	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 3q3z:A6, See in JSmol MgRNA representative site for type trans-2OP

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Site type: trans-2O_ph

Schematic drawing for
trans-2O_ph
MgRNA type trans-2OP

List of all 1227 Mg²⁺ binding sites with the site type trans-2O_ph in RNA crystal structures 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 ^#", "PDB ID" 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
1ehz	A580	trans-2O_ph	4	0.51	0.52	0.83	no
1fjg	A1604	trans-2O_ph	2	0.07	0.47	0.55	no
1fjg	A1618	trans-2O_ph	2	0.15	0.57	0.66	no
1hnw	A1602	trans-2O_ph	2	0.07	0.75	0.48	no
1hnw	A1616	trans-2O_ph	2	0.27	0.15	0.59	no
1hnw	A1621	trans-2O_ph	2	0.11	0.27	0.35	no
1hnx	A1617	trans-2O_ph	2	0.17	0.28	0.68	no
1hnx	A1603	trans-2O_ph	2	0.11	0.41	0.55	no
1hnz	A1603	trans-2O_ph	2	0.11	0.47	0.55	no
1hnz	A1617	trans-2O_ph	2	0.14	0.41	0.76	no
1hr0	A1602	trans-2O_ph	2	0.22	0.50	0.69	no
1i95	A1574	trans-2O_ph	2	0.08	0.59	0.71	no
1ibk	A1597	trans-2O_ph	2	0.17	0.59	0.49	no
1ibl	A1596	trans-2O_ph	2	0.21	0.44	0.39	no
1ibm	A1597	trans-2O_ph	2	0.13	0.42	0.46	no
1jj2	08077	trans-2O_ph	6	0.99	0.92	0.84	yes
1jj2	08094	trans-2O_ph	4	0.41	0.48	0.66	no
1jj2	08015	trans-2O_ph	6	0.85	0.86	0.77	yes
1k73	A8015	trans-2O_ph	6	0.67	0.74	0.44	no
1k73	A8077	trans-2O_ph	6	0.57	0.82	0.75	yes
1k73	A8094	trans-2O_ph	4	0.40	0.45	0.71	no
1k8a	A8015	trans-2O_ph	6	0.82	0.89	0.55	yes
1k8a	A8077	trans-2O_ph	6	0.85	0.86	0.54	yes
1k8a	A8094	trans-2O_ph	4	0.52	0.32	0.66	no
1k9m	A8094	trans-2O_ph	4	0.75	0.46	0.71	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

Site type: trans-2Oph

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

Site type: trans-2O_ph