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 2qbf 2QBF (3.3Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with ribosome recycling factor (rrf). this file contains the 30s subunit of the second 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in List of all 62 Mg2+ binding sites in the PDB structure 2qbf 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 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2qbf A1603 Ob 6   1.00   0.95   0.99 yes 2qbf A1578 Ob 6   0.85   0.85   0.98 yes 2qbf A1583 Nb 6   0.96   0.98   0.95 yes 2qbf A1549 Nb 6   0.99   0.96   0.97 yes 2qbf A1576 2Nb 6   0.90   0.96   0.88 yes 2qbf A1564 Oph 6   0.88   0.89   0.99 yes 2qbf A1574 Oph 6   0.99   0.95   0.93 yes 2qbf A1553 Oph 6   0.87   0.88   0.98 yes 2qbf A1593 Oph 6   0.98   0.95   0.97 yes 2qbf A1598 Oph·Pout 6   0.88   0.87   0.96 yes 2qbf A1585 Oph·Pout 6   0.85   0.86   0.96 yes 2qbf A1581 Oph·Pout 6   0.93   0.89   0.96 yes 2qbf A1573 Oph·Pout 6   0.91   0.88   0.93 yes 2qbf A1599 Oph·Pout 6   0.82   0.82   0.99 yes 2qbf A1552 Oph·Pout 6   0.97   0.93   0.95 yes 2qbf A1602 Oph·Pout 6   0.90   0.90   0.96 yes 2qbf A1543 Oph·2Pout 6   0.95   0.95   0.75 yes 2qbf A1586 Oph·2Pout 6   0.96   0.97   0.98 yes 2qbf A1560 Oph·3Pout 6   0.83   0.83   0.89 yes 2qbf A1547 Oph·3Pout 6   0.90   0.91   0.96 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].

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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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