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 1 of 67 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1nji A8097 2Ob 6   0.70   0.72   0.73 yes 4dr2 A1761 2Ob 6   0.67   0.70   0.97 yes 1yjw 78097 2Ob 6   0.58   0.71   0.82 yes 1yjn 08097 2Ob 6   0.56   0.49   0.90 no 3v23 A3310 2Ob 6   0.54   0.74   0.96 yes 3v23 A3357 2Ob 6   0.54   0.75   0.85 yes 4dr6 A1613 2Ob 6   0.53   0.56   0.58 no 4dr3 A1632 2Ob 5   0.53   0.71   0.56 yes 4dv7 A1626 2Ob 5   0.52   0.72   0.56 yes 2otj 08097 2Ob 6   0.52   0.76   0.74 yes 4dv6 A1775 2Ob 5   0.52   0.73   0.39 no 3v2d A3258 2Ob 6   0.52   0.74   1.00 yes 4ji3 A1784 2Ob 5   0.51   0.69   0.97 yes 4nxn A1629 2Ob 5   0.51   0.69   0.55 yes 4dv5 A1686 2Ob 5   0.51   0.74   0.85 yes 2r8s R1004 2Ob 6   0.51   0.85   0.99 yes 4dv5 A1625 2Ob 5   0.51   0.73   0.54 yes 4ji7 A1654 2Ob 5   0.51   0.70   0.63 yes 1jj2 08097 2Ob 6   0.50   0.71   0.90 yes 3v23 A3322 2Ob 6   0.50   0.71   0.77 no 4dr7 A1650 2Ob 5   0.50   0.49   0.96 no 1vqm 08096 2Ob 6   0.49   0.77   0.76 no 1kc8 A8097 2Ob 6   0.49   0.66   0.98 no 1s72 08097 2Ob 6   0.48   0.73   0.87 no 2otj 08096 2Ob 6   0.47   0.83   0.84 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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