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 4e8q 4E8Q (2.84Å) -- RNA : Structure of oceanobacillus iheyensis group ii intron in a ligand-free state in the presence of tl+ and mg2+ List of all 30 Mg2+ binding sites in the PDB structure 4e8q 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4e8q A446 Ob 1   0.02  0   0.85 no 4e8q A423 Ob 2   0.22   0.14   0.98 no 4e8q A420 Oph 1   0.08  0   0.80 no 4e8q A426 Oph 2   0.15   0.12   0.95 no 4e8q A434 Oph 1   0.01  0   0.87 no 4e8q A439 Oph 1   0.08  0   0.83 no 4e8q A441 Oph 1   0.06  0   0.68 no 4e8q A422 Oph 1   0.07  0   0.88 no 4e8q A447 Oph 1   0.13  0   0.68 no 4e8q A418 Oph 1   0.18  0   0.85 no 4e8q A435 Oph 1   0.08  0   0.54 no 4e8q A437 Oph 1   0.10  0   0.88 no 4e8q A436 Oph·Or 2   0.04   0.19   0.79 no 4e8q A419 Oph·Nb 2   0.22   0.20   0.81 no 4e8q A443 Oph·Ob·Nb 3   0.45   0.20   0.54 no 4e8q A438 cis-2Oph 2   0.09   0.12   0.82 no 4e8q A427 cis-2Oph 3   0.32   0.14   0.87 no 4e8q A432 cis-2Oph 3   0.42   0.28   0.94 no 4e8q A431 trans-2Oph 3   0.14   0.29   0.91 no 4e8q A421 trans-2Oph 2   0.15   0.73   0.96 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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