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

Representative site 1vs8:B2991, See in JSmol MgRNA representative site for type trans,cis-4OP

Click on the image to toggle views

Site type: trans,cis-4O_ph

Schematic drawing for
trans,cis-4O_ph
MgRNA type trans,cis-4OP

List of all 107 Mg²⁺ binding sites with the site type trans,cis-4O_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"
Page 1 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
3r8s	A3013	trans,cis-4O_ph	6	0.95	0.90	0	no
4tpd	A3110	trans,cis-4O_ph	6	0.82	0.91	0.09	no
3knm	A2978	trans,cis-4O_ph	4	0.41	0.56	0.13	no
1vvy	A3054	trans,cis-4O_ph	4	0.69	0.49	0.20	no
3orb	A3011	trans,cis-4O_ph	6	0.60	0.63	0.24	no
3i1n	A3013	trans,cis-4O_ph	6	0.54	0.66	0.24	no
3f1f	A5645	trans,cis-4O_ph	4	0.33	0.65	0.28	no
1vw0	A3112	trans,cis-4O_ph	4	0.87	0.68	0.28	no
3d5d	A3147	trans,cis-4O_ph	4	0.18	0.36	0.31	no
3oi3	A2993	trans,cis-4O_ph	4	0.31	0.56	0.33	no
3d5b	A3132	trans,cis-4O_ph	4	0.16	0.55	0.33	no
2z4n	B2994	trans,cis-4O_ph	6	0.92	0.82	0.34	no
2qp1	B2993	trans,cis-4O_ph	6	0.63	0.45	0.36	no
2qox	B2992	trans,cis-4O_ph	6	0.82	0.67	0.39	no
2qbc	B3512	trans,cis-4O_ph	6	0.96	0.74	0.41	no
2qov	B2944	trans,cis-4O_ph	6	0.87	0.87	0.45	no
3ohj	A2993	trans,cis-4O_ph	4	0.33	0.55	0.45	no
4kiz	A3109	trans,cis-4O_ph	5	0.59	0.52	0.47	no
2vhn	Z4073	trans,cis-4O_ph	6	0.24	0.65	0.48	no
2qbk	B2993	trans,cis-4O_ph	6	0.88	0.72	0.48	no
4ji6	A1605	trans,cis-4O_ph	6	0.42	0.57	0.49	no
2z4l	B2992	trans,cis-4O_ph	6	0.79	0.87	0.50	no
3pip	X2951	trans,cis-4O_ph	4	0.17	0.29	0.50	no
3kno	A2951	trans,cis-4O_ph	4	0.25	0.39	0.50	no
1vvs	A3110	trans,cis-4O_ph	4	0.60	0.55	0.51	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,cis-4Oph

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

Site type: trans,cis-4O_ph