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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3i20:A2945, See in JSmolMgRNA representative site for type OP-PO Click on the image to toggle views


Site type: Oph·Pout

Schematic drawing for
Oph·Pout
MgRNA type OP-PO
List of all 1301 Mg2+ binding sites with the site type Oph·Pout 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
2i2v B2926 Oph·Pout A:B1156(OP2) B3129, B3130, B3131, B3132, B3133 A:B1155 U:B999, G:B1157, C:B998
2i2v B2913 Oph·Pout A:B1664(OP2) B3067, B3068, B3069, B3070, B3071 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666
2i2v B2965 Oph·Pout U:B419(OP1) B3316, B3317, B3318, B3319, B3320 G:B230 G:B230
2otj 08084 Oph·Pout A:01742(OP2) 03654, 07841, 09255, 09382, 09763 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
2otj 08039 Oph·Pout U:0115(OP2) 03993, 05129, 07809, 07810, 09922 G:0112 A:0114 A:0119, G:0118, A:0117
2otl 08092 Oph·Pout C:01844(OP2) 03656, 03671, 07882, 09387 A:01843 A:01845
2otl 08039 Oph·Pout U:0115(OP2) 03977, 05121, 07796, 09917 G:0112 A:0114 A:0119, G:0118
2otl 08084 Oph·Pout A:01742(OP2) 03646, 07828, 09250, 09375, 09757 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
2otl 08068 Oph·Pout A:02568(OP2) 03764, 04844, 07873, 09740, E5607 G:02567 A:02569, A:02568
2qal A2025 Oph·Pout C:A934(OP1) A2026, A2027, A2028, A2029, A2030 U:A1345
2qal A2322 Oph·Pout G:A111(OP2) A2323, A2324, A2325, A2326, A2327 C:A110 G:A112, G:A111
2qal A2213 Oph·Pout A:A1433(OP2) A2214, A2215, A2216, A2217, A2218 A:A1434 A:A1434, G:A1435
2qal A2170 Oph·Pout A:A572(OP1) A2171, A2172, A2173, A2174, A2175 A:A573 A:A819
2qal A2288 Oph·Pout G:A100(OP2) A2289, A2290, A2291, A2292, A2293 A:A101 G:A64, G:A100, A:A101
2qal A2316 Oph·Pout C:A352(OP2) A2317, A2318, A2319, A2320, A2321 G:A354 G:A331, C:A352, C:A330 C:A330, A:A59, G:A354
2qam B3394 Oph·Pout A:B1678(OP2) B3933, B3934, B3935, B3936, B3937 A:B1679 A:B1678, A:B1679
2qam B3276 Oph·Pout U:B567(OP1) B3835, B3836, B3837, B3838, B3839 G:B809 U:B810
2qam B3151 Oph·Pout A:B945(OP1) B3733, B3734, B3735, B3736, B3737 G:B831 G:B831, U:B832
2qam B3032 Oph·Pout G:B2588(OP2) B3638, B3639, B3640, C274, C275 A:B2589 A:B2589
2qam B3376 Oph·Pout A:B1664(OP2) B3918, B3919, B3920, B3921, B3922 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666
2qam B3124 Oph·Pout G:B1187(OP2) B3712, B3713, B3714, B3715, R128 C:B816 G:B1185 G:B818, G:B1187
2qan A2324 Oph·Pout C:A536(OP1) A2325, A2326, A2327, A2328, A2329 C:A504 C:A522
2qan A2334 Oph·Pout C:A352(OP2) A2335, A2336, A2337, A2338, A2339 G:A354 C:A330, C:A352 C:A330, A:A59, G:A354
2qan A2056 Oph·Pout C:A934(OP1) A2057, A2058, A2059, A2060, A2061 U:A1345
2qan A2239 Oph·Pout A:A1433(OP2) A2240, A2241, A2242, A2243, A2244 A:A1434 A:A1434, G:A1435

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>