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 4kj3

4KJ3 (2.9Å) -- RIBOSOME : Control of ribosomal subunit rotation by elongation factor g
List of all 143 Mg²⁺ binding sites in the PDB structure 4kj3 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
4kj3	A3131	Mg²⁺ not bound by RNA	0	0	0	0.69	no
4kj3	A3079	Mg²⁺ not bound by RNA	0	0	0	0.88	no
4kj3	A3135	Mg²⁺ not bound by RNA	0	0	0	0.93	no
4kj3	A3021	P_out·B_out	1	0.02	0	0.24	no
4kj3	A3057	N_b	1	0.02	0	0.56	no
4kj3	A3136	O_b	1	0.23	0	0.69	no
4kj3	L201	Mg²⁺ not bound by RNA	1	0.01	0	0.97	no
4kj3	A3025	B_out	1	0.03	0	0.91	no
4kj3	A3133	O_ph	1	0.01	0	0.60	no
4kj3	A3006	O_ph	1	0.03	0	0.38	no
4kj3	A3091	Mg²⁺ not bound by RNA	1	0.15	0	0.93	no
4kj3	A3124	Mg²⁺ not bound by RNA	1	0.01	0	0.63	no
4kj3	A3069	N_b	1	0.02	0	0.85	no
4kj3	A3083	O_ph	1	0.11	0	0.52	no
4kj3	A3088	2B_out	1	0.08	0	0.86	no
4kj3	A3076	O_ph	2	0.03	0.15	0.74	no
4kj3	A3003	O_ph	2	0.22	0.18	0.57	no
4kj3	A3023	O_ph·P_out	2	0.21	0.07	0.54	no
4kj3	A3070	2B_out	2	0.11	0.12	0.64	no
4kj3	A3036	2O_r	2	0.33	0.08	0.95	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 4kj3

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

List of Mg²⁺ binding sites in structure 4kj3