MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df4:B3602, See in JSmolClick on the image to toggle views Site type: Pout·Rout·2Bout Schematic drawing for Pout·Rout·2Bout List of all 93 Mg2+ binding sites with the site type Pout·Rout·2Bout 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 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vq9 08076 Pout·Rout·2Bout 4   0.11   0.41   0.94 no 3ccv 08060 Pout·Rout·2Bout 4   0.25   0.61   0.78 no 4qcp A3276 Pout·Rout·2Bout 4   0.50   0.65   0.77 no 3v2f A3292 Pout·Rout·2Bout 4   0.49   0.62   0.66 no 4tpb A3064 Pout·Rout·2Bout 4   0.67   0.64   0.92 yes 3v2f A3329 Pout·Rout·2Bout 4   0.49   0.92   0.81 no 1vql 08068 Pout·Rout·2Bout 4   0.47   0.59   0.69 no 4dh9 A1957 Pout·Rout·2Bout 4   0.49   0.97   0.92 no 3i56 08085 Pout·Rout·2Bout 5   0.16   0.67   0.71 no 3ofb A1575 Pout·Rout·2Bout 5   0.82   0.80   0.80 yes 1vqp 08076 Pout·Rout·2Bout 5   0.29   0.61   0.69 no 3i56 28060 Pout·Rout·2Bout 5   0.14   0.67   0.95 no 3cc7 08060 Pout·Rout·2Bout 5   0.25   0.77   0.99 no 3ora A1575 Pout·Rout·2Bout 5   0.82   0.79   0.86 yes 4dv1 A1822 Pout·Rout·2Bout 5   0.80   0.80   0.61 yes 2qal A2109 Pout·Rout·2Bout 5   0.81   0.80   0.99 yes 1yjw 78107 Pout·Rout·2Bout 5   0.58   0.59   0.53 no 4kjb A3080 Pout·Rout·2Bout 5   0.31   0.30   1.00 no 1q82 A8076 Pout·Rout·2Bout 5   0.63   0.67   0.66 yes 4kj7 A3081 Pout·Rout·2Bout 5   0.58   0.49   0.44 no 3v2d A3664 Pout·Rout·2Bout 5   0.62   0.76   0.83 yes 2xzn 015 Pout·Rout·2Bout 6   0.12   1.00   1.00 no 4qct A3619 Pout·Rout·2Bout 6   0.75   0.99   0.82 yes 2xzn 017 Pout·Rout·2Bout 6   0.12   0.99   1.00 no 2xzm 047 Pout·Rout·2Bout 6   0.12   1.00   1.00 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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>