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 4qd1 4QD1 (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 50s subunit List of all 666 Mg2+ binding sites in the PDB structure 4qd1 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 34 | « 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 4qd1 A3198 Or 1   0.02  0   0.82 no 4qd1 A3129 Or 1   0.04  0   0.78 no 4qd1 A3142 Or 1   0.01  0   0.80 no 4qd1 A3002 Or 1   0.05  0   0.80 no 4qd1 A3162 Or 1   0.01  0   0.84 no 4qd1 A3605 Or 2   0.14   0.08   0.89 no 4qd1 A3013 Or 1   0.02  0   0.77 no 4qd1 A3603 Or 3   0.26   0.38   0.92 no 4qd1 A3277 Ob 1   0.03  0   0.88 no 4qd1 A3466 Ob 2   0.14   0.13   0.91 no 4qd1 A3220 Ob 1   0.05  0   0.93 no 4qd1 A3519 Ob 4   0.41   0.68   0.94 no 4qd1 A3530 Ob 3   0.27   0.31   0.85 no 4qd1 A3573 Ob 2   0.14   0.08   0.96 no 4qd1 A3398 Ob 3   0.26   0.36   0.68 no 4qd1 A3001 Ob 1   0.17  0   0.91 no 4qd1 A3381 Ob 3   0.26   0.30   0.64 no 4qd1 B3007 Ob 4   0.39   0.46   0.98 no 4qd1 B3005 Ob 1   0.01  0   0.79 no 4qd1 A3607 Ob 2   0.14   0.09   0.91 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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