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 4b3r 4B3R (3Å) -- RIBOSOME : Crystal structure of the 30s ribosome in complex with compound 30 List of all 201 Mg2+ binding sites in the PDB structure 4b3r 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 9 of 11 | « Previous | Next » | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4b3r A2631 Mg2+ not bound by RNA 0  0  0   0.93 no 4b3r A2718 Oph·Ob 2   0.14   0.25   0.94 no 4b3r A2652 other RNA-inner types 4   0.12   0.46   0.94 no 4b3r A2704 poly-nuclear Mg2+ site 3   0.06   0.27   0.94 no 4b3r K1120 Mg2+ bound by non-RNA 4   0.11   0.88   0.94 no 4b3r A2688 Nb 1   0.01  0   0.94 no 4b3r A2741 Mg2+ not bound by RNA 0  0  0   0.95 no 4b3r A2714 Ob 1   0.03  0   0.95 no 4b3r A2660 Ob 1   0.04  0   0.95 no 4b3r A2701 Oph 1   0.03  0   0.95 no 4b3r A2621 other RNA-inner types 3   0.07   0.33   0.95 no 4b3r A2663 cis-2Oph 2   0.03   0.29   0.95 no 4b3r A2691 Nb 1   0.07  0   0.95 no 4b3r A2625 trans-2Oph·Or 3   0.12   0.69   0.95 no 4b3r A2624 Oph·2Ob 3   0.07   0.47   0.95 no 4b3r A2720 poly-nuclear Mg2+ site 3   0.13   0.44   0.96 no 4b3r A2559 poly-nuclear Mg2+ site 2   0.04   0.18   0.96 no 4b3r A2556 Mg2+ not bound by RNA 0  0  0   0.97 no 4b3r J1099 Oph 1   0.03  0   0.97 no 4b3r A2750 Mg2+ not bound by RNA 0  0  0   0.97 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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