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 4kiy 4KIY (2.9Å) -- RIBOSOME/ANTIBIOTIC : Control of ribosomal subunit rotation by elongation factor g List of all 44 Mg2+ binding sites in the PDB structure 4kiy 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 2 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4kiy A1623 Oph·Nb 6   0.61   0.33   0.65 no 4kiy A1626 Oph·Nb 4   0.51   0.52   0.74 no 4kiy A1613 cis-2Oph 4   0.73   0.31   0.54 no 4kiy A1616 cis-2Oph 3   0.54   0.25   0.27 no 4kiy A1634 fac-3Oph 5   0.80   0.49   0.59 no 4kiy A1638 mer-3Oph 5   0.66   0.57   0.92 no 4kiy A1619 mer-3Oph 4   0.45   0.50   0.59 no 4kiy A1608 mer-3Oph 4   0.51   0.62   0.96 yes 4kiy A1601 Bout 3   0.35   0.13   0.41 no 4kiy A1610 3Bout 4   0.38   0.52   0.48 no 4kiy A1640 Pout 4   0.65   0.36   0.80 no 4kiy A1615 Pout·Bout 1   0.01  0   0.23 no 4kiy N201 Pout·Bout 3   0.49   0.19   0.69 no 4kiy A1622 Pout·2Bout 3   0.36   0.32   0.88 no 4kiy A1621 Pout·3Bout 4   0.61   0.37   0.98 no 4kiy A1611 2Pout·2Bout 5   0.75   0.69   0.67 yes 4kiy A1631 2Pout·3Bout 3   0.43   0.36   0.82 no 4kiy A1635 2Pout·3Bout 3   0.19   0.24   0.50 no 4kiy U101 Mg2+ bound by non-RNA 2   0.05   0.80   0.85 no 4kiy A1628 poly-nuclear Mg2+ site 4   0.47   0.30   0.67 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].

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