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 4kj3 4KJ3 (2.9Å) -- RIBOSOME : Control of ribosomal subunit rotation by elongation factor g List of all 143 Mg2+ binding sites in the PDB structure 4kj3 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 4kj3 A3021 Pout·Bout 1   0.02  0   0.24 no 4kj3 A3095 Ob·Nb 4   0.15   0.62   0.30 no 4kj3 A3085 Oph 3   0.45   0.10   0.30 no 4kj3 A3080 Oph 2   0.07   0.11   0.34 no 4kj3 A3129 2Bout 3   0.17   0.38   0.37 no 4kj3 A3006 Oph 1   0.03  0   0.38 no 4kj3 A3030 poly-nuclear Mg2+ site 4   0.40   0.68   0.38 no 4kj3 A3047 Oph·Pout 4   0.34   0.37   0.38 no 4kj3 A3001 Bout 4   0.59   0.41   0.38 no 4kj3 A3066 trans-2Oph·Ob 4   0.21   0.32   0.41 no 4kj3 A3017 2Pout·Rout·4Bout 5   0.17   0.70   0.41 no 4kj3 A3018 Oph·Pout 4   0.11   0.45   0.42 no 4kj3 A3089 Oph 3   0.25   0.26   0.42 no 4kj3 A3061 2Pout·Bout 3   0.22   0.18   0.42 no 4kj3 A3134 2Pout 3   0.27   0.33   0.46 no 4kj3 A3104 other RNA-inner types 5   0.39   0.63   0.47 no 4kj3 A3010 cis-2Oph 4   0.26   0.34   0.47 no 4kj3 A3020 2Bout 3   0.45   0.23   0.47 no 4kj3 A3086 Oph·Or 4   0.11   0.38   0.47 no 4kj3 A3084 3Pout·Bout 3   0.12   0.45   0.50 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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