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 4qcy

4QCY (2.8Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the pre- attack state of peptide bond formation containing short substrate- mimic cytidine-cytidine-puromycin in the a site and acylated trna in the p site. this entry contains the 30s subunit
List of all 228 Mg²⁺ binding sites in the PDB structure 4qcy 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
4qcy	M201	Mg²⁺ bound by non-RNA	4	0.34	0.71	0.66	no
4qcy	J201	Mg²⁺ not bound by RNA	0	0	0	0.96	no
4qcy	D301	Mg²⁺ not bound by RNA	0	0	0	0.84	no
4qcy	D303	Mg²⁺ not bound by RNA	0	0	0	0	no
4qcy	N502	Mg²⁺ bound by non-RNA	2	0.04	0.83	0.85	no
4qcy	N503	P_out·2B_out	2	0.25	0.29	0.80	no
4qcy	F3001	Mg²⁺ not bound by RNA	1	0.01	0	0.93	no
4qcy	V3001	O_ph	1	0.01	0	0.57	no
4qcy	A3001	Mg²⁺ bound by non-RNA	2	0.05	0.17	0.95	no
4qcy	E3001	Mg²⁺ not bound by RNA	1	0.29	0	0.70	no
4qcy	K3001	Mg²⁺ bound by non-RNA	4	0.19	0.68	0.78	no
4qcy	A3002	Mg²⁺ bound by non-RNA	4	0.16	0.32	0.80	no
4qcy	E3002	Mg²⁺ not bound by RNA	4	0.42	0.63	0.91	no
4qcy	X3002	Mg²⁺ not bound by RNA	0	0	0	0.93	no
4qcy	X3003	Mg²⁺ not bound by RNA	0	0	0	0.80	no
4qcy	A3003	Mg²⁺ bound by non-RNA	2	0.07	0.33	0.67	no
4qcy	X3004	trans-2O_ph·O_b	3	0.24	0.56	0.70	no
4qcy	A3004	Mg²⁺ not bound by RNA	0	0	0	0.77	no
4qcy	A3005	O_ph	1	0.01	0	0.96	no
4qcy	X3005	Mg²⁺ not bound by RNA	0	0	0	0.79	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 4qcy

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

List of Mg²⁺ binding sites in structure 4qcy