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

Representative site 2r8s:R1004, See in JSmol MgRNA representative site for type 2OB

Click on the image to toggle views

Site type: 2O_b

Schematic drawing for
2O_b
MgRNA type 2OB

List of all 1662 Mg²⁺ binding sites with the site type 2O_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 6 of 67 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
3oi3	A3177	2O_b	2	0.05	0.13	0.89	no
4kfh	A2377	2O_b	2	0.06	0.13	0.73	no
3pyr	A3433	2O_b	2	0.05	0.13	0.89	no
3v25	A3224	2O_b	2	0.03	0.13	0.88	no
4ji5	A1671	2O_b	2	0.03	0.13	0.92	no
4kfk	A2412	2O_b	2	0.04	0.13	0.54	no
4lfc	A1727	2O_b	2	0.05	0.13	0.98	no
4lfa	A1627	2O_b	2	0.04	0.13	0.69	no
4qcw	A3004	2O_b	2	0.07	0.13	0.83	no
1vy1	A3208	2O_b	2	0.05	0.13	0.85	no
2vqe	Z189	2O_b	2	0.05	0.13	0.55	no
4nvv	A3043	2O_b	2	0.04	0.13	0.70	no
4qd0	A3009	2O_b	2	0.05	0.13	0.84	no
4qcv	A3036	2O_b	2	0.06	0.13	0.90	no
3t1h	A1603	2O_b	2	0.05	0.13	0.88	no
3i9b	A1554	2O_b	2	0.10	0.13	0.67	no
4qcx	A3186	2O_b	2	0.07	0.13	0.90	no
3knj	A1569	2O_b	2	0.04	0.13	0.57	no
4nxn	A1782	2O_b	2	0.04	0.13	0.60	no
4qcn	A3067	2O_b	2	0.09	0.13	0.57	no
2uxb	G3059	2O_b	2	0.06	0.13	0.57	no
4dv7	A1698	2O_b	3	0.19	0.13	0.97	no
3kiw	A3104	2O_b	2	0.07	0.13	0.90	no
4qct	A3094	2O_b	2	0.08	0.13	0.97	no
3oh7	A2915	2O_b	2	0.04	0.13	0.77	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: 2Ob

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

Site type: 2O_b