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 4tp7 4TP7 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 50s subunit of the second 70s ribosome with virginiamycin m1 bound. List of all 168 Mg2+ binding sites in the PDB structure 4tp7 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 9 | « 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 4tp7 A3100 2Bout 6   0.74   1.00   0.66 yes 4tp7 A3063 3Pout·2Bout 6   0.74   0.99   0.66 yes 4tp7 A3014 3Pout·Bout 6   0.74   0.99   0.67 yes 4tp7 A3026 4Pout 5   0.68   0.68   0.67 yes 4tp7 A3113 cis-2Oph 5   0.46   0.87   0.68 no 4tp7 A3155 Ob 1   0.03  0   0.68 no 4tp7 Q201 Mg2+ not bound by RNA 0  0  0   0.68 no 4tp7 A3028 2Pout·2Rout·Bout 5   0.81   0.81   0.69 yes 4tp7 A3123 cis-2Oph 6   0.78   0.78   0.69 yes 4tp7 A3066 Oph·3Pout 6   0.84   0.82   0.69 yes 4tp7 A3072 2Pout·4Bout 6   0.74   0.99   0.70 yes 4tp7 A3136 Pout·3Bout 6   0.74   0.99   0.70 yes 4tp7 A3052 4Pout·Bout 6   0.75   0.99   0.70 yes 4tp7 A3127 Oph·2Pout 4   0.40   0.67   0.70 no 4tp7 A3138 Oph 1   0.04  0   0.70 no 4tp7 A3104 Pout·3Bout 6   0.74   0.99   0.70 yes 4tp7 A3165 Mg2+ not bound by RNA 0  0  0   0.71 no 4tp7 A3121 5Pout 4   0.67   0.64   0.72 yes 4tp7 A3149 Mg2+ not bound by RNA 0  0  0   0.72 no 4tp7 A3125 2Pout·2Bout 4   0.66   0.99   0.72 yes

^# 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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