MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2288, See in JSmolClick on the image to toggle views Site type: 4Bout Schematic drawing for 4Bout List of all 252 Mg2+ binding sites with the site type 4Bout 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 11 | « 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 4nw1 A3460 4Bout 1   0.13  0   1.00 no 4dv0 A1604 4Bout 1   0.02  0   0.91 no 4qcp A3306 4Bout 2   0.14   0.16   0.94 no 4nvx A3345 4Bout 2   0.24   0.26   0.89 no 4nvx A3560 4Bout 2   0.25   0.26   0.87 no 4nw1 A3339 4Bout 2   0.25   0.26   0.84 no 4qcp A3502 4Bout 2   0.25   0.29   0.71 no 4ji4 A1648 4Bout 2   0.32   0.29   0.80 no 4qcr A3405 4Bout 2   0.25   0.30   0.67 no 4qcx A3557 4Bout 2   0.25   0.30   0.71 no 4dr5 A1647 4Bout 2   0.31   0.30   0.66 no 4kix A3064 4Bout 4   0.90   0.30   0.28 no 4qcp A3580 4Bout 2   0.25   0.31   0.77 no 4qct A3596 4Bout 2   0.25   0.31   0.75 no 4dha A3716 4Bout 2   0.23   0.33   0.80 no 4kiz B1203 4Bout 4   0.59   0.36   0.89 no 4nw1 A3303 4Bout 3   0.38   0.37   0.96 no 3v2f A3611 4Bout 2   0.26   0.37   0.94 no 4kix A3092 4Bout 3   0.06   0.37   0.55 no 3v2f A3348 4Bout 2   0.25   0.40   0.77 no 1k73 A8100 4Bout 4   0.50   0.40   0.80 no 1qvf 08100 4Bout 4   0.30   0.40   0.64 no 4dha A3693 4Bout 3   0.37   0.41   0.95 no 1kd1 A8100 4Bout 5   0.50   0.41   0.71 no 1yi2 08100 4Bout 4   0.31   0.42   0.74 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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