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 3ccj 3CCJ (2.7Å) -- RIBOSOME : Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation c2534u List of all 93 Mg2+ binding sites in the PDB structure 3ccj 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 2 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3ccj Y8077 2Bout 3   0.13   0.98   0.82 no 3ccj 08036 2Pout·Bout 3   0.08   0.51   0.75 no 3ccj 08042 Mg2+ bound by non-RNA 3   0.09   0.61   0.91 no 3ccj 08047 4Pout 3   0.11   0.34   0.49 no 3ccj 08085 Mg2+ not bound by RNA 3   0.24   0.27   0.51 no 3ccj T8057 Mg2+ not bound by RNA 3   0.09   0.47   0.69 no 3ccj 08048 cis-2Oph 3   0.30   0.69   0.53 no 3ccj 08052 Mg2+ bound by non-RNA 4   0.24   0.74   0.76 no 3ccj 08049 Pout·Bout 4   0.17   0.39   0.42 no 3ccj 08060 2Pout·Rout·2Bout 4   0.18   0.65   0.98 no 3ccj 08017 Nb 4   0.31   0.83   0.46 no 3ccj 08043 Oph·3Pout 4   0.31   0.56   0.98 no 3ccj 08071 Oph·2Pout 4   0.13   0.35   0.47 no 3ccj 08044 poly-nuclear Mg2+ site 4   0.16   0.48   0.84 no 3ccj 08061 poly-nuclear Mg2+ site 4   0.21   0.44   0.91 no 3ccj 08035 Oph·2Pout 4   0.16   0.40   0.81 no 3ccj 08089 Nb 4   0.13   0.53   0.77 no 3ccj 08030 3Pout 4   0.06   0.55   0.78 no 3ccj 08034 Mg2+ bound by non-RNA 4   0.33   0.68   0.97 no 3ccj 08068 cis-2Oph 4   0.21   0.64   0.73 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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