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

	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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List of Mg²⁺ binding sites in structure 4tp9

4TP9 (2.8Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to dalfopristin and quinupristin. this file contains the 50s subunit of the first 70s ribosome with dalfopristin and quinupristin bound.
List of all 194 Mg²⁺ binding sites in the PDB structure 4tp9 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"
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Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
4tp9	A3103	cis-2O_ph	6	0.87	0.87	0.31	no
4tp9	A3121	cis-2O_ph	6	0.84	0.76	0.29	no
4tp9	A3069	cis-2O_ph	6	0.88	0.74	0.71	yes
4tp9	A3059	cis-2O_ph	6	0.76	0.79	0.38	no
4tp9	A3053	cis-2O_ph	6	0.92	0.97	0.68	yes
4tp9	B201	cis-2O_ph	6	0.83	0.86	0.82	yes
4tp9	A3047	cis-2O_ph	6	0.79	0.81	0.29	no
4tp9	A3033	cis-2O_ph	6	0.90	0.91	0.63	yes
4tp9	A3188	cis-2O_ph	2	0.10	0.18	0.33	no
4tp9	A3011	cis-2O_ph	6	0.92	0.94	0.38	no
4tp9	A3125	trans-2O_ph	6	0.82	0.93	0.40	no
4tp9	A3024	trans-2O_ph	6	0.99	0.93	0.21	no
4tp9	A3065	trans-2O_ph	6	0.80	0.73	0.32	no
4tp9	A3109	trans-2O_ph	5	0.57	0.47	0.24	no
4tp9	A3194	cis-2O_ph·O_b	3	0.23	0.38	0.60	no
4tp9	A3107	cis-2O_ph·O_b	6	0.88	0.85	0	no
4tp9	A3164	cis-2O_ph·O_b	3	0.32	0.67	0.89	no
4tp9	A3126	cis-2O_ph·N_b	6	0.83	0.85	0.89	yes
4tp9	A3129	cis-2O_ph·N_b	6	0.70	0.69	0.42	no
4tp9	A3110	fac-3O_ph	6	0.65	0.75	0.29	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

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 4tp9

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

List of Mg²⁺ binding sites in structure 4tp9