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 4a1a

4A1A (3.52Å) -- RIBOSOME : T.thermophila 60s ribosomal subunit in complex with initiation factor 6. this file contains 5s rrna, 5.8s rrna and proteins of molecule 3.
List of all 209 Mg²⁺ binding sites in the PDB structure 4a1a 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
4a1a	0100	O_ph	7	0.86	0.88	0.98	no
4a1a	0277	Mg²⁺ not bound by RNA	7	0.84	0.89	0.98	no
4a1a	0174	Mg²⁺ not bound by RNA	7	0.83	0.90	0.98	no
4a1a	0317	Mg²⁺ not bound by RNA	6	0.75	0.92	0.97	no
4a1a	050	Mg²⁺ not bound by RNA	6	0.74	0.93	1.00	no
4a1a	0143	Mg²⁺ not bound by RNA	6	0.77	0.96	1.00	no
4a1a	0135	Mg²⁺ not bound by RNA	6	0.77	0.96	1.00	no
4a1a	0261	Mg²⁺ not bound by RNA	6	0.74	0.97	1.00	no
4a1a	0267	Mg²⁺ not bound by RNA	6	0.75	0.97	1.00	no
4a1a	0140	Mg²⁺ not bound by RNA	6	0.76	0.97	1.00	no
4a1a	0162	Mg²⁺ not bound by RNA	6	0.76	0.97	1.00	no
4a1a	055	P_out	6	0.76	0.97	1.00	yes
4a1a	063	2P_out·4B_out	6	0.75	0.98	1.00	yes
4a1a	0226	Mg²⁺ not bound by RNA	6	0.75	0.98	1.00	no
4a1a	0269	Mg²⁺ not bound by RNA	6	0.78	0.98	1.00	no
4a1a	0265	Mg²⁺ not bound by RNA	6	0.76	0.98	1.00	no
4a1a	0320	Mg²⁺ not bound by RNA	6	0.76	0.98	1.00	no
4a1a	0108	Mg²⁺ not bound by RNA	6	0.74	0.98	1.00	no
4a1a	0233	Mg²⁺ not bound by RNA	6	0.76	0.98	1.00	no
4a1a	0321	Mg²⁺ not bound by RNA	6	0.75	0.98	1.00	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 4a1a

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

List of Mg²⁺ binding sites in structure 4a1a