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 7 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 A3077 2Pout 4   0.67   0.65   0.70 yes 4tpb A3102 3Pout 4   0.67   0.65   0.76 yes 4tpb A3080 3Pout·4Bout 4   0.67   0.65   0.95 yes 4tpb A3115 2Pout·2Bout 4   0.67   0.65   0.81 yes 4tpb A3039 3Pout 4   0.67   0.65   0.95 yes 4tpb A3025 5Pout 4   0.67   0.65   0.72 yes 4tpb A3094 Pout·3Bout 4   0.67   0.64   0.95 yes 4tpb A3110 fac-3Oph 5   0.52   0.64   0.61 yes 4tpb A3063 3Pout·Rout·2Bout 4   0.67   0.64   0.96 yes 4tpb A3064 Pout·Rout·2Bout 4   0.67   0.64   0.92 yes 4tpb A3024 fac-3Oph 6   0.61   0.63   0.90 yes 4tpb A3108 fac-3Oph 6   0.58   0.60   1.00 no 4tpb A3114 Oph·Or 5   0.57   0.59   0.79 no 4tpb A3041 trans,cis-4Oph 4   0.10   0.58   0.72 no 4tpb A3047 cis-2Oph 5   0.57   0.56   0.90 no 4tpb A3128 Oph·2Pout 4   0.52   0.48   0.80 no 4tpb A3105 Oph·3Pout 4   0.52   0.47   0.61 no 4tpb A3158 other RNA-inner types 3   0.08   0.46   0.73 no 4tpb A3123 Oph·Or 5   0.54   0.45   0.82 no 4tpb A3116 5Pout·Bout 3   0.36   0.43   0.63 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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