	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
	Back to Classification Home	Download this subset in: CSV, XML, JSON

Representative site 4ji7:A1885, See in JSmol MgRNA representative site for type 2RO-BO

Click on the image to toggle views

Site type: 2R_out·B_out

Schematic drawing for
2R_out·B_out
MgRNA type 2RO-BO

List of all 16 Mg²⁺ binding sites with the site type 2R_out·B_out 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 1

Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
3v27	A3528	2R_out·B_out	5	0.62	0.80	0.98	yes
3v27	A3652	2R_out·B_out	6	0.73	0.98	0.49	no
3v29	A3540	2R_out·B_out	4	0.51	0.94	0.87	yes
3v2d	A3484	2R_out·B_out	3	0.38	0.62	0.78	no
4dha	A3709	2R_out·B_out	2	0.25	0.32	0.77	no
4dr3	A1828	2R_out·B_out	6	0.96	0.99	0.34	no
4ji6	A1852	2R_out·B_out	6	0.98	0.99	0.29	no
4ji7	A1885	2R_out·B_out	6	0.94	0.99	0.91	yes
4ji8	A1886	2R_out·B_out	6	0.97	0.97	0.25	no
4ji8	A1827	2R_out·B_out	6	0.85	0.96	0.31	no
4nvx	A3222	2R_out·B_out	1	0.02	0	0.65	no
4p95	A604	2R_out·B_out	5	0.45	0.80	0.35	no
4qcn	A3618	2R_out·B_out	1	0.12	0	0.95	no
4qcr	A3779	2R_out·B_out	1	0.12	0	0.61	no
4qct	A3617	2R_out·B_out	3	0.37	0.67	0.87	no
4qcx	A3464	2R_out·B_out	1	0.12	0	0.86	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

Abbreviations used for Mg²⁺ "Site type"	Mg²⁺ inner-sphere ligands	Geometry for inner-sphere O_P	Mg²⁺ outer-sphere moieties
Site type used in the classification is a string abbreviation of ligand composition in Mg²⁺ coordination sphere
Abbreviations used for Mg²⁺ "Site type"	O_ph phosphate oxygen (OP1/OP2) O_r ribose oxygen (O2'/O4') or oxygen bridging phosphate and ribose (O3'/O5') O_b nucleobase oxygen N_b nucleobase nitrogen	*cis-* two O_P ligands adopt cis- isoform *trans-* two O_P ligands adopt trans- isoform *fac-* three O_P ligands adopt fac- isoform *mer-* three O_P ligands adopt mer- isoform	P_out phosphate moiety R_out ribose moiety B_out 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].

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

Site type: 2Rout·Bout

MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures

Site type: 2R_out·B_out