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 4nw0

4NW0 (3.1Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of antibiotic ge82832 bound to 70s ribosome
List of all 179 Mg²⁺ binding sites in the PDB structure 4nw0 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
4nw0	A3039	Mg²⁺ not bound by RNA	0	0	0	0.85	no
4nw0	A3057	Mg²⁺ not bound by RNA	0	0	0	0.80	no
4nw0	A3030	Mg²⁺ not bound by RNA	0	0	0	0.78	no
4nw0	A3037	Mg²⁺ not bound by RNA	0	0	0	0.78	no
4nw0	A3040	Mg²⁺ not bound by RNA	0	0	0	0.54	no
4nw0	A3053	Mg²⁺ not bound by RNA	0	0	0	0.83	no
4nw0	A3021	Mg²⁺ not bound by RNA	0	0	0	0.72	no
4nw0	A3029	Mg²⁺ not bound by RNA	0	0	0	0.77	no
4nw0	A3035	Mg²⁺ not bound by RNA	0	0	0	0.89	no
4nw0	A3036	Mg²⁺ not bound by RNA	0	0	0	0.80	no
4nw0	A3016	Mg²⁺ not bound by RNA	0	0	0	0.97	no
4nw0	A3018	Mg²⁺ not bound by RNA	0	0	0	0.94	no
4nw0	A3041	Mg²⁺ not bound by RNA	0	0	0	0.75	no
4nw0	A3042	Mg²⁺ not bound by RNA	0	0	0	0.78	no
4nw0	A3005	Mg²⁺ not bound by RNA	0	0	0	0.84	no
4nw0	A3015	Mg²⁺ not bound by RNA	0	0	0	0.74	no
4nw0	A3024	Mg²⁺ not bound by RNA	0	0	0	0.80	no
4nw0	A3031	Mg²⁺ not bound by RNA	0	0	0	0.99	no
4nw0	A3033	Mg²⁺ not bound by RNA	0	0	0	0.79	no
4nw0	A3060	Mg²⁺ not bound by RNA	0	0	0	0.55	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 4nw0

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

List of Mg²⁺ binding sites in structure 4nw0