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 3cc2 3CC2 (2.4Å) -- RIBOSOME : The refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution with rrna sequence for the 23s rrna and genome-derived sequences for r-proteins List of all 116 Mg2+ binding sites in the PDB structure 3cc2 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 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3cc2 08113 Nb 6   0.32   0.95   0.94 no 3cc2 08099 Or 4   0.33   0.61   0.67 no 3cc2 08024 Nb 5   0.33   0.61   0.52 no 3cc2 08115 poly-nuclear Mg2+ site 6   0.34   0.87   0.71 no 3cc2 08112 Nb 6   0.34   0.86   0.70 no 3cc2 08070 Oph·Ob 5   0.34   0.51   0.49 no 3cc2 08043 poly-nuclear Mg2+ site 5   0.34   0.79   0.97 no 3cc2 Y8108 Mg2+ not bound by RNA 6   0.35   0.72   0.85 no 3cc2 08067 Mg2+ bound by non-RNA 5   0.37   0.88   0.82 no 3cc2 08107 2Pout·Rout·2Bout 5   0.38   0.66   0.72 no 3cc2 08098 Nb 6   0.38   0.87   0.87 no 3cc2 08105 poly-nuclear Mg2+ site 6   0.38   0.79   0.74 no 3cc2 08089 cis-2Oph·Nb 6   0.38   0.87   0.94 no 3cc2 08041 Oph·2Or 6   0.38   0.78   0.87 no 3cc2 08075 2Or 6   0.41   0.83   0.84 no 3cc2 08097 2Ob 6   0.42   0.77   0.84 no 3cc2 08093 Oph·Or 6   0.42   0.80   0.70 no 3cc2 08045 Oph·2Pout 5   0.42   0.78   0.84 no 3cc2 08111 Nb 6   0.43   0.93   0.84 no 3cc2 08053 Ob 6   0.43   0.88   0.72 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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