	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
	Back to Classification Home	Download this subset in: CSV, XML, JSON

Representative site 1hr2:A5, See in JSmol MgRNA representative site for type OB-NB

Click on the image to toggle views

Site type: O_b·N_b

Schematic drawing for
O_b·N_b
MgRNA type OB-NB

List of all 592 Mg²⁺ binding sites with the site type O_b·N_b 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"
Page 1 of 24 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
1cx0	B402	O_b·N_b	2	0.10	0.12	0.95	no
1drz	B402	O_b·N_b	2	0.08	0.09	0.82	no
1gid	A272	O_b·N_b	2	0.21	0.14	0.77	no
1gid	B271	O_b·N_b	2	0.18	0.13	0.93	no
1hnw	A1610	O_b·N_b	3	0.10	0.39	0.48	no
1hnx	A1611	O_b·N_b	3	0.21	0.20	0.65	no
1hnz	A1580	O_b·N_b	2	0.31	0.13	0.53	no
1hr2	B6	O_b·N_b	6	0.97	0.87	0.99	yes
1hr2	A5	O_b·N_b	6	0.99	0.89	0.96	yes
1i96	A1547	O_b·N_b	2	0.04	0.55	0.78	no
1i97	A1547	O_b·N_b	2	0.06	0.31	0.65	no
1ibk	A1636	O_b·N_b	2	0.04	0.15	0.33	no
1ibk	A1644	O_b·N_b	2	0.05	0.28	0.30	no
1jj2	08102	O_b·N_b	6	0.29	0.83	0.68	no
1k73	A8102	O_b·N_b	6	0.30	0.78	0.91	no
1m1k	A8102	O_b·N_b	6	0.32	0.65	0.72	no
1m90	A8102	O_b·N_b	6	0.34	0.85	0.84	no
1mms	D360	O_b·N_b	6	0.29	0.58	0.64	no
1n32	A1678	O_b·N_b	2	0.06	0.23	0.51	no
1n32	A1675	O_b·N_b	2	0.05	0.11	0.57	no
1n32	A1673	O_b·N_b	2	0.06	0.11	0.47	no
1n33	A1609	O_b·N_b	2	0.04	0.13	0.42	no
1nji	A8102	O_b·N_b	6	0.31	0.86	0.69	no
1q7y	A8102	O_b·N_b	5	0.49	0.59	0.81	no
1q86	A8102	O_b·N_b	6	0.41	0.83	0.79	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: Ob·Nb

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

Site type: O_b·N_b