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 1 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 4kj1 A3103 Oph·Or 4   0.66   0.46  0 no 3d5b A100 Oph·Or 2   0.03   0.61  0 no 3d5d A2936 Oph·Or 2   0.10   0.40  0 no 3v6u A1703 Oph·Or 2   0.31   0.18   0.01 no 1vw0 A3162 Oph·Or 2   0.19   0.07   0.01 no 2v46 Z287 Oph·Or 3   0.22   0.41   0.02 no 2j00 Z227 Oph·Or 2   0.08   0.45   0.02 no 2v46 Z500 Oph·Or 2   0.65   0.51   0.02 no 2x9t Z506 Oph·Or 2   0.02   0.30   0.03 no 2j00 Z502 Oph·Or 2   0.14   0.13   0.03 no 3v6v A1702 Oph·Or 2   0.20   0.07   0.03 no 3f1g A5042 Oph·Or 2   0.06   0.54   0.04 no 3t1h A1629 Oph·Or 2   0.03   0.41   0.04 no 1vvu A3092 Oph·Or 2   0.10   0.23   0.04 no 1vvq A3216 Oph·Or 2   0.06   0.31   0.04 no 4tp5 A3105 Oph·Or 5   0.61   0.49   0.04 no 2v48 G2209 Oph·Or 2   0.08   0.15   0.05 no 3f1h A5207 Oph·Or 2   0.08   0.34   0.05 no 1vvr A1611 Oph·Or 2   0.16   0.19   0.05 no 1vxt A3088 Oph·Or 2   0.06   0.14   0.06 no 3t1h A1711 Oph·Or 2   0.06   0.07   0.06 no 3f1h A5219 Oph·Or 2   0.04   0.79   0.07 no 3t1y A1640 Oph·Or 2   0.28   0.62   0.07 no 3g78 A459 Oph·Or 3   0.55   0.45   0.08 no 1vvs A3211 Oph·Or 2   0.11   0.20   0.09 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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