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 8 of 67 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2vqf Z189 2Ob 2   0.06   0.14   0.62 no 4ji8 A1617 2Ob 2   0.03   0.14   0.80 no 2wdh Z489 2Ob 2   0.05   0.14   0.64 no 3t1h A1756 2Ob 2   0.05   0.14   0.27 no 1vvu A3222 2Ob 2   0.07   0.14   0.64 no 3kix a1618 2Ob 2   0.04   0.14   0.21 no 3pyr A2992 2Ob 2   0.04   0.14   0.71 no 4dr3 A1836 2Ob 2   0.03   0.14   0.88 no 4ej9 A7083 2Ob 2   0.03   0.14   0.82 no 4qcn A3047 2Ob 2   0.08   0.14   0.97 no 3v26 A1634 2Ob 2   0.05   0.14   0.70 no 4l6j A4798 2Ob 2   0.04   0.14   0.60 no 4ji0 A1827 2Ob 2   0.04   0.14   0.98 no 4qcy A3064 2Ob 2   0.06   0.14   0.76 no 3r8s A3078 2Ob 2   0.03   0.14   0.04 no 4nxn A1650 2Ob 2   0.03   0.14   0.61 no 3ohk A3162 2Ob 2   0.05   0.14   0.86 no 3oi5 A3194 2Ob 2   0.05   0.14   0.99 no 3t1y A1699 2Ob 2   0.05   0.14   0.27 no 4b3s A2655 2Ob 2   0.10   0.14   0.82 no 3t1y A1736 2Ob 2   0.04   0.14   0.19 no 4qcr B215 2Ob 3   0.15   0.14   0.65 no 4l6j A5121 2Ob 2   0.04   0.14   0.96 no 4nw1 A3055 2Ob 2   0.04   0.14   0.99 no 4ji5 A1746 2Ob 2   0.27   0.14   0.79 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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