MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

	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 2otj

2OTJ (2.9Å) -- RIBOSOME : 13-deoxytedanolide bound to the large subunit of haloarcula marismortui
List of all 117 Mg²⁺ binding sites in the PDB structure 2otj 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 3 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
2otj	08099	O_r	4	0.37	0.50	0.66	no
2otj	08106	poly-nuclear Mg²⁺ site	5	0.26	0.41	0.59	no
2otj	08113	poly-nuclear Mg²⁺ site	6	0.34	0.95	0.94	no
2otj	T8073	Mg²⁺ not bound by RNA	6	0.18	0.75	0.69	no
2otj	38078	Mg²⁺ bound by non-RNA	6	0.92	0.57	0.35	no
2otj	08010	Mg²⁺ bound by non-RNA	6	0.28	0.79	0.29	no
2otj	08043	poly-nuclear Mg²⁺ site	4	0.28	0.30	0.99	no
2otj	08064	poly-nuclear Mg²⁺ site	6	0.15	0.86	1.00	no
2otj	08067	Mg²⁺ bound by non-RNA	5	0.40	0.83	0.99	no
2otj	08085	poly-nuclear Mg²⁺ site	6	0.18	0.63	0.81	no
2otj	08115	poly-nuclear Mg²⁺ site	4	0.42	0.39	0.53	no
2otj	08116	poly-nuclear Mg²⁺ site	6	0.19	0.76	0.86	no
2otj	38118	Mg²⁺ bound by non-RNA	3	0.49	0.05	0.24	no
2otj	Y8109	Mg²⁺ not bound by RNA	6	0.33	0.78	0.94	no
2otj	08048	cis-2O_ph	5	0.94	0.87	0.79	yes
2otj	K8069	Mg²⁺ bound by non-RNA	6	0.75	0.84	0.97	yes
2otj	08054	cis-2O_ph	6	0.85	0.91	0.97	yes
2otj	08061	cis-2O_ph	6	0.89	0.81	0.77	yes
2otj	08074	cis-2O_ph	6	0.95	0.83	0.76	yes
2otj	08080	cis-2O_ph	6	0.57	0.66	0.95	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

Abbreviations used for Mg²⁺ "Site type"	Mg²⁺ inner-sphere ligands	Geometry for inner-sphere O_P	Mg²⁺ outer-sphere moieties
Site type used in the classification is a string abbreviation of ligand composition in Mg²⁺ coordination sphere
Abbreviations used for Mg²⁺ "Site type"	O_ph phosphate oxygen (OP1/OP2) O_r ribose oxygen (O2'/O4') or oxygen bridging phosphate and ribose (O3'/O5') O_b nucleobase oxygen N_b nucleobase nitrogen	*cis-* two O_P ligands adopt cis- isoform *trans-* two O_P ligands adopt trans- isoform *fac-* three O_P ligands adopt fac- isoform *mer-* three O_P ligands adopt mer- isoform	P_out phosphate moiety R_out ribose moiety B_out 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].

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

List of Mg2+ binding sites in structure 2otj

MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures

List of Mg²⁺ binding sites in structure 2otj