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 2uub Z1195 2Ob 2   0.04   0.17   0.94 no 1hr0 A1547 2Ob 2   0.03   0.14   0.81 no 1hnw A1548 2Ob 2   0.05   0.16   0.75 no 1ibk A1548 2Ob 2   0.03   0.20   0.58 no 1fjg A1549 2Ob 2   0.04   0.18   0.84 no 3oto A1550 2Ob 2   0.04   0.17   0.63 no 3i9b A1554 2Ob 2   0.10   0.13   0.67 no 3ohd A1556 2Ob 2   0.06   0.16   0.99 no 3ohc A1559 2Ob 2   0.05   0.15   0.74 no 3knn A1561 2Ob 2   0.42   0.09   0.64 no 3d5c A1564 2Ob 2   0.06   0.15   0.09 no 1hnz A1566 2Ob 2   0.04   0.20   0.71 no 1fjg A1567 2Ob 2   0.04   0.19   0.77 no 3i8g A1568 2Ob 2   0.14   0.27   0.94 no 3oi4 A1569 2Ob 2   0.07   0.19   0.84 no 3knj A1569 2Ob 2   0.04   0.13   0.57 no 3oi2 A1571 2Ob 2   0.05   0.11   0.86 no 3ohc A1573 2Ob 2   0.03   0.18   0.68 no 3d5c A1573 2Ob 2   0.06   0.11   0.33 no 2xfz Z1574 2Ob 2   0.13   0.20   0.69 no 3knh A1575 2Ob 2   0.06   0.15   0.62 no 3huy A1575 2Ob 2   0.06   0.16   0.45 no 3sfs A1576 2Ob 2   0.06   0.11   0.56 no 2qoy A1577 2Ob 4   0.37   0.45   0.97 no 3kix a1578 2Ob 2   0.04   0.22   0.94 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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