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 1k8a 1K8A (3Å) -- RIBOSOME : Co-crystal structure of carbomycin a bound to the 50s ribosomal subunit of haloarcula marismortui List of all 119 Mg2+ binding sites in the PDB structure 1k8a 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 1k8a A8100 Ob 5   0.41   0.42   0.78 no 1k8a A8053 Ob 6   0.38   0.81   0.98 no 1k8a A8111 Nb 6   0.49   0.82   0.69 no 1k8a A8112 Nb 6   0.59   0.70   0.87 yes 1k8a A8024 Nb 5   0.18   0.70   0.67 no 1k8a A8098 Nb 6   0.50   0.77   0.45 no 1k8a A8102 Nb 3   0.43   0.14   0.81 no 1k8a A8113 Nb 6   0.34   0.66   0.83 no 1k8a A8046 Nb 4   0.46   0.46   0.81 no 1k8a A8075 2Or 6   0.47   0.57   0.87 no 1k8a A8088 Or·Ob 2   0.03   0.18   0.76 no 1k8a A8097 2Ob 6   0.35   0.87   0.71 no 1k8a A8042 2Ob 5   0.40   0.57   0.89 no 1k8a A8011 2Nb 6   0.26   0.92   0.88 no 1k8a A8117 2Or·Nb 6   0.29   0.82   0.55 no 1k8a A8050 Oph 2   0.09   0.12   0.96 no 1k8a A8022 Oph 1   0.03  0   0.61 no 1k8a A8084 Oph·Pout 6   0.99   0.92   0.88 yes 1k8a A8039 Oph·Pout 6   0.95   0.76   0.82 yes 1k8a A8104 Oph·Pout 3   0.08   0.37   0.73 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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