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 12 of 36 | « Previous | Next » | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4qcp A3608 cis-2Oph·Ob 5   0.28   0.41   0.80 no 4qcp A3463 cis-2Oph·Nb 5   0.34   0.49   0.69 no 4qcp A3189 fac-3Oph 3   0.06   0.41   0.90 no 4qcp A3416 fac-3Oph 5   0.36   0.60   0.99 no 4qcp A3466 fac-3Oph 5   0.35   0.83   0.94 no 4qcp A3567 fac-3Oph 5   0.38   0.79   0.89 no 4qcp A3411 fac-3Oph 6   0.49   0.78   0.92 no 4qcp A3430 mer-3Oph 5   0.36   0.90   0.83 no 4qcp A3536 Bout 1   0.12  0   0.93 no 4qcp A3649 Bout 3   0.37   0.43   0.94 no 4qcp A3646 Oph·Pout 2   0.15   0.21   0.78 no 4qcp A3067 Nb 1   0.01  0   0.96 no 4qcp A3500 Mg2+ not bound by RNA 1   0.12  0   0.90 no 4qcp A3651 Mg2+ not bound by RNA 1   0.12  0   0.83 no 4qcp A3657 Mg2+ not bound by RNA 1   0.12  0   0.92 no 4qcp B3013 Mg2+ not bound by RNA 1   0.12  0   0.88 no 4qcp A3005 Oph 1   0.04  0   0.96 no 4qcp A3007 Mg2+ not bound by RNA 0  0  0   0.80 no 4qcp A3008 other RNA-inner types 4   0.18   0.47   0.72 no 4qcp A3175 Mg2+ not bound by RNA 0  0  0   0.76 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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