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 1vqk 08097 2Ob 5   0.23   0.66   0.75 no 4dr3 A1766 2Ob 2   0.03   0.66   0.95 no 3ccv 08033 2Ob 5   0.19   0.65   0.72 no 3v2f A3530 2Ob 5   0.42   0.65   0.92 no 4dv4 A1821 2Ob 2   0.03   0.65   0.53 no 3cme 08033 2Ob 5   0.12   0.65   0.96 no 3v2f A3397 2Ob 4   0.29   0.64   0.96 no 4kj2 A1604 2Ob 4   0.16   0.64   0.93 no 1yij 08043 2Ob 5   0.35   0.64   0.98 no 3v2d A3638 2Ob 5   0.27   0.64   0.89 no 3cxc 08042 2Ob 6   0.21   0.63   0.87 no 4nvv A3293 2Ob 2   0.04   0.63   0.85 no 3u5d 14116 2Ob 2   0.04   0.63   0.60 no 3cc4 08033 2Ob 5   0.15   0.62   0.88 no 4qcy X3007 2Ob 2   0.03   0.62   0.70 no 4ji1 A1666 2Ob 2   0.05   0.61   0.68 no 3v2d A3274 2Ob 5   0.40   0.61   0.93 no 2j02 Z451 2Ob 2   0.09   0.61   0.25 no 1o3z A303 2Ob 4   0.09   0.61   0.68 no 3d5a A1580 2Ob 2   0.04   0.60   0.33 no 4dr7 A1885 2Ob 3   0.07   0.60   0.72 no 3v25 A3102 2Ob 3   0.05   0.60   0.96 no 3v28 A1654 2Ob 2   0.05   0.59   0.90 no 3v25 A3388 2Ob 4   0.28   0.59   0.76 no 4dha A3527 2Ob 5   0.42   0.59   0.80 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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