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 13 of 67 | « Previous | Next » | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3k0j E707 2Ob 2   0.17   0.09   0.65 no 3u56 B2207 2Ob 5   0.21   0.81   0.51 no 4ox9 A1607 2Ob 2   0.14   0.27   0.86 no 3skl B203 2Ob 2   0.08   0.17   0.46 no 3oto A1550 2Ob 2   0.04   0.17   0.63 no 3ivn B101 2Ob 2   0.03   0.21   0.97 no 3oh7 A2915 2Ob 2   0.04   0.13   0.77 no 4lf6 A1611 2Ob 2   0.04   0.20   0.69 no 4qco A3009 2Ob 2   0.12   0.11   0.92 no 3l26 C9 2Ob 6   0.34   0.75   0.38 no 4ox9 A1609 2Ob 2   0.08   0.19   0.62 no 4g5v A1617 2Ob 2   0.05   0.15   0.79 no 4lf4 A1611 2Ob 2   0.03   0.19   0.73 no 3v29 A3012 2Ob 2   0.05   0.21   0.89 no 3ohd A1556 2Ob 2   0.06   0.16   0.99 no 4jya A1613 2Ob 2   0.03   0.19   0.57 no 4dr6 A1613 2Ob 6   0.53   0.56   0.58 no 4eja A7014 2Ob 2   0.06   0.17   0.74 no 3ohc A1559 2Ob 2   0.05   0.15   0.74 no 3v23 A3014 2Ob 2   0.05   0.18   0.91 no 4lf6 A1619 2Ob 2   0.10   0.51   0.75 no 4lf8 A1618 2Ob 2   0.13   0.57   0.63 no 4eja A7016 2Ob 2   0.03   0.15   0.70 no 4lf7 A1618 2Ob 2   0.13   0.57   0.63 no 3ivn A101 2Ob 2   0.03   0.17   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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