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 3i1p

3I1P (3.19Å) -- RIBOSOME : Crystal structure of the e. coli 70s ribosome in an intermediate state of ratcheting
List of all 137 Mg²⁺ binding sites in the PDB structure 3i1p 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 4 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
3i1p	A2911	O_ph·N_b	6	0.74	0.72	0.84	yes
3i1p	A2975	O_ph·N_b	6	0.72	0.66	0.71	yes
3i1p	A3021	cis-2O_ph	6	0.76	0.75	0.89	yes
3i1p	A3001	cis-2O_ph	6	0.71	0.70	0.65	yes
3i1p	A2985	cis-2O_ph	6	0.79	0.82	0.76	yes
3i1p	A2944	cis-2O_ph	6	0.71	0.70	0.80	yes
3i1p	A2969	cis-2O_ph	6	0.78	0.80	0.97	yes
3i1p	A2983	cis-2O_ph	6	0.81	0.78	0.68	yes
3i1p	A3007	cis-2O_ph	5	0.59	0.61	0.69	yes
3i1p	A2951	cis-2O_ph	6	0.78	0.80	0.97	yes
3i1p	A3030	cis-2O_ph	5	0.44	0.74	0.97	no
3i1p	A3008	cis-2O_ph	5	0.49	0.87	0.82	no
3i1p	A3012	trans-2O_ph	4	0.39	0.40	0.76	no
3i1p	A2940	trans-2O_ph	6	0.75	0.96	0.75	yes
3i1p	A2927	trans-2O_ph	6	0.84	0.95	0.95	yes
3i1p	A3005	cis-2O_ph·O_b	6	0.44	0.77	0.78	no
3i1p	A3016	cis-2O_ph·O_b	6	0.47	0.59	0.72	no
3i1p	A3022	cis-2O_ph·N_b	6	0.62	0.58	0.73	no
3i1p	A3027	cis-2O_ph·N_b	6	0.58	0.57	0.79	no
3i1p	A3024	cis-2O_ph·N_b	6	0.66	0.74	0.92	yes

^# 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 3i1p

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

List of Mg²⁺ binding sites in structure 3i1p