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 6 of 12 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4qcy A3164 cis-2Oph·Nb 4   0.18   0.30   0.89 no 4qcy A3022 cis-2Oph·2Ob 4   0.66   0.71   0.69 yes 4qcy A3092 fac-3Oph 3   0.17   0.22   0.70 no 4qcy A3107 fac-3Oph 3   0.37   0.21   0.77 no 4qcy A3015 other RNA-inner types 3   0.09   0.43   0.53 no 4qcy A3052 other RNA-inner types 3   0.17   0.37   0.73 no 4qcy A3026 other RNA-inner types 4   0.26   0.38   0.81 no 4qcy A3016 other RNA-inner types 4   0.11   0.55   0.66 no 4qcy A3133 other RNA-inner types 4   0.28   0.42   0.78 no 4qcy A3065 other RNA-inner types 3   0.10   0.57   0.75 no 4qcy A3103 other RNA-inner types 3   0.09   0.27   0.59 no 4qcy A3096 other RNA-inner types 4   0.12   0.59   0.78 no 4qcy A3011 other RNA-inner types 3   0.23   0.25   0.99 no 4qcy A3078 other RNA-inner types 3   0.10   0.51   0.85 no 4qcy A3158 other RNA-inner types 4   0.29   0.92   0.98 no 4qcy A3169 Rout 3   0.38   0.43   0.80 no 4qcy A3186 Bout 1   0.12  0   0.91 no 4qcy A3203 Bout 1   0.12  0   0.81 no 4qcy A3195 Bout 1   0.12  0   0.93 no 4qcy A3201 Bout 1   0.12  0   0.81 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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