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 3oi3

3OI3 (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 372 Mg²⁺ binding sites in the PDB structure 3oi3 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
3oi3	A3046	Mg²⁺ bound by non-RNA	4	0.23	0.40	0.64	no
3oi3	A3047	O_ph	1	0.11	0	0.70	no
3oi3	A3048	cis-2O_ph	2	0.22	0.16	0.88	no
3oi3	A3049	Mg²⁺ not bound by RNA	0	0	0	0.74	no
3oi3	A3050	O_ph	1	0.04	0	0.94	no
3oi3	A3051	O_ph	1	0.11	0	0.49	no
3oi3	A3052	Mg²⁺ bound by non-RNA	4	0.30	0.71	0.46	no
3oi3	A3053	O_b	1	0.03	0	0.83	no
3oi3	A3054	O_ph·O_r	2	0.06	0.31	0.90	no
3oi3	A3055	O_b	1	0.03	0	0.81	no
3oi3	A3056	Mg²⁺ not bound by RNA	1	0.06	0	0.46	no
3oi3	A3057	O_b	1	0.03	0	0.77	no
3oi3	A3058	Mg²⁺ not bound by RNA	0	0	0	0.50	no
3oi3	A3059	poly-nuclear Mg²⁺ site	2	0.04	0.24	0.82	no
3oi3	A3060	Mg²⁺ not bound by RNA	0	0	0	0.64	no
3oi3	A3061	O_b	1	0.06	0	0.61	no
3oi3	A3062	Mg²⁺ not bound by RNA	0	0	0	0.54	no
3oi3	A3063	Mg²⁺ not bound by RNA	0	0	0	0.57	no
3oi3	A3064	other RNA-inner types	4	0.07	0.36	0.69	no
3oi3	A3065	O_ph·O_b	2	0.04	0.22	0.77	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 3oi3

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

List of Mg²⁺ binding sites in structure 3oi3