MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2121, See in JSmolClick on the image to toggle views Site type: 2Pout·Rout·2Bout Schematic drawing for 2Pout·Rout·2Bout List of all 93 Mg2+ binding sites with the site type 2Pout·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 3 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 1kc8 A8108 2Pout·Rout·2Bout 5   0.53   0.55   0.75 no 1q7y A8108 2Pout·Rout·2Bout 5   0.57   0.53   0.94 no 1yjn 08107 2Pout·Rout·2Bout 5   0.57   0.68   0.60 yes 1kqs 08108 2Pout·Rout·2Bout 5   0.59   0.57   0.66 no 4kiz A3129 2Pout·Rout·2Bout 4   0.60   0.35   0.90 no 4dv5 A1844 2Pout·Rout·2Bout 4   0.61   0.65   0.36 no 4qcx A3377 2Pout·Rout·2Bout 5   0.63   0.80   0.81 yes 4nw1 A3335 2Pout·Rout·2Bout 5   0.63   0.81   0.70 yes 4qcn A3690 2Pout·Rout·2Bout 5   0.63   0.80   0.87 yes 1kd1 A8108 2Pout·Rout·2Bout 5   0.67   0.47   0.55 no 4kj7 A3032 2Pout·Rout·2Bout 4   0.67   0.22   0.94 no 4gaq A1615 2Pout·Rout·2Bout 4   0.67   0.65   0.99 yes 1q82 A8108 2Pout·Rout·2Bout 5   0.67   0.49   1.00 no 3oas A2967 2Pout·Rout·2Bout 6   0.74   1.00   0.60 yes 3i20 A2960 2Pout·Rout·2Bout 6   0.74   0.99   1.00 yes 4bpe A5019 2Pout·Rout·2Bout 6   0.74   0.99   1.00 yes 4tpf A3083 2Pout·Rout·2Bout 6   0.75   0.99   0.94 yes 4bpo A5019 2Pout·Rout·2Bout 6   0.75   0.99   1.00 yes 4tpb A3082 2Pout·Rout·2Bout 6   0.75   0.99   0.91 yes 4bpp A5019 2Pout·Rout·2Bout 6   0.75   0.99   1.00 yes 3ofc A2919 2Pout·Rout·2Bout 6   0.75   0.98   0.43 no 3i20 A2920 2Pout·Rout·2Bout 6   0.75   0.99   1.00 yes 4too A3130 2Pout·Rout·2Bout 6   0.76   0.99   0.85 yes 4dha A3647 2Pout·Rout·2Bout 6   0.76   0.97   0.75 yes 4dv7 A1864 2Pout·Rout·2Bout 5   0.80   0.81   0.52 yes

^# 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>