MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4m:A1592, See in JSmolClick on the image to toggle views Site type: Pout Schematic drawing for Pout List of all 731 Mg2+ binding sites with the site type Pout in RNA crystal structures 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 #", "PDB ID" or "Mg2+ ID" Page 1 of 30 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4qd0 A3090 Pout 1   0.12  0   0.92 no 4kj7 A3055 Pout 1   0.12  0   0.48 no 2vhp Z4035 Pout 1   0.02  0   0.65 no 4nvw A3077 Pout 1   0.13  0   0.99 no 3v23 A3041 Pout 1   0.02  0   0.92 no 3g78 A449 Pout 1   0.05  0   0.65 no 4ji8 A1637 Pout 1   0.14  0   0.71 no 4e8n A426 Pout 1   0.04  0   0.83 no 4dhc A3069 Pout 1   0.02  0   0.86 no 4dr5 A1663 Pout 1   0.16  0   0.97 no 4kjc A1638 Pout 1   0.07  0   0.82 no 4nvx A3501 Pout 1   0.12  0   0.64 no 4kj8 A1614 Pout 1   0.03  0   0.56 no 4e8v A404 Pout 1   0.08  0   0.94 no 3r1l C1023 Pout 1   0.03  0   0.96 no 2cv2 C902 Pout 1   0.02  0   0.99 no 4far A416 Pout 1   0.06  0   0.89 no 3bo3 B1019 Pout 1   0.02  0   0.71 no 4qcz B3008 Pout 1   0.12  0   0.90 no 4kj1 A3057 Pout 1   0.03  0   0.33 no 2vhp Z4009 Pout 1   0.02  0   0.87 no 1q81 A8024 Pout 1   0.03  0   0.71 no 2z75 B303 Pout 1   0.02  0   0.86 no 4e8q A433 Pout 1   0.11  0   0.96 no 2vhm Z4100 Pout 1   0.03  0   0.13 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

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout 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].

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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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