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 1m1k 1M1K (3.2Å) -- RIBOSOME : Co-crystal structure of azithromycin bound to the 50s ribosomal subunit of haloarcula marismortui List of all 117 Mg2+ binding sites in the PDB structure 1m1k 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 1m1k A8099 Or 4   0.29   0.56   0.94 no 1m1k A8053 Ob 6   0.33   0.93   0.88 no 1m1k A8111 Nb 6   0.59   0.72   0.74 yes 1m1k A8113 Nb 6   0.54   0.56   0.84 no 1m1k A8098 Nb 6   0.76   0.38   0.85 no 1m1k A8112 Nb 6   0.46   0.77   0.95 no 1m1k A8114 Nb 6   0.38   0.77   0.93 no 1m1k A8024 Nb 5   0.32   0.63   0.86 no 1m1k A8046 Nb 4   0.47   0.44   0.82 no 1m1k A8075 2Or 6   0.34   0.81   0.82 no 1m1k A8066 Or·Ob 2   0.06   0.18   0.80 no 1m1k A8097 2Ob 6   0.39   0.84   0.95 no 1m1k A8042 2Ob 6   0.33   0.79   0.94 no 1m1k A8102 Ob·Nb 6   0.32   0.65   0.72 no 1m1k A8011 2Nb 6   0.26   0.74   0.90 no 1m1k A8117 2Or·Nb 5   0.62   0.39   0.86 no 1m1k A8047 Oph·Pout 4   0.64   0.60   0.73 yes 1m1k A8039 Oph·Pout 6   0.82   0.78   0.92 yes 1m1k A8051 Oph·Pout 4   0.49   0.55   0.82 no 1m1k A8084 Oph·Pout 6   0.98   0.94   0.99 yes

^# 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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