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

	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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List of Mg²⁺ binding sites in structure 2wh1

2WH1 (3.45Å) -- RIBOSOME : Insights into translational termination from the structure of rf2 bound to the ribosome
List of all 173 Mg²⁺ binding sites in the PDB structure 2wh1 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 ^#", "Site type" or "Mg²⁺ ID"
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Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
2wh1	Z1	Mg²⁺ not bound by RNA	0	0	0	0.67	no
2wh1	Z3	Mg²⁺ not bound by RNA	0	0	0	0.61	no
2wh1	Z6	Mg²⁺ not bound by RNA	1	0.05	0	0.48	no
2wh1	Z7	Mg²⁺ not bound by RNA	1	0.01	0	0.32	no
2wh1	Z8	fac-3O_ph	3	0.20	0.51	0.63	no
2wh1	Z12	mer-3O_ph	3	0.23	0.52	0.69	no
2wh1	Z13	trans-2O_ph	2	0.05	0.57	0.48	no
2wh1	Z15	O_ph	1	0.05	0	0.64	no
2wh1	Z16	cis-2O_ph·O_r	3	0.15	0.53	0.71	no
2wh1	Z18	cis-2O_ph·O_r	3	0.10	0.20	0.52	no
2wh1	Z20	O_ph	1	0.05	0	0.57	no
2wh1	Z22	Mg²⁺ not bound by RNA	0	0	0	0.34	no
2wh1	Z24	N_b	1	0.05	0	0.52	no
2wh1	Z25	O_b	1	0.01	0	0.48	no
2wh1	Z26	poly-nuclear Mg²⁺ site	1	0.02	0	0.53	no
2wh1	Z29	other RNA-inner types	3	0.10	0.37	0.53	no
2wh1	Z30	O_ph	1	0.02	0	0.41	no
2wh1	Z31	O_ph	1	0.09	0	0.95	no
2wh1	Z32	O_ph	1	0.06	0	0.69	no
2wh1	Z34	cis-2O_ph	2	0.03	0.12	0.62	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

List of Mg2+ binding sites in structure 2wh1

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

List of Mg²⁺ binding sites in structure 2wh1