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 3cd6 3CD6 (2.75Å) -- RIBOSOME : Co-cystal of large ribosomal subunit mutant g2616a with cc-puromycin List of all 93 Mg2+ binding sites in the PDB structure 3cd6 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 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 3cd6 08078 Or 4   0.09   0.74   0.71 no 3cd6 08083 Ob 5   0.14   0.79   0.77 no 3cd6 08033 Ob 3   0.06   0.42   0.92 no 3cd6 08090 Ob 5   0.11   0.58   0.88 no 3cd6 08040 Nb 2   0.05   0.31   0.57 no 3cd6 08080 Nb 2   0.03   0.51   0.86 no 3cd6 08036 Nb 4   0.12   0.64   0.79 no 3cd6 08077 Nb 5   0.17   0.82   0.93 no 3cd6 08017 Nb 4   0.18   0.55   0.57 no 3cd6 08059 2Or 6   0.20   0.74   0.75 no 3cd6 08032 2Ob 6   0.16   0.76   0.90 no 3cd6 08076 2Ob 6   0.21   0.73   0.96 no 3cd6 08075 2Ob·Nb 6   0.22   0.76   0.79 no 3cd6 08093 2Or·Nb 5   0.15   0.50   0.95 no 3cd6 08037 Oph 3   0.10   0.29   0.67 no 3cd6 08065 Oph·Pout 6   0.34   0.91   0.91 no 3cd6 08038 Oph·Pout 2   0.07   0.14   0.94 no 3cd6 08073 Oph·Pout 2   0.04   0.12   0.45 no 3cd6 08081 Oph·Pout 2   0.07   0.41   0.73 no 3cd6 08029 Oph·Pout 5   0.16   0.46   0.90 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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