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 3d5d 3D5D (3.21Å) -- RIBOSOME : Structural basis for translation termination on the 70s ribosome. this file contains the 50s subunit of the second 70s ribosome. the entire crystal structure contains two 70s ribosomes as described in remark 400. List of all 807 Mg2+ binding sites in the PDB structure 3d5d 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 41 | « 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 3d5d A3639 Or 1   0.05  0   0.29 no 3d5d A3528 Or 1   0.06  0   0.05 no 3d5d A3541 Or 1   0.02  0   0.42 no 3d5d A3622 Or 1   0.02  0   0.21 no 3d5d A3429 Or 1   0.03  0   0.61 no 3d5d A3604 Or 1   0.02  0   0.43 no 3d5d A3482 Or 1   0.02  0   0.56 no 3d5d A3527 Or 1   0.02  0   0.23 no 3d5d B761 Or 1   0.02  0   0.26 no 3d5d B495 Or 1   0.01  0   0.30 no 3d5d A3457 Or 1   0.04  0   0.25 no 3d5d B754 Or 1   0.02  0   0.18 no 3d5d A3507 Or 1   0.02  0   0.35 no 3d5d A3506 Or 1   0.06  0   0.16 no 3d5d A3573 Or 1   0.02  0   0.30 no 3d5d A3315 Ob 1   0.01  0   0.16 no 3d5d A3301 Ob 1   0.02  0   0.17 no 3d5d A3278 Ob 1   0.01  0   0.28 no 3d5d A3244 Ob 1   0.02  0   0.40 no 3d5d A3601 Ob 1   0.01  0   0.17 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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