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 14 of 67 | « Previous | Next » | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4qcr A3622 2Ob 3   0.15   0.22   0.92 no 4qco A3009 2Ob 2   0.12   0.11   0.92 no 4ji3 A1756 2Ob 2   0.18   0.30   0.92 no 4qcn A3347 2Ob 4   0.28   0.45   0.92 no 3v27 A3194 2Ob 3   0.04   0.42   0.92 no 3i9b A1764 2Ob 2   0.07   0.21   0.92 no 3ccq 08076 2Ob 6   0.32   0.89   0.92 no 4dr3 A1788 2Ob 2   0.04   0.16   0.92 no 1vq4 08097 2Ob 6   0.31   0.85   0.92 no 3oi3 A3030 2Ob 2   0.06   0.12   0.92 no 3kit A3056 2Ob 2   0.09   0.18   0.92 no 4g5v A1969 2Ob 2   0.06   0.26   0.92 no 4dhc A3496 2Ob 4   0.30   0.42   0.92 no 4dv7 A1739 2Ob 2   0.03   0.16   0.92 no 3ccq 08032 2Ob 6   0.22   0.85   0.92 no 1vqn 08096 2Ob 6   0.41   0.86   0.92 no 3v23 A3519 2Ob 5   0.41   0.71   0.91 no 4aqy A2549 2Ob 2   0.08   0.21   0.91 no 2vqe Z14 2Ob 2   0.06   0.19   0.91 no 1xnq A210 2Ob 2   0.05   0.18   0.91 no 4aqy A2683 2Ob 2   0.05   0.15   0.91 no 3kiy A3169 2Ob 2   0.03   0.21   0.91 no 3oi1 A3115 2Ob 2   0.04   0.15   0.91 no 4b3t A2657 2Ob 2   0.04   0.21   0.91 no 4qct A3220 2Ob 3   0.13   0.51   0.91 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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