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 3ccq

3CCQ (2.9Å) -- RIBOSOME : Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation a2488u
List of all 93 Mg²⁺ binding sites in the PDB structure 3ccq 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
3ccq	08047	O_r	5	0.30	0.44	0.79	no
3ccq	08078	O_r	4	0.24	0.58	0.71	no
3ccq	08083	O_b	6	0.31	0.93	0.87	no
3ccq	08017	N_b	3	0.19	0.43	0.93	no
3ccq	08036	N_b	4	0.17	0.46	0.84	no
3ccq	08069	N_b	4	0.13	0.49	0.89	no
3ccq	08088	N_b	6	0.35	0.73	0.92	no
3ccq	08090	N_b	4	0.13	0.50	0.76	no
3ccq	08077	N_b	5	0.25	0.74	0.95	no
3ccq	08031	2O_r	5	0.16	0.53	0.84	no
3ccq	08059	2O_r	6	0.37	0.86	0.73	no
3ccq	08076	2O_b	6	0.32	0.89	0.92	no
3ccq	08033	2O_b	4	0.12	0.49	0.77	no
3ccq	08032	2O_b	6	0.22	0.85	0.92	no
3ccq	08080	O_b·N_b	6	0.23	0.74	0.65	no
3ccq	08093	2O_r·N_b	6	0.26	0.72	0.97	no
3ccq	08082	O_ph	1	0.03	0	0.94	no
3ccq	A8051	O_ph	3	0.17	0.51	0.91	no
3ccq	08038	O_ph	2	0.10	0.20	0.84	no
3ccq	08071	O_ph·P_out	4	0.14	0.67	0.88	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 3ccq

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

List of Mg²⁺ binding sites in structure 3ccq