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 4kja 4KJA (2.9Å) -- RIBOSOME/ANTIBIOTIC : Control of ribosomal subunit rotation by elongation factor g List of all 43 Mg2+ binding sites in the PDB structure 4kja 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 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4kja U101 Bout 2   0.06   0.57   0.64 no 4kja E201 Mg2+ not bound by RNA 0  0  0   0.58 no 4kja V802 Mg2+ not bound by RNA 4   0.19   0.54   0.77 no 4kja A1601 Ob 3   0.12   0.43   0.88 no 4kja A1602 Oph 1   0.02  0   0.92 no 4kja A1603 Nb 4   0.86   0.73   0.86 yes 4kja A1604 Oph·2Ob 4   0.26   0.26   0.98 no 4kja A1605 Oph·2Pout 3   0.33   0.13   0.70 no 4kja A1606 Oph·2Pout 4   0.35   0.36   0.53 no 4kja A1607 Oph·Pout 3   0.50   0.21   0.93 no 4kja A1608 cis-2Oph 4   0.65   0.43   0.97 no 4kja A1609 Oph·Pout 4   0.40   0.28   0.56 no 4kja A1610 Nb 1   0.06  0   0.81 no 4kja A1611 Pout 2   0.30   0.19   0.14 no 4kja A1612 Oph·Pout 3   0.14   0.18   0.24 no 4kja A1613 Oph·Pout 3   0.43   0.31   0.80 no 4kja A1614 2Pout·Rout 5   0.42   0.62   0.46 no 4kja A1615 Oph 5   0.50   0.34   0.76 no 4kja A1616 Pout·2Bout 2   0.34   0.05   0.63 no 4kja A1617 cis-2Oph·Nb 4   0.41   0.35   0.51 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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