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

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

List of Mg²⁺ binding sites in structure 4tp7

4TP7 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 50s subunit of the second 70s ribosome with virginiamycin m1 bound.
List of all 168 Mg²⁺ binding sites in the PDB structure 4tp7 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 ^#", "Site type" or "Mg²⁺ ID"
Page 1 of 9 | « 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
4tp7	A3142	Mg²⁺ not bound by RNA	0	0	0	0.63	no
4tp7	A3166	Mg²⁺ not bound by RNA	0	0	0	0.54	no
4tp7	A3147	Mg²⁺ not bound by RNA	0	0	0	0.54	no
4tp7	A3165	Mg²⁺ not bound by RNA	0	0	0	0.71	no
4tp7	A3143	Mg²⁺ not bound by RNA	0	0	0	0.58	no
4tp7	A3148	Mg²⁺ not bound by RNA	0	0	0	0.75	no
4tp7	A3156	Mg²⁺ not bound by RNA	0	0	0	0.95	no
4tp7	A3157	Mg²⁺ not bound by RNA	0	0	0	0.57	no
4tp7	Q201	Mg²⁺ not bound by RNA	0	0	0	0.68	no
4tp7	A3161	Mg²⁺ not bound by RNA	0	0	0	0.58	no
4tp7	A3149	Mg²⁺ not bound by RNA	0	0	0	0.72	no
4tp7	A3163	O_ph	1	0.01	0	0.85	no
4tp7	A3153	O_ph	1	0.01	0	0.57	no
4tp7	A3154	O_b	1	0.02	0	0.51	no
4tp7	A3155	O_b	1	0.03	0	0.68	no
4tp7	A3138	O_ph	1	0.04	0	0.70	no
4tp7	A3152	cis-2O_ph	2	0.04	0.35	0.73	no
4tp7	A3141	O_ph	1	0.05	0	0.78	no
4tp7	A3144	N_b	1	0.06	0	0.97	no
4tp7	A3164	O_b·2N_b	3	0.06	0.28	0.82	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

List of Mg2+ binding sites in structure 4tp7

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

List of Mg²⁺ binding sites in structure 4tp7