0.90 no 4kvb A1624 Ob 1   0.11  0   0.92 no 4kvb A1638 Nb 1   0.13  0   0.62 no 4kvb A1648 Nb 1   0.02  0   0.56 no 4kvb A1739 2Or 3   0.28   0.26   0.69 no 4kvb A1726 2Or 2   0.24   0.20   0.76 no 4kvb A1606 Or·Ob 2   0.27   0.50   0.76 no 4kvb A1702 2Ob 2   0.05   0.22   0.98 no 4kvb A1747 2Ob 2   0.18   0.25   0.81 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>