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 4kvb

4KVB (4.2Å) -- RIBOSOME : Thermus thermophilus hb27 30s ribosomal subunit lacking ribosomal protein s17
List of all 144 Mg²⁺ binding sites in the PDB structure 4kvb 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
4kvb	A1609	O_b·2N_b	3	0.10	0.25	0.31	no
4kvb	A1722	O_ph·O_r	2	0.17	0.10	0.31	no
4kvb	A1645	O_b·2N_b	3	0.36	0.32	0.32	no
4kvb	A1633	Mg²⁺ not bound by RNA	0	0	0	0.33	no
4kvb	A1635	Mg²⁺ not bound by RNA	0	0	0	0.33	no
4kvb	A1655	Mg²⁺ not bound by RNA	0	0	0	0.33	no
4kvb	A1636	O_ph	1	0.06	0	0.35	no
4kvb	A1695	Mg²⁺ not bound by RNA	0	0	0	0.37	no
4kvb	A1661	Mg²⁺ not bound by RNA	0	0	0	0.38	no
4kvb	A1637	Mg²⁺ not bound by RNA	0	0	0	0.38	no
4kvb	A1611	Mg²⁺ not bound by RNA	0	0	0	0.39	no
4kvb	A1701	O_ph	2	0.17	0.16	0.39	no
4kvb	A1659	Mg²⁺ not bound by RNA	0	0	0	0.39	no
4kvb	U101	Mg²⁺ not bound by RNA	3	0.27	0.30	0.40	no
4kvb	A1649	poly-nuclear Mg²⁺ site	1	0.01	0	0.41	no
4kvb	A1651	O_ph	1	0.14	0	0.42	no
4kvb	A1670	Mg²⁺ bound by non-RNA	2	0.24	0.14	0.42	no
4kvb	A1729	O_ph	1	0.15	0	0.42	no
4kvb	A1630	Mg²⁺ not bound by RNA	0	0	0	0.43	no
4kvb	A1707	trans-2O_ph	2	0.27	0.67	0.44	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 4kvb

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

List of Mg²⁺ binding sites in structure 4kvb