	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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Representative site 3r8s:A3026, See in JSmol MgRNA representative site for type cis-2OP

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Site type: cis-2O_ph

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

List of all 6585 Mg²⁺ binding sites with the site type cis-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
1i96	A1576	cis-2O_ph	3	0.38	0.53	0.95	no
1i96	A1573	cis-2O_ph	2	0.08	0.54	0.74	no
1i96	A1566	cis-2O_ph	2	0.13	0.23	0.89	no
1i97	A1566	cis-2O_ph	2	0.12	0.21	0.91	no
1i97	A1577	cis-2O_ph	3	0.42	0.68	0.73	no
1i9v	A301	cis-2O_ph	2	0.10	0.15	0.89	no
1ibk	A1607	cis-2O_ph	2	0.06	0.07	0.43	no
1ibk	A1599	cis-2O_ph	2	0.18	0.27	0.45	no
1ibk	A1550	cis-2O_ph	2	0.48	0.31	0.39	no
1ibk	A1571	cis-2O_ph	2	0.26	0.19	0.36	no
1ibk	A1546	cis-2O_ph	2	0.14	0.19	0.41	no
1ibk	A1574	cis-2O_ph	2	0.21	0.12	0.33	no
1ibl	A1570	cis-2O_ph	2	0.18	0.20	0.40	no
1ibl	A1607	cis-2O_ph	2	0.16	0.17	0.34	no
1ibl	A1551	cis-2O_ph	2	0.39	0.44	0.35	no
1ibl	A1606	cis-2O_ph	2	0.06	0.16	0.34	no
1ibl	A1546	cis-2O_ph	2	0.21	0.19	0.40	no
1ibl	A1598	cis-2O_ph	2	0.07	0.22	0.33	no
1ibl	A214	cis-2O_ph	2	0.07	0.18	0.43	no
1ibl	A1655	cis-2O_ph	2	0.04	0.18	0.33	no
1ibm	A1575	cis-2O_ph	2	0.41	0.11	0.29	no
1ibm	A1571	cis-2O_ph	2	0.22	0.23	0.42	no
1ibm	A1599	cis-2O_ph	2	0.13	0.15	0.41	no
1ibm	A1608	cis-2O_ph	2	0.10	0.09	0.38	no
1ibm	A1550	cis-2O_ph	2	0.13	0.17	0.41	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: cis-2Oph

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

Site type: cis-2O_ph