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	A3136	O_b	1	0.23	0	0.69	no
4kj3	A3004	O_b	3	0.23	0.28	0.85	no
4kj3	A3092	O_b	3	0.30	0.24	0.57	no
4kj3	A3130	O_b	6	0.52	0.42	0.99	no
4kj3	A3009	O_b	3	0.39	0.23	0.95	no
4kj3	A3015	O_b	2	0.05	0.50	0.85	no
4kj3	A3069	N_b	1	0.02	0	0.85	no
4kj3	A3057	N_b	1	0.02	0	0.56	no
4kj3	A3042	N_b	3	0.25	0.19	0.95	no
4kj3	B1201	N_b	4	0.28	0.44	0.63	no
4kj3	A3077	N_b	4	0.38	0.32	0.75	no
4kj3	A3036	2O_r	2	0.33	0.08	0.95	no
4kj3	A3126	2O_r	3	0.16	0.33	0.84	no
4kj3	A3071	O_b·N_b	4	0.41	0.51	0.93	no
4kj3	A3095	O_b·N_b	4	0.15	0.62	0.30	no
4kj3	B1203	O_b·N_b	3	0.25	0.35	0.69	no
4kj3	A3044	2N_b	4	0.24	0.52	0.59	no
4kj3	A3083	O_ph	1	0.11	0	0.52	no
4kj3	A3076	O_ph	2	0.03	0.15	0.74	no
4kj3	A3026	O_ph	4	0.69	0.35	0.56	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