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 3oi5

3OI5 (3.1Å) -- RIBOSOME/ANTIBIOTIC : Structure of the thermus thermophilus 70s ribosome complexed with telithromycin. this file contains the 50s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes.
List of all 328 Mg²⁺ binding sites in the PDB structure 3oi5 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
3oi5	A46	O_ph	1	0.19	0	0.77	no
3oi5	A91	O_ph	1	0.05	0	0.70	no
3oi5	A101	O_ph	1	0.12	0	0.93	no
3oi5	5105	Mg²⁺ not bound by RNA	1	0.10	0	0.89	no
3oi5	A138	O_b	1	0.01	0	0.82	no
3oi5	R141	Mg²⁺ bound by non-RNA	3	0.18	0.17	0.84	no
3oi5	A155	Mg²⁺ not bound by RNA	0	0	0	0.51	no
3oi5	A159	cis-2O_ph	2	0.08	0.34	0.90	no
3oi5	A160	cis-2O_ph	2	0.14	0.08	0.82	no
3oi5	A161	2O_b	2	0.04	0.20	0.94	no
3oi5	A162	Mg²⁺ not bound by RNA	0	0	0	0.84	no
3oi5	A163	O_ph	1	0.02	0	0.87	no
3oi5	A164	Mg²⁺ not bound by RNA	0	0	0	0.87	no
3oi5	A165	O_b	1	0.22	0	0.50	no
3oi5	A166	Mg²⁺ not bound by RNA	0	0	0	0.58	no
3oi5	A167	other RNA-inner types	4	0.11	0.40	0.99	no
3oi5	A168	O_ph·O_b	2	0.06	0.24	0.86	no
3oi5	A169	Mg²⁺ not bound by RNA	0	0	0	0.79	no
3oi5	A170	O_b	1	0.11	0	0.77	no
3oi5	B174	Mg²⁺ not bound by RNA	0	0	0	0.95	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 3oi5

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

List of Mg²⁺ binding sites in structure 3oi5