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 3v2e

3V2E (2.7Å) -- RIBOSOME/INHIBITOR : Crystal structure of yfia bound to the 70s ribosome. this pdb entry contains coordinates for the 30s subunit with bound yfia of the 2nd ribosome in the asu
List of all 206 Mg²⁺ binding sites in the PDB structure 3v2e 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
3v2e	A1641	Mg²⁺ not bound by RNA	0	0	0	0.97	no
3v2e	A1602	Mg²⁺ not bound by RNA	0	0	0	0.94	no
3v2e	A1632	Mg²⁺ not bound by RNA	0	0	0	0.99	no
3v2e	A1626	Mg²⁺ not bound by RNA	0	0	0	0.79	no
3v2e	A1610	Mg²⁺ not bound by RNA	0	0	0	0.77	no
3v2e	A1630	Mg²⁺ not bound by RNA	0	0	0	0.87	no
3v2e	A1644	Mg²⁺ not bound by RNA	0	0	0	0.77	no
3v2e	A1642	Mg²⁺ not bound by RNA	0	0	0	0.94	no
3v2e	A1650	Mg²⁺ not bound by RNA	0	0	0	0.85	no
3v2e	A1617	Mg²⁺ not bound by RNA	0	0	0	0.76	no
3v2e	A1601	Mg²⁺ not bound by RNA	0	0	0	0.86	no
3v2e	A1612	Mg²⁺ not bound by RNA	0	0	0	0.88	no
3v2e	A1629	Mg²⁺ not bound by RNA	0	0	0	0.81	no
3v2e	A1609	Mg²⁺ not bound by RNA	0	0	0	0.94	no
3v2e	A1625	O_b	1	0.01	0	0.99	no
3v2e	A1611	Mg²⁺ not bound by RNA	1	0.01	0	0.84	no
3v2e	A1616	O_ph	1	0.01	0	0.90	no
3v2e	A1628	O_b	1	0.01	0	0.74	no
3v2e	A1647	O_ph	1	0.01	0	0.69	no
3v2e	A1605	O_ph	1	0.01	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 3v2e

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

List of Mg²⁺ binding sites in structure 3v2e