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	A1712	Mg²⁺ not bound by RNA	0	0	0	0.66	no
4gkj	A1654	Mg²⁺ not bound by RNA	0	0	0	0.85	no
4gkj	A1708	Mg²⁺ not bound by RNA	0	0	0	0.98	no
4gkj	A1704	Mg²⁺ not bound by RNA	0	0	0	0.99	no
4gkj	A1701	Mg²⁺ not bound by RNA	0	0	0	0.93	no
4gkj	A1665	Mg²⁺ not bound by RNA	0	0	0	0.83	no
4gkj	A1672	Mg²⁺ not bound by RNA	0	0	0	0.85	no
4gkj	A1700	Mg²⁺ not bound by RNA	0	0	0	0.86	no
4gkj	A1632	O_b	1	0.01	0	0.79	no
4gkj	A1780	poly-nuclear Mg²⁺ site	1	0.01	0	0.73	no
4gkj	A1753	O_r	1	0.01	0	0.88	no
4gkj	A1781	O_ph	1	0.01	0	0.98	no
4gkj	A1771	O_b	1	0.01	0	0.80	no
4gkj	A1625	O_ph	1	0.01	0	0.91	no
4gkj	A1602	O_b	1	0.01	0	0.63	no
4gkj	A1694	O_b	1	0.01	0	0.54	no
4gkj	A1765	O_ph	1	0.01	0	0.80	no
4gkj	A1749	O_b	1	0.01	0	0.98	no
4gkj	A1777	O_ph	1	0.02	0	0.51	no
4gkj	A1615	N_b	1	0.02	0	0.98	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