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

	MgRNA: Classification of Mg²⁺ binding sites in RNA crystal structures
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List of Mg²⁺ binding sites in structure 4kfh

4KFH (3.4Å) -- RIBOSOME : Crystal structure of the 70s ribosome bound with the q253p mutant of release factor rf2. 30s of the a subunit
List of all 614 Mg²⁺ binding sites in the PDB structure 4kfh 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"
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Mg²⁺ ion		Site type	Validation parameters
PDB ID	Mg²⁺ ID	Site type	Coordination Number	Qv ^#	Qs ^#	Qe ^#	benchmark dataset
4kfh	A1960	O_b	1	0.02	0	0.48	no
4kfh	A1776	O_b	1	0.01	0	0.52	no
4kfh	A1995	O_b	1	0.02	0	0.60	no
4kfh	A1847	O_b	1	0.02	0	0.70	no
4kfh	A2198	O_b	1	0.01	0	0.41	no
4kfh	A2167	O_b	1	0.03	0	0.46	no
4kfh	A1956	O_b	1	0.03	0	0.65	no
4kfh	A1676	O_b	1	0.01	0	0.77	no
4kfh	A1659	N_b	1	0.02	0	0.74	no
4kfh	A1609	N_b	1	0.03	0	0.47	no
4kfh	A1610	N_b	1	0.01	0	0.44	no
4kfh	A2418	N_b	1	0.01	0	0.51	no
4kfh	A1989	N_b	1	0.02	0	0.60	no
4kfh	A1877	N_b	1	0.02	0	0.62	no
4kfh	A2033	N_b	1	0.02	0	0.87	no
4kfh	A2063	N_b	1	0.07	0	0.43	no
4kfh	A1933	N_b	1	0.05	0	0.46	no
4kfh	A2175	N_b	1	0.05	0	0.43	no
4kfh	A2575	N_b	1	0.02	0	0.60	no
4kfh	A2060	N_b	1	0.01	0	0.74	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 4kfh

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

List of Mg²⁺ binding sites in structure 4kfh