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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2i2v:B2959, See in JSmolMgRNA representative site for type PO-RO-3BO Click on the image to toggle views


Site type: Pout·Rout·3Bout

Schematic drawing for
Pout·Rout·3Bout
MgRNA type PO-RO-3BO
List of all 32 Mg2+ binding sites with the site type Pout·Rout·3Bout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4qcn A3565 Pout·Rout·3Bout A4893, A4894, A4895, A4896, A4897 U:A1977 G:A1976 G:A1971, G:A1972, G:A1970
4qcp A3633 Pout·Rout·3Bout A4944, A4945, A4946, A4947 U:A1955 G:A1954 G:A1948, G:A1949, G:A1950
4qcr A3588 Pout·Rout·3Bout A4914, A4915, A4916, A4917, A4918 U:A1977 G:A1976 G:A1971, G:A1970, G:A1972
4qcr B214 Pout·Rout·3Bout B323, B324, B325, B326, B327, B328 G:B75 A:B100 G:B76, G:B75, U:B77
4qcx A3388 Pout·Rout·3Bout A4314, A4315, A4316, A4317, A4318, A4319 U:A1267 G:A1266 G:A2010, U:A2011, G:A2009
4tp3 A3061 Pout·Rout·3Bout A3474, A3475, A3476, A3477 A:A2033 A:A2033 U:A2026, G:A2027, U:A2028
4tpb A3061 Pout·Rout·3Bout A3474, A3475, A3476, A3477 A:A2033 A:A2033 U:A2026, G:A2027, U:A2028

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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>