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 3uz7

3UZ7 (3Å) -- RIBOSOME : Crystal structure analysis of ribosomal decoding. this entry contains the 30s ribosomal subunit of the second 70s molecule in the asymmetric unit for the cognate trna-tyr complex.
List of all 261 Mg²⁺ binding sites in the PDB structure 3uz7 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 14 | « 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
3uz7	R102	Mg²⁺ not bound by RNA	1	0.02	0	0.86	no
3uz7	C103	Mg²⁺ not bound by RNA	0	0	0	0	no
3uz7	C105	cis-2O_ph	2	0.08	0.15	0.89	no
3uz7	B106	Mg²⁺ not bound by RNA	0	0	0	0.46	no
3uz7	C108	Mg²⁺ not bound by RNA	0	0	0	0	no
3uz7	D108	Mg²⁺ not bound by RNA	0	0	0	0	no
3uz7	B112	N_b	1	0.01	0	0.65	no
3uz7	B113	Mg²⁺ not bound by RNA	0	0	0	0.99	no
3uz7	D117	Mg²⁺ not bound by RNA	0	0	0	0.74	no
3uz7	D118	Mg²⁺ not bound by RNA	0	0	0	0	no
3uz7	B118	Mg²⁺ not bound by RNA	0	0	0	0.81	no
3uz7	C120	Mg²⁺ not bound by RNA	0	0	0	0	no
3uz7	C122	Mg²⁺ not bound by RNA	0	0	0	0.81	no
3uz7	C123	Mg²⁺ not bound by RNA	0	0	0	0.98	no
3uz7	C124	O_b·N_b	2	0.03	0.23	0.97	no
3uz7	C125	Mg²⁺ not bound by RNA	0	0	0	0.93	no
3uz7	C126	Mg²⁺ not bound by RNA	0	0	0	0	no
3uz7	B127	N_b	1	0.01	0	0.98	no
3uz7	C128	Mg²⁺ not bound by RNA	0	0	0	0.88	no
3uz7	C136	2O_b	2	0.03	0.15	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

List of Mg2+ binding sites in structure 3uz7

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

List of Mg²⁺ binding sites in structure 3uz7