MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2r8s:R1004, See in JSmolClick on the image to toggle views Site type: 2Ob Schematic drawing for 2Ob List of all 1662 Mg2+ binding sites with the site type 2Ob in RNA crystal structures 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 #", "PDB ID" or "Mg2+ ID" Page 11 of 67 | « Previous | Next » | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2uub Z1195 2Ob 2   0.04   0.17   0.94 no 2wdg Z519 2Ob 2   0.05   0.21   0.94 no 1m1k A8042 2Ob 6   0.33   0.79   0.94 no 3v25 A3406 2Ob 5   0.42   0.76   0.94 no 3v2c A1782 2Ob 4   0.29   0.52   0.94 no 3i8g A1568 2Ob 2   0.14   0.27   0.94 no 4khp A1685 2Ob 2   0.07   0.23   0.94 no 4dr6 A1907 2Ob 3   0.06   0.48   0.94 no 1vw0 A3155 2Ob 2   0.03   0.16   0.94 no 3i8h A1883 2Ob 2   0.06   0.28   0.94 no 4qd1 A3267 2Ob 2   0.04   0.21   0.94 no 4qcs A3161 2Ob 3   0.15   0.18   0.94 no 3ox0 A120 2Ob 2   0.07   0.18   0.94 no 3kiy A3055 2Ob 2   0.06   0.19   0.94 no 3v27 A3154 2Ob 2   0.03   0.14   0.94 no 4l6j A5177 2Ob 2   0.03   0.20   0.94 no 4nvx A3618 2Ob 4   0.28   0.49   0.94 no 4dv3 A1748 2Ob 2   0.05   0.10   0.94 no 3v27 A3020 2Ob 2   0.04   0.14   0.94 no 4dv5 A1744 2Ob 2   0.05   0.10   0.93 no 4qd1 A3512 2Ob 3   0.15   0.26   0.93 no 3cma 08075 2Ob 6   0.21   0.92   0.93 no 4qd1 A3247 2Ob 3   0.09   0.41   0.93 no 4qco A3061 2Ob 2   0.04   0.15   0.93 no 3kix a1656 2Ob 2   0.03   0.45   0.93 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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