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 4qcy 4QCY (2.8Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the pre- attack state of peptide bond formation containing short substrate- mimic cytidine-cytidine-puromycin in the a site and acylated trna in the p site. this entry contains the 30s subunit List of all 228 Mg2+ binding sites in the PDB structure 4qcy 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 4 of 12 | « 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 4qcy A3059 Nb 1   0.03  0   0.77 no 4qcy A3008 cis-2Oph 2   0.04   0.17   0.86 no 4qcy A3080 Oph 1   0.04  0   0.73 no 4qcy A3055 Oph 1   0.04  0   0.79 no 4qcy A3061 Oph 1   0.04  0   0.66 no 4qcy N502 Mg2+ bound by non-RNA 2   0.04   0.83   0.85 no 4qcy A3116 Oph 1   0.04  0   0.88 no 4qcy A3062 Oph 1   0.05  0   0.73 no 4qcy A3068 Oph 1   0.05  0   0.87 no 4qcy A3025 Ob 1   0.05  0   0.62 no 4qcy A3074 2Ob 2   0.05   0.21   0.79 no 4qcy A3001 Mg2+ bound by non-RNA 2   0.05   0.17   0.95 no 4qcy A3046 poly-nuclear Mg2+ site 1   0.05  0   0.88 no 4qcy A3009 poly-nuclear Mg2+ site 2   0.05   0.38   0.73 no 4qcy A3105 cis-2Oph 2   0.05   0.30   0.99 no 4qcy A3084 Or·Ob 2   0.05   0.12   0.68 no 4qcy A3047 Oph·Or 2   0.05   0.29   0.92 no 4qcy A3019 trans-2Oph 2   0.06   0.47   0.74 no 4qcy A3064 2Ob 2   0.06   0.14   0.76 no 4qcy A3037 2Ob 2   0.07   0.18   0.65 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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