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 4kjb 4KJB (2.9Å) -- RIBOSOME : Control of ribosomal subunit rotation by elongation factor g List of all 141 Mg2+ binding sites in the PDB structure 4kjb 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 4kjb S201 Mg2+ not bound by RNA 0  0  0   0.52 no 4kjb A3131 Mg2+ not bound by RNA 0  0  0   0.94 no 4kjb A3082 Pout 1   0.01  0   0.94 no 4kjb A3133 Oph 1   0.02  0   0.27 no 4kjb B1202 Oph 1   0.03  0   0.95 no 4kjb A3093 Pout 2   0.03   0.50   0.49 no 4kjb A3069 Nb 1   0.03  0   0.95 no 4kjb A3073 Oph·2Pout 2   0.04   0.17   0.35 no 4kjb A3014 2Pout 2   0.04   0.31   0.78 no 4kjb A3060 Mg2+ not bound by RNA 2   0.04   0.20   0.49 no 4kjb A3090 2Bout 2   0.05   0.17   0.93 no 4kjb A3094 Ob·Nb 3   0.06   0.31   0.56 no 4kjb A3059 Oph 2   0.06   0.52   0.25 no 4kjb B1201 2Pout 3   0.06   0.53   0.97 no 4kjb A3068 Or 2   0.06   0.40   0.77 no 4kjb A3033 Oph·Or 2   0.07   0.21   0.98 no 4kjb A3134 Oph·Pout 3   0.07   0.61   0.62 no 4kjb A3018 Mg2+ bound by non-RNA 3   0.09   0.49   0.88 no 4kjb L201 Mg2+ bound by non-RNA 2   0.09   0.51   0.80 no 4kjb A3051 cis-2Oph 3   0.09   0.21   0.42 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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