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 4byd 4BYD (3.35Å) -- RIBOSOME : Structure of thermus thermophilus 30s ribosome List of all 103 Mg2+ binding sites in the PDB structure 4byd 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 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4byd A2578 Or 1   0.03  0   0.47 no 4byd A2564 Or 1   0.08  0   0.55 no 4byd A2574 Ob 1   0.16  0   0.69 no 4byd A2603 Ob 1   0.02  0   0.90 no 4byd A2554 Ob 1   0.18  0   0.79 no 4byd A2606 Ob 1   0.04  0   0.84 no 4byd A2581 Ob 1   0.02  0   0.69 no 4byd A2599 Ob 1   0.02  0   0.98 no 4byd A2565 Ob 1   0.01  0   0.83 no 4byd A2542 Nb 1   0.03  0   0.85 no 4byd A2546 Nb 1   0.30  0   0.78 no 4byd A2584 Nb 1   0.02  0   0.75 no 4byd A2594 2Ob 2   0.11   0.20   0.93 no 4byd A2582 2Ob 2   0.21   0.29   0.99 no 4byd A2543 2Ob 2   0.12   0.40   0.60 no 4byd A2600 Ob·Nb 2   0.04   0.30   0.77 no 4byd A2555 2Nb 2   0.04   0.17   0.80 no 4byd A2602 Oph 1   0.01  0   0.89 no 4byd A2592 Oph 1   0.04  0   0.91 no 4byd A3114 Oph 1   0.01  0   0.83 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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