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 3v25 3V25 (3Å) -- RIBOSOME : Crystal structure of rmf bound to the 70s ribosome. this pdb entry contains coordinates for the 50s subunit of the 2nd ribosome in the asu List of all 425 Mg2+ binding sites in the PDB structure 3v25 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 22 | « 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 3v25 A3075 Or 1   0.03  0   0.93 no 3v25 A3130 Or 1   0.05  0   0.87 no 3v25 A3009 Or 1   0.01  0   0.92 no 3v25 A3207 Ob 1   0.02  0   0.88 no 3v25 A3154 Ob 1   0.03  0   0.99 no 3v25 A3178 Ob 1   0.02  0   1.00 no 3v25 A3131 Ob 1   0.02  0   0.94 no 3v25 A3068 Ob 1   0.02  0   1.00 no 3v25 A3135 Ob 1   0.02  0   0.84 no 3v25 A3175 Ob 1   0.03  0   0.79 no 3v25 A3021 Ob 1   0.01  0   0.84 no 3v25 A3306 Ob 4   0.40   0.57   0.98 no 3v25 A3006 Ob 1   0.03  0   0.95 no 3v25 A3163 Ob 1   0.02  0   0.91 no 3v25 A3096 Ob 2   0.05   0.27   0.92 no 3v25 A3151 Ob 1   0.04  0   0.69 no 3v25 A3039 Ob 1   0.02  0   0.93 no 3v25 A3032 Ob 1   0.02  0   0.69 no 3v25 D301 Ob 5   0.55   0.61   0.94 yes 3v25 A3389 Nb 2   0.14   0.12   0.78 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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