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 2aw7 2AW7 (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli at 3.5 a resolution. this file contains the 30s subunit of the second 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in remark 400. List of all 62 Mg2+ binding sites in the PDB structure 2aw7 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 2aw7 A1604 Ob 6   0.88   0.86   0.94 yes 2aw7 A1579 Ob 6   0.90   0.91   0.97 yes 2aw7 A1584 Nb 6   0.94   0.96   0.97 yes 2aw7 A1549 Nb 6   0.94   0.95   0.93 yes 2aw7 A1577 2Nb 6   0.87   0.91   0.73 yes 2aw7 A1574 Oph 6   0.93   0.94   0.89 yes 2aw7 A1575 Oph 6   0.92   0.89   0.87 yes 2aw7 A1564 Oph 6   0.85   0.86   0.98 yes 2aw7 A1603 Oph 6   0.88   0.86   0.97 yes 2aw7 A1599 Oph·Pout 6   0.98   0.97   0.92 yes 2aw7 A1594 Oph·Pout 6   0.97   0.94   0.95 yes 2aw7 A1586 Oph·Pout 6   0.92   0.93   0.95 yes 2aw7 A1552 Oph·Pout 6   0.91   0.89   0.78 yes 2aw7 A1600 Oph·Pout 6   0.83   0.83   0.99 yes 2aw7 A1582 Oph·Pout 6   0.94   0.91   0.90 yes 2aw7 A1597 Oph·2Pout 6   0.86   0.85   0.91 yes 2aw7 A1590 Oph·2Pout 5   0.99   0.73   0.93 yes 2aw7 A1587 Oph·2Pout 6   0.82   0.82   0.89 yes 2aw7 A1553 Oph·2Pout 6   0.95   0.97   0.93 yes 2aw7 A1543 Oph·2Pout 6   0.95   0.96   0.63 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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