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 4ji8 A1617 2Ob 2   0.03   0.14   0.80 no 2uu9 Z1018 2Ob 2   0.06   0.24   0.54 no 3i9b A1554 2Ob 2   0.10   0.13   0.67 no 4b3m A2557 2Ob 2   0.16   0.20   0.68 no 3owi A127 2Ob 2   0.08   0.20   0.65 no 3pyt A2910 2Ob 2   0.04   0.15   0.08 no 4nvv A3019 2Ob 2   0.07   0.40   0.89 no 4nvz A3019 2Ob 2   0.04   0.33   0.90 no 4kx1 A1620 2Ob 2   0.13   0.92   0.73 no 4qcx A3020 2Ob 2   0.17   0.15   0.77 no 3v27 A3020 2Ob 2   0.04   0.14   0.94 no 4dhc A3021 2Ob 2   0.03   0.38   0.91 no 3t1y A1622 2Ob 2   0.14   0.18   0.43 no 3oxb A124 2Ob 2   0.10   0.22   0.99 no 3uyf A1691 2Ob 2   0.03   0.18   0.67 no 4nvu A3022 2Ob 2   0.03   0.19   0.87 no 4gkj A1624 2Ob 2   0.07   0.12   0.78 no 4dv4 A1625 2Ob 2   0.03   0.17   0.86 no 2uuc Z1026 2Ob 2   0.13   0.44   0.73 no 3v27 A3023 2Ob 2   0.06   0.25   0.64 no 1vvv A1624 2Ob 2   0.15   0.15   0.35 no 1hnz A1566 2Ob 2   0.04   0.20   0.71 no 4gkk A1627 2Ob 2   0.06   0.22   0.94 no 4g5k A1659 2Ob 2   0.26   0.19   0.98 no 3v2d A3638 2Ob 5   0.27   0.64   0.89 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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