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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qov:B2933, See in JSmolMgRNA representative site for type OP-3PO Click on the image to toggle views


Site type: Oph·3Pout

Schematic drawing for
Oph·3Pout
MgRNA type OP-3PO
List of all 867 Mg2+ binding sites with the site type Oph·3Pout 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 1 of 35 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tpf A3074 Oph·3Pout A:A2518(OP2) A3533, A3534, A3535, A3536, A3537 U:A2519, C:A2540, A:A2541 C:A2517 A:A2541
4tpf A3044 Oph·3Pout G:A1333(OP2) A3388, A3389, A3390, A3391, A3392 U:A1313, G:A1334, G:A1332 C:A1335
4tpf A3070 Oph·3Pout A:A2270(OP2) A3512, A3513, A3514, A3515, A3516 G:A2269, A:A2267, G:A2271 A:A2270, G:A2271, U:A2272
4tpf A3131 Oph·3Pout A:A1009(OP2) A3777, A3778, A3779, A3780 A:A1010, C:A1006, C:A1007 A:A1010
4tpf A3122 Oph·3Pout G:A1828(OP2) A3742, A3743, A3744, A3745, C306 U:A1827, G:A1972, C:A1788 G:A1828
4tpf A3066 Oph·3Pout A:A2062(OP1) A3493, A3494, A3495, A3496, A3497 G:A2061, C:A2443, G:A2444 G:A2444, G:A2445
4tpf A3050 Oph·3Pout U:A1647(OP2) A3415, A3416, A3417, A3418, A3419 A:A1272, A:A1618, C:A1617 C:A1646, A:A1616 G:A1271
4tpf A3033 Oph·3Pout C:A946(OP2) A3344, A3345, A3346, A3347 A:A945, G:A822, C:A823 A:A821, C:A944
4tpf A3006 Oph·3Pout A:A218(OP2) A3223, A3224, A3225, A3226, A3227 A:A217, U:A427, A:A428 A:A218, A:A219, G:A220
4tpe A1619 Oph·3Pout C:A578(OP1) A1786, A1787, A1788, A1789, A1790 C:A817, C:A576, U:A820 G:A575
4tpd A3043 Oph·3Pout G:A1333(OP2) A3392, A3393, A3394, A3395, A3396 C:A1314, G:A1334, G:A1332 G:A1334, G:A1333
4tpd A3007 Oph·3Pout G:A297(OP2) A3228, A3229, A3230, A3231, A3232 U:A296, G:A298, G:A338 G:A298, G:A297
4tpd A3118 Oph·3Pout G:A862(OP2) A3730, A3731, A3732, A3733, A3734 A:A861, A:A910, A:A863 G:A862, A:A863
4tpd A3073 Oph·3Pout A:A2518(OP2) A3537, A3538, A3539, A3540, A3541 U:A2519, C:A2540, A:A2541 C:A2517 A:A2541
4tpd A3009 Oph·3Pout G:A450(OP2) A3238, A3239, A3240, A3241, E301 U:A451, G:A452, A:A449
4tpd A3056 Oph·3Pout G:A1828(OP1) A3454, A3455, A3456, A3457, A3458 A:A1773, G:A1973, A:A1772
4tpd A3040 Oph·3Pout A:A2005(OP1) A3384, A3385, A3386, A3387 A:A1268, A:A1269, C:A2006 A:A1269
4tpc A1609 Oph·3Pout C:A578(OP1) A1739, A1740, A1741, A1742, A1743 C:A576, C:A817, U:A820 G:A575
4tpb A3065 Oph·3Pout A:A2062(OP1) A3492, A3493, A3494, A3495, A3496 G:A2061, C:A2443, G:A2444 G:A2444
4tpb A3130 Oph·3Pout A:A1009(OP2) A3776, A3777, A3778, A3779 A:A1010, C:A1006, C:A1007 A:A1010
4tpb A3121 Oph·3Pout G:A1828(OP2) A3741, A3742, A3743, A3744, C306 U:A1827, G:A1972, C:A1788 G:A1828
4tpb A3049 Oph·3Pout U:A1647(OP2) A3415, A3416, A3417, A3418, A3419 A:A1618, A:A1272, C:A1617 A:A1616, C:A1646 G:A1271
4tpb A3118 Oph·3Pout A:A1938(OP2) A3726, A3727, A3728, A3729, A3730 A:A1937, C:A1957, C:A1958 G:A1770
4tpb A3006 Oph·3Pout A:A218(OP2) A3223, A3224, A3225, A3226, A3227 A:A217, U:A427, A:A428 A:A218, A:A219, G:A220
4tpb A3054 Oph·3Pout C:A1774(OP1) A3440, A3441, A3442, A3443, A3444 U:A1775, A:A1787, A:A1786 A:A1772 G:A1776, C:A1788, A:A1789, A:A1787

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>