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 4qco 4QCO (2.6Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the pre- attack state of peptide bond formation containing acylated trna- substrates in the a and p sites. this entry contains the 30s subunit of the second 70s ribosome in the asu. List of all 172 Mg2+ binding sites in the PDB structure 4qco 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 4qco A3035 Or 1   0.01  0   0.80 no 4qco W3001 Or 1   0.06  0   0.69 no 4qco A3157 Ob 4   0.41   0.72   0.99 no 4qco A3016 Ob 1   0.03  0   0.68 no 4qco A3100 Ob 2   0.14   0.16   0.93 no 4qco A3112 Ob 2   0.14   0.10   0.86 no 4qco A3015 Ob 1   0.18  0   0.94 no 4qco A3030 Ob 1   0.02  0   0.78 no 4qco A3003 Ob 1   0.01  0   0.98 no 4qco A3086 Ob 2   0.14   0.11   0.85 no 4qco A3106 Ob 2   0.14   0.08   0.93 no 4qco A3032 Ob 1   0.02  0   0.66 no 4qco A3111 Ob 4   0.39   0.65   0.80 no 4qco A3121 Nb 2   0.14   0.13   0.77 no 4qco A3060 Nb 1   0.05  0   0.96 no 4qco A3005 Nb 1   0.06  0   0.98 no 4qco A3062 Nb 1   0.10  0   0.93 no 4qco A3038 2Or 2   0.05   0.10   0.92 no 4qco A3053 2Ob 2   0.11   0.09   0.91 no 4qco A3009 2Ob 2   0.12   0.11   0.92 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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