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 4qcp 4QCP (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 50s subunit of the second 70s ribosome in the asu. List of all 707 Mg2+ binding sites in the PDB structure 4qcp 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 13 of 36 | « Previous | Next » | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4qcp A3564 poly-nuclear Mg2+ site 4   0.28   0.38   0.82 no 4qcp D303 Mg2+ bound by non-RNA 4   0.39   0.65   0.82 no 4qcp A3128 Oph 1   0.02  0   0.82 no 4qcp A3098 Oph 1   0.04  0   0.82 no 4qcp A3524 Oph·2Ob 4   0.18   0.51   0.82 no 4qcp A3386 Bout 2   0.25   0.29   0.82 no 4qcp F303 poly-nuclear Mg2+ site 3   0.07   0.43   0.82 no 4qcp A3361 Oph·Pout 6   0.64   0.82   0.82 yes 4qcp A3615 Mg2+ not bound by RNA 1   0.12  0   0.82 no 4qcp A3165 fac-3Oph 3   0.34   0.32   0.82 no 4qcp A3136 Oph 1   0.03  0   0.82 no 4qcp A3342 Oph·Ob 3   0.15   0.11   0.82 no 4qcp A3033 Mg2+ not bound by RNA 0  0  0   0.83 no 4qcp A3510 Mg2+ not bound by RNA 2   0.25   0.28   0.83 no 4qcp A3384 Pout·3Bout 6   0.75   1.00   0.83 yes 4qcp A3549 Pout·Bout 5   0.62   0.80   0.83 yes 4qcp A3617 cis-2Oph·Or 4   0.19   0.27   0.83 no 4qcp A3532 3Bout 4   0.49   0.64   0.83 no 4qcp F302 Mg2+ not bound by RNA 0  0  0   0.83 no 4qcp A3155 Ob 2   0.17   0.13   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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