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 12 of 67 | « Previous | Next » | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4qcy A3030 2Ob 2   0.03   0.18   0.79 no 3kis a1670 2Ob 2   0.03   0.17   0.93 no 2uub Z1083 2Ob 2   0.03   0.19   0.81 no 3v27 B206 2Ob 2   0.03   0.17   0.72 no 4qcv A3195 2Ob 2   0.03   0.18   0.80 no 4dv4 A1625 2Ob 2   0.03   0.17   0.86 no 4l6j A5625 2Ob 2   0.03   0.17   0.64 no 1xmo A1632 2Ob 2   0.03   0.18   0.40 no 1vxs A1667 2Ob 2   0.03   0.14   0.47 no 3uyd A2014 2Ob 2   0.03   0.18   0.80 no 1vxi A1650 2Ob 2   0.03   0.19   0.89 no 4duz A1781 2Ob 2   0.04   0.18   0.68 no 4g5v A1654 2Ob 2   0.04   0.18   0.89 no 3v23 A3109 2Ob 2   0.04   0.18   0.69 no 3v25 A3071 2Ob 2   0.04   0.46   0.89 no 3f1f A5322 2Ob 2   0.04   0.23   0.72 no 4dv6 A1766 2Ob 2   0.04   0.15   0.92 no 3knj A1569 2Ob 2   0.04   0.13   0.57 no 4nw0 A3043 2Ob 2   0.04   0.28   0.58 no 3uz4 A1764 2Ob 2   0.04   0.16   0.76 no 1vx9 A3221 2Ob 2   0.04   0.16   0.24 no 4duz A1696 2Ob 2   0.04   0.73   0.59 no 4ji0 A1827 2Ob 2   0.04   0.14   0.98 no 4dv3 A1755 2Ob 2   0.04   0.53   0.71 no 4l6j A5121 2Ob 2   0.04   0.14   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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