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 4gkj

4GKJ (3.3Å) -- RIBOSOME/ANTIBIOTIC : Structure of the thermus thermophilus 30s ribosomal subunit complexed with a human mitochondrial anticodon stem loop (asl) of transfer rna methionine (trnamet) bound to an mrna with an aug-codon in the a-site and paromomycin.
List of all 166 Mg²⁺ binding sites in the PDB structure 4gkj 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
4gkj	N101	Mg²⁺ not bound by RNA	0	0	0	0.79	no
4gkj	B301	Mg²⁺ not bound by RNA	0	0	0	0.93	no
4gkj	A1601	Mg²⁺ not bound by RNA	0	0	0	0.80	no
4gkj	A1602	O_b	1	0.01	0	0.63	no
4gkj	A1603	O_b	1	0.05	0	0.86	no
4gkj	A1604	Mg²⁺ not bound by RNA	0	0	0	0.90	no
4gkj	A1605	Mg²⁺ not bound by RNA	0	0	0	0.86	no
4gkj	A1606	Mg²⁺ not bound by RNA	0	0	0	0.76	no
4gkj	A1607	Mg²⁺ not bound by RNA	0	0	0	0.93	no
4gkj	A1608	Mg²⁺ not bound by RNA	0	0	0	0.70	no
4gkj	A1609	Mg²⁺ not bound by RNA	0	0	0	0.59	no
4gkj	A1610	O_b	1	0.04	0	0.95	no
4gkj	A1612	Mg²⁺ not bound by RNA	0	0	0	0.92	no
4gkj	A1613	Mg²⁺ not bound by RNA	0	0	0	0	no
4gkj	A1614	Mg²⁺ not bound by RNA	0	0	0	0.67	no
4gkj	A1615	N_b	1	0.02	0	0.98	no
4gkj	A1616	Mg²⁺ not bound by RNA	0	0	0	0.86	no
4gkj	A1617	Mg²⁺ not bound by RNA	0	0	0	0.72	no
4gkj	A1618	O_ph	1	0.04	0	0.99	no
4gkj	A1619	Mg²⁺ not bound by RNA	0	0	0	0.82	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 4gkj

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

List of Mg²⁺ binding sites in structure 4gkj