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

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Representative site 2qoz:B2982, See in JSmolMgRNA representative site for type PO-3BO         Click on the image to toggle views


Site type: Pout·3Bout

Schematic drawing for
Pout·3Bout

MgRNA type PO-3BO
List of all 341 Mg2+ binding sites with the site type Pout·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"
Page 2 of 14 | | | 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
2i2p A1563 Pout·3Bout A1703, A1704, A1705, A1706, K165, K168 A:A781 G:A799, G:A800, U:A798
2i2t B2922 Pout·3Bout B3105, B3106, B3107, B3108, B3109, B3110 U:B1267 G:B2010, U:B2011, G:B2012
2i2t B2937 Pout·3Bout B3180, B3181, B3182, B3183, B3184, B3185 G:B649 C:B650, G:B651, U:B652
2i2t B2982 Pout·3Bout B3388, B3389, B3390, B3391, B3392, B3393 A:B2386 C:B2326, A:B2386, U:B2387
2i2t B3021 Pout·3Bout B3545, B3546, B3547, B3548, B3549, N768 G:B2004 G:B1651, G:B1649, A:B1650
2i2u A1546 Pout·3Bout A1611, A1612, A1613, A1614, A1615, A1616 G:A803 U:A772, G:A773, G:A771
2i2u A1554 Pout·3Bout A1652, A1653, A1654, A1655, A1656, A1657 A:A781 G:A800, U:A798, G:A799
2i2u A1553 Pout·3Bout A1646, A1647, A1648, A1649, A1650, A1651 G:A266 G:A257, G:A258, G:A259
2i2v B3022 Pout·3Bout B3546, B3547, B3548, B3549, B3550, N1068 G:B2004 G:B1651, G:B1649, A:B1650
2nz4 S9004 Pout·3Bout H14, H17, S9005, S9006, S9007, S9008 C:S52 G:S53, G:S54, A:S28
2nz4 R9002 Pout·3Bout G9016, G9017, R9019, R9020, R9021, R9022 C:R52 G:R53, A:R28, G:R54
2nz4 P9005 Pout·3Bout P9011, P9012, P9013, P9014, P9015, P9016 C:P52 A:P28, G:P54, G:P53
2qal A2084 Pout·3Bout A2085, A2087, A2088, A2089, N2086, N2090 A:A1360 C:A980, G:A1361, A:A1360
2qal A2122 Pout·3Bout A2123, A2124, A2125, A2126, A2127, A2128 A:A781 U:A798, G:A799, G:A800
2qao B3074 Pout·3Bout B3679, B3680, B3681, B3682, B3683, B3684 A:B2033 G:B2027, U:B2028, G:B2029
2qao B3133 Pout·3Bout B3727, B3728, B3729, B3730, B3731, B3732 A:B616 G:B617, G:B618, G:B619
2qao B3308 Pout·3Bout B3871, B3872, B3873, B3874, B3875, B3876 A:B2386 C:B2326, U:B2387, A:B2386
2qb9 A2084 Pout·3Bout A2428, A2429, A2430, A2431, A2432, N2090 A:A1360 C:A980, G:A1361, A:A1360
2qb9 A2115 Pout·3Bout A2451, A2452, A2453, A2454, A2455, A2456 G:A266 G:A257, G:A258, G:A259
2qb9 A2122 Pout·3Bout A2457, A2458, A2459, A2460, A2461, A2462 A:A781 U:A798, G:A799, G:A800
2qba B3309 Pout·3Bout B3865, B3866, B3867, B3868, B3869, B3870 A:B616 G:B618, G:B619, G:B617
2qbb A2141 Pout·3Bout A2484, A2485, A2486, A2487, A2488, A2489 G:A266 G:A257, G:A258, G:A259
2qbb A2148 Pout·3Bout A2490, A2491, A2492, A2493, A2494, A2495 A:A781 G:A800, U:A798, G:A799
2qbc B3074 Pout·3Bout B3680, B3681, B3682, B3683, B3684, B3685 A:B2033 G:B2027, U:B2028, G:B2029
2qbd A2044 Pout·3Bout A2045, A2046, A2047, A2048, A2049, A2050 A:A315 G:A318, G:A319, A:A320

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>