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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qbd:A2237, See in JSmolMgRNA representative site for type OP-OB Click on the image to toggle views


Site type: Oph·Ob

Schematic drawing for
Oph·Ob
MgRNA type OP-OB
List of all 554 Mg2+ binding sites with the site type Oph·Ob 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"
Page 6 of 23 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2avy A1592 Oph·Ob A:A195(OP2) U:A180(O4) A1840, A1841, A1842, A1843 C:A194, A:A179 A:A181, A:A179
2aw4 B2976 Oph·Ob A:B2033(OP1) U:B2028(O4) B3352, B3353, B3354, B3355
2aw4 B2943 Oph·Ob A:B453(OP1) G:B450(O6) B3197, B3198, B3199, B3200 A:B454, A:B449 A:B449
2aw4 B2919 Oph·Ob C:B2248(OP2) U:B2249(O4) B3080, B3081, B3082, B3083 C:B2066, A:B2247, G:B2253
2aw4 B2996 Oph·Ob A:B1342(OP2) U:B1602(O4) B3430, B3431, B3432, B3433 G:B1601
2aw7 A1583 Oph·Ob G:A558(OP1) G:A299(O6) A1805, A1806, A1807, A1808 A:A560 G:A297 A:A300, A:A298, G:A566
2aw7 A1596 Oph·Ob A:A195(OP2) U:A180(O4) A1866, A1867, A1868, A1869 C:A194, A:A179 A:A181, A:A179
2aw7 A1585 Oph·Ob A:A533(OP1) U:A516(O4) A1814, A1815, A1816, A1817 A:A532 G:A517, G:A515
2aw7 A1589 Oph·Ob U:A1095(OP2) G:A1108(O6) A1832, A1833, A1834, A1835 C:A1096 G:A1094 C:A1109
2awb B2966 Oph·Ob A:B453(OP1) G:B450(O6) B3314, B3315, B3316, B3317 A:B454, A:B471 A:B449
2awb B2982 Oph·Ob C:B2248(OP2) U:B2249(O4) B3388, B3389, B3390, B3391 C:B2066, G:B2253 A:B2247
2awb B2997 Oph·Ob A:B1342(OP2) U:B1602(O4) B3442, B3443, B3444, B3445 G:B1601
2i2p A1586 Oph·Ob U:A1095(OP2) G:A1108(O6) A1814, A1815, A1816, A1817 C:A1096 C:A1109
2i2p A1593 Oph·Ob A:A195(OP2) U:A180(O4) A1849, A1850, A1851, A1852 C:A194, A:A179 A:A181
2i2p A1580 Oph·Ob G:A558(OP1) G:A299(O6) A1787, A1788, A1789, A1790 A:A560 G:A297 A:A300, G:A566
2i2p A1582 Oph·Ob A:A533(OP1) U:A516(O4) A1796, A1797, A1798, A1799 G:A515, G:A517
2i2t B2996 Oph·Ob A:B1342(OP2) U:B1602(O4) B3440, B3441, B3442, B3443 G:B1601
2i2t B2919 Oph·Ob C:B2248(OP2) U:B2249(O4) B3090, B3091, B3092, B3093 C:B2066, A:B2247, G:B2253
2i2t B2943 Oph·Ob A:B453(OP1) G:B450(O6) B3207, B3208, B3209, B3210 A:B449
2i2u A1564 Oph·Ob A:A533(OP1) U:A516(O4) A1700, A1701, A1702, A1703 G:A517, G:A515
2i2u A1562 Oph·Ob G:A558(OP1) G:A299(O6) A1691, A1692, A1693, A1694 A:A560 G:A297 A:A300, G:A566
2i2u A1570 Oph·Ob A:A195(OP2) U:A180(O4) A1728, A1729, A1730, A1731 C:A194, A:A179 A:A181
2i2v B2997 Oph·Ob A:B1342(OP2) U:B1602(O4) B3450, B3451, B3452, T953 G:B1601
2i2v B2982 Oph·Ob C:B2248(OP2) U:B2249(O4) B3397, B3398, B3399, B3400 A:B2247, C:B2066, G:B2253
2i2v B2966 Oph·Ob A:B453(OP1) G:B450(O6) B3321, B3322, B3323, B3324 A:B449

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>