MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON 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" Page 1 of 11 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4a1a 0100 Oph 7   0.86   0.88   0.98 no 4a1a 0324 2Bout 6   0.75   0.99   1.00 yes 4a1a 0117 3Bout 6   0.75   0.99   1.00 yes 4a1a 0347 3Bout 6   0.75   0.99   1.00 yes 4a1a 066 3Bout 6   0.75   0.99   1.00 yes 4a1a 0199 Pout 6   0.75   0.99   1.00 yes 4a1a 055 Pout 6   0.76   0.97   1.00 yes 4a1a 054 Pout 6   0.74   0.99   1.00 yes 4a1a 08 Pout·Rout 6   0.75   0.99   1.00 yes 4a1a 0334 Pout·Bout 6   0.75   0.99   1.00 yes 4a1a 079 Pout·3Bout 6   0.76   0.99   1.00 yes 4a1a 0345 Pout·3Bout 6   0.75   0.99   1.00 yes 4a1a 0204 Pout·4Bout 6   0.75   0.99   1.00 yes 4a1a 05 2Pout 6   0.75   1.00   1.00 yes 4a1a 063 2Pout·4Bout 6   0.75   0.98   1.00 yes 4a1a 0325 2Pout·4Bout 6   0.75   0.99   1.00 yes 4a1a 09 Mg2+ not bound by RNA 6   0.76   1.00   1.00 no 4a1a 06 Mg2+ not bound by RNA 6   0.75   0.99   1.00 no 4a1a 03 Mg2+ not bound by RNA 6   0.75   0.99   1.00 no 4a1a 0277 Mg2+ not bound by RNA 7   0.84   0.89   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

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout 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].

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