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

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Representative site 4ji1:A1760, See in JSmolMgRNA representative site for type 3PO-2RO        Click on the image to toggle views

Site type: 3Pout·2Rout

Schematic drawing for

MgRNA type 3PO-2RO
List of all 11 Mg2+ binding sites with the site type 3Pout·2Rout 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
3i22 A2978 3Pout·2Rout A3394, A3395, A3396, A3397, A3398 G:A2447, G:A2502, C:A2501 A:A575, U:A576
3oxb A111 3Pout·2Rout A149, A150, A151, A152, A153 A:A21, U:A20, C:A15 A:A13, C:B24
3v2d A3149 3Pout·2Rout A4099, A4100, A4101, A4102, A4103 G:A690, A:A781, A:A782 U:A1777, G:A780
4bpe A5003 3Pout·2Rout A2144, A2145, A2146, A2147, A2189, A2352 A:A1014, G:A844, G:A1013 U:A842, A:A843
4bpn A5003 3Pout·2Rout A6018, A6019, A6020, A6021, A6022, A6023 G:A1013, A:A1014, G:A844 A:A843, U:A842
4bpo A5064 3Pout·2Rout A2226, A2227, A2228, A2234, A2269, A2270 A:A1180, U:A1420, G:A1419 U:A1241, G:A1240
4bpp A5003 3Pout·2Rout A7059, A7060, A7061, A7062, A7063, A7064 G:A1013, A:A1014, G:A844 A:A843, U:A842
4duy A1789 3Pout·2Rout A2126, A2127, A2128, A2129, A2130, A2131 C:A1200, C:A1051, U:A1052 C:A962, G:A963
4ji1 A1760 3Pout·2Rout A2249, A2250, A2251, A2252, A2253, A2254 C:A1051, U:A1052, C:A1200 C:A962, G:A963
4ji5 A1697 3Pout·2Rout A1911, A1912, A1913, A1914, A1915, A1916 G:A1215, C:A984, G:A1050 C:A1214, G:A1048
4ji7 A1824 3Pout·2Rout A2458, A2459, A2460, A2461, A2462, A2463 C:A984, G:A1050, G:A1215 C:A1214, G:A1050

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>