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 4tpb 4TPB (2.8Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to dalfopristin and quinupristin. this file contains the 50s subunit of the second 70s ribosome with dalfopristin and quinupristin bound. List of all 171 Mg2+ binding sites in the PDB structure 4tpb 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 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 4tpb A3108 fac-3Oph 6   0.58   0.60   1.00 no 4tpb A3020 2Nb 6   0.75   0.75   0.99 yes 4tpb A3125 cis-2Oph·Nb 6   0.64   0.71   0.99 yes 4tpb A3042 2Pout 5   0.81   0.80   0.99 yes 4tpb A3081 Oph·Pout 6   0.84   0.83   0.99 yes 4tpb A3079 Oph·Nb 6   0.75   0.97   0.98 yes 4tpb A3132 Ob 6   0.85   0.86   0.98 yes 4tpb A3098 Oph·2Pout 6   0.86   0.86   0.98 yes 4tpb A3076 Oph·2Pout 5   0.71   0.66   0.98 yes 4tpb A3147 Mg2+ not bound by RNA 0  0  0   0.98 no 4tpb A3155 Mg2+ not bound by RNA 0  0  0   0.98 no 4tpb A3101 Ob 6   0.89   0.87   0.96 yes 4tpb A3008 Pout·Bout 5   0.81   0.80   0.96 yes 4tpb A3022 Ob 6   0.86   0.85   0.96 yes 4tpb A3117 Oph·2Pout 6   0.85   0.85   0.96 yes 4tpb B202 Ob 6   0.85   0.84   0.96 yes 4tpb A3063 3Pout·Rout·2Bout 4   0.67   0.64   0.96 yes 4tpb A3039 3Pout 4   0.67   0.65   0.95 yes 4tpb A3121 Oph·3Pout 6   0.86   0.86   0.95 yes 4tpb A3134 Oph·Pout 6   0.92   0.93   0.95 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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