MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3428, See in JSmolClick on the image to toggle views Site type: Oph·Or Schematic drawing for Oph·Or List of all 1185 Mg2+ binding sites with the site type Oph·Or 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 2 of 48 | « 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 1k8a A8093 Oph·Or 6   0.44   0.73   0.71 no 1k9m A8093 Oph·Or 6   0.54   0.49   0.80 no 1kc8 A8093 Oph·Or 6   0.42   0.67   0.70 no 1kd1 A8093 Oph·Or 6   0.50   0.69   0.62 yes 1kqs 08014 Oph·Or 6   0.90   0.75   0.92 yes 1kqs 08093 Oph·Or 6   0.47   0.70   0.56 no 1l8v A308 Oph·Or 2   0.11   0.35   0.96 no 1l8v B314 Oph·Or 2   0.10   0.42   0.88 no 1m1k A8093 Oph·Or 6   0.68   0.74   0.69 yes 1m90 A8093 Oph·Or 6   0.46   0.71   0.67 no 1mms D375 Oph·Or 5   0.23   0.66   0.49 no 1n32 A1582 Oph·Or 2   0.18   0.19   0.38 no 1n32 A1558 Oph·Or 2   0.14   0.14   0.55 no 1n33 A469 Oph·Or 3   0.30   0.34   0.29 no 1n33 A1557 Oph·Or 2   0.19   0.08   0.43 no 1n33 A1578 Oph·Or 2   0.28   0.12   0.35 no 1n8r A8093 Oph·Or 6   0.56   0.56   0.48 no 1nji A8093 Oph·Or 6   0.43   0.74   0.75 no 1q82 A8093 Oph·Or 6   0.46   0.58   0.99 no 1q86 A8093 Oph·Or 6   0.53   0.72   0.41 no 1qvf 08093 Oph·Or 6   0.47   0.78   0.92 no 1qvg 08093 Oph·Or 6   0.43   0.82   0.58 no 1s72 08093 Oph·Or 6   0.40   0.80   0.70 no 1vq4 08014 Oph·Or 6   0.57   0.72   0.87 yes 1vq4 08093 Oph·Or 6   0.39   0.83   0.76 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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