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 1vq5

1VQ5 (2.6Å) -- RIBOSOME : The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui
List of all 118 Mg²⁺ binding sites in the PDB structure 1vq5 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
1vq5	08049	cis-2O_ph	3	0.30	0.26	0.84	no
1vq5	08044	Mg²⁺ bound by non-RNA	5	0.31	0.92	0.91	no
1vq5	08097	2O_b	6	0.32	0.84	0.94	no
1vq5	08104	cis-2O_ph	4	0.32	0.86	0.93	no
1vq5	98095	cis-2O_ph	3	0.33	0.29	1.00	no
1vq5	08041	O_ph·2O_r	6	0.33	0.59	0.68	no
1vq5	28076	R_out·2B_out	5	0.33	0.63	0.75	no
1vq5	08116	poly-nuclear Mg²⁺ site	6	0.33	0.75	0.80	no
1vq5	08046	N_b	4	0.33	0.60	0.99	no
1vq5	08094	trans-2O_ph	4	0.33	0.48	0.68	no
1vq5	08085	O_ph·2P_out	6	0.34	0.63	0.84	no
1vq5	08098	N_b	5	0.34	0.82	0.88	no
1vq5	08102	O_b·N_b	5	0.35	0.76	0.92	no
1vq5	08024	N_b	4	0.35	0.49	0.66	no
1vq5	08070	O_ph·O_b	5	0.37	0.56	0.53	no
1vq5	08092	O_ph·P_out	4	0.37	0.66	0.59	no
1vq5	08111	N_b	6	0.38	0.93	0.95	no
1vq5	08110	O_ph·N_b	5	0.39	0.78	0.94	no
1vq5	08067	Mg²⁺ bound by non-RNA	5	0.40	0.86	0.71	no
1vq5	08093	O_ph·O_r	6	0.40	0.85	0.63	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 1vq5

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

List of Mg²⁺ binding sites in structure 1vq5