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 4byb A2584 Oph·Or 2   0.33   0.02   0.89 no 3kix a1652 Oph·Or 2   0.50   0.02   0.51 no 2j02 Z152 Oph·Or 2   0.27   0.03   0.39 no 3kis a1650 Oph·Or 2   0.51   0.03   0.56 no 2wdh Z200 Oph·Or 2   0.49   0.03   0.62 no 1vvs A3218 Oph·Or 2   0.16   0.03   0.09 no 1vvv A1611 Oph·Or 2   0.30   0.03   0.09 no 1vvq A3198 Oph·Or 2   0.47   0.03   0.58 no 1vy2 A1612 Oph·Or 2   0.23   0.03   0.23 no 1vvp A1616 Oph·Or 2   0.22   0.03   0.15 no 1ibk A1557 Oph·Or 2   0.20   0.03   0.34 no 2j02 Z440 Oph·Or 2   0.38   0.03   0.26 no 2v48 G2502 Oph·Or 2   0.38   0.04   0.24 no 2xfz Z1707 Oph·Or 2   0.52   0.04   0.46 no 4byd A2577 Oph·Or 2   0.36   0.04   0.82 no 4ji6 A1743 Oph·Or 2   0.16   0.04   0.40 no 3huw A1551 Oph·Or 2   0.11   0.04   0.33 no 2wdg Z502 Oph·Or 2   0.20   0.04   0.86 no 4g5m A1818 Oph·Or 2   0.35   0.04   0.57 no 1hnz A1559 Oph·Or 2   0.16   0.04   0.54 no 2wdh Z514 Oph·Or 2   0.16   0.05   0.64 no 4tp4 A1645 Oph·Or 2   0.60   0.05   0.63 no 3kni A3112 Oph·Or 2   0.21   0.05   0.75 no 2f4v A1566 Oph·Or 2   0.25   0.05   0.16 no 2wdm Z735 Oph·Or 2   0.31   0.05   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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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