	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
1n8r	A8077	trans-2O_ph	6	0.20	0.83	0.70	no
1nji	A8077	trans-2O_ph	6	0.71	0.77	0.62	yes
1nji	A8094	trans-2O_ph	4	0.51	0.53	0.78	no
1nji	A8015	trans-2O_ph	6	0.01	0.81	0.28	no
1o3z	B302	trans-2O_ph	7	0.65	0.68	0.44	no
1q7y	A8094	trans-2O_ph	4	0.29	0.58	0.89	no
1q7y	A8077	trans-2O_ph	6	0.18	0.76	0.63	no
1q7y	A8015	trans-2O_ph	6	0.55	0.87	0.30	no
1q81	A8077	trans-2O_ph	6	0.58	0.69	0.99	yes
1q81	A8015	trans-2O_ph	6	0.95	0.89	0.84	yes
1q82	A8094	trans-2O_ph	4	0.51	0.34	0.81	no
1q82	A8077	trans-2O_ph	6	0.44	0.78	0.97	no
1q82	A8015	trans-2O_ph	6	0.24	0.63	0.41	no
1q86	A8015	trans-2O_ph	6	0.56	0.87	0.39	no
1q86	A8077	trans-2O_ph	6	0.60	0.92	0.89	yes
1q86	A8094	trans-2O_ph	4	0.40	0.39	0.74	no
1qvf	08077	trans-2O_ph	6	0.80	0.86	0.92	yes
1qvf	08094	trans-2O_ph	4	0.38	0.48	0.82	no
1qvf	08015	trans-2O_ph	5	0.84	0.76	0.68	yes
1qvg	08077	trans-2O_ph	6	0.57	0.81	0.91	yes
1qvg	08015	trans-2O_ph	6	0.40	0.95	0.34	no
1s72	08094	trans-2O_ph	4	0.41	0.49	0.64	no
1s72	08077	trans-2O_ph	6	0.97	0.93	0.85	yes
1s72	08015	trans-2O_ph	6	0.87	0.88	0.76	yes
1u6b	B1025	trans-2O_ph	3	0.08	0.73	0.97	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