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 4lf4 A1611 2Ob 2   0.03   0.19   0.73 no 3uyf A1691 2Ob 2   0.03   0.18   0.67 no 3uz3 A2200 2Ob 2   0.03   0.16   0.76 no 3ohk A3088 2Ob 2   0.03   0.19   0.91 no 4dh9 A1827 2Ob 2   0.03   0.19   0.79 no 4dv3 A1726 2Ob 2   0.03   0.32   0.75 no 4kfh A2523 2Ob 2   0.03   0.12   0.69 no 4duy A1729 2Ob 2   0.03   0.37   0.62 no 4ji2 A1757 2Ob 2   0.03   0.32   0.71 no 3uz6 A2074 2Ob 2   0.03   0.45   0.75 no 3d5b A3406 2Ob 2   0.03   0.18   0.19 no 4aqy A2584 2Ob 2   0.03   0.15   0.88 no 4g5v A1974 2Ob 2   0.03   0.38   0.87 no 3pyo A3557 2Ob 2   0.03   0.23   0.61 no 3u5d 14372 2Ob 2   0.03   0.15   0.95 no 3u5d 14170 2Ob 2   0.03   0.22   0.74 no 3hux A3111 2Ob 2   0.03   0.21   0.45 no 3uz6 A2333 2Ob 2   0.03   0.18   0.64 no 2x9t Z487 2Ob 2   0.03   0.16   0.76 no 1vxj A3144 2Ob 2   0.03   0.20   0.79 no 3kiw A3067 2Ob 2   0.03   0.15   0.95 no 3oi1 A3119 2Ob 2   0.03   0.42   0.92 no 4kx2 A3152 2Ob 2   0.03   0.16   0.89 no 4dv7 A1761 2Ob 2   0.03   0.12   0.73 no 4nxn A1650 2Ob 2   0.03   0.14   0.61 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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