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 4duy

4DUY (3.39Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u13c
List of all 302 Mg²⁺ binding sites in the PDB structure 4duy 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
4duy	A1655	Mg²⁺ not bound by RNA	1	0.16	0	0.97	no
4duy	A1739	Mg²⁺ not bound by RNA	0	0	0	0.99	no
4duy	A1661	poly-nuclear Mg²⁺ site	1	0.16	0	0.78	no
4duy	A1712	O_b	1	0.01	0	0.92	no
4duy	A1736	Mg²⁺ not bound by RNA	0	0	0	0.86	no
4duy	A1670	Mg²⁺ not bound by RNA	0	0	0	0.93	no
4duy	A1671	Mg²⁺ not bound by RNA	0	0	0	0.67	no
4duy	A1860	O_ph	1	0.03	0	0.66	no
4duy	A1875	Mg²⁺ not bound by RNA	0	0	0	0.83	no
4duy	A1706	poly-nuclear Mg²⁺ site	2	0.19	0.07	0.55	no
4duy	A1640	O_ph	2	0.17	0.09	0.51	no
4duy	N102	Mg²⁺ bound by non-RNA	2	0.03	0.11	0.78	no
4duy	A1710	2O_r	2	0.03	0.11	0.83	no
4duy	A1703	O_ph·O_b	3	0.20	0.11	0.96	no
4duy	A1676	O_ph·O_r	2	0.03	0.12	0.90	no
4duy	A1718	Mg²⁺ bound by non-RNA	2	0.04	0.13	0.86	no
4duy	A1667	B_out	2	0.03	0.13	0.78	no
4duy	F201	Mg²⁺ not bound by RNA	2	0.03	0.14	0.89	no
4duy	A1680	cis-2O_ph	3	0.20	0.14	0.67	no
4duy	A1747	2O_b	2	0.03	0.15	0.75	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 4duy

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

List of Mg²⁺ binding sites in structure 4duy