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

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Representative site 1vs6:B2982, See in JSmolMgRNA representative site for type 2PO-RO-3BO     Click on the image to toggle views


Site type: 2Pout·Rout·3Bout

Schematic drawing for
2Pout·Rout·3Bout

MgRNA type 2PO-RO-3BO
List of all 39 Mg2+ binding sites with the site type 2Pout·Rout·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"
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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
1feu B311 2Pout·Rout·3Bout B10, B12, B13, B17, B251 U:B74, G:B75 A:C99 G:B76, G:B75, U:B77
1vs6 B2956 2Pout·Rout·3Bout B3260, B3261, B3262, B3263, B3264, B3265 A:B1253, A:B582 C:B1251 G:B583, C:B584, A:B582
1vs6 B2982 2Pout·Rout·3Bout B3382, B3383, B3384, B3385, B3386, B3387 A:B2386, G:B2325 U:B2384 C:B2326, A:B2386, U:B2387
2aw4 B2982 2Pout·Rout·3Bout B3378, B3379, B3380, B3381, B3382, B3383 A:B2386, G:B2325 U:B2384 C:B2326, A:B2386, U:B2387
2i2t B2956 2Pout·Rout·3Bout B3268, B3269, B3270, B3271, B3272, B3273 A:B1253, A:B582 C:B1251 G:B583, C:B584, A:B582
2qam B3450 2Pout·Rout·3Bout B3979, B3980, B3981, B3982, B3983, B3984 A:B2386, G:B2325 U:B2384 C:B2326, A:B2386, U:B2387
2qba B3450 2Pout·Rout·3Bout B3976, B3977, B3978, B3979, B3980, B3981 A:B2386, G:B2325 U:B2384 C:B2326, A:B2386, U:B2387
2qbe B3302 2Pout·Rout·3Bout B3857, B3858, B3859, B3860, B3861, B3862 A:B1253, A:B582 C:B1251 G:B583, C:B584, A:B582
2qbk B2959 2Pout·Rout·3Bout B3276, B3277, B3278, B3279, B3280, B3281 A:B582, A:B1253 C:B1251 A:B582, G:B583, G:B585
2qoz B2956 2Pout·Rout·3Bout B3752, B3753, B3754, B3755, B3756, B3757 A:B1253, A:B582 C:B1251 G:B583, C:B584, G:B585
2qp1 B2959 2Pout·Rout·3Bout B3783, B3784, B3785, B3786, B3787, B3788 A:B582, A:B1253 C:B1251 C:B584, A:B582, G:B585
3df2 B3450 2Pout·Rout·3Bout B4451, B4452, B4453, B4454, B4455, B4456 A:B2386, G:B2325 U:B2384 G:B2325, C:B2326, A:B2386
3i1n A2920 2Pout·Rout·3Bout A3124, A3125, A3126, A3127, A3128, Q226 A:A1253, A:A582 C:A1251 G:A583, C:A584, A:A582
3i1r A2985 2Pout·Rout·3Bout A3418, A3419, A3420, A3421, A3422, A3423 A:A574, C:A2055 A:A2054 U:A2034, G:A2035, A:A574
3i22 A2905 2Pout·Rout·3Bout A3043, A3044, A3045, A3046, A3047, A3048 A:A28, A:A447 A:A447 G:A473, G:A474, G:A30
3i22 A2977 2Pout·Rout·3Bout A3388, A3389, A3390, A3391, A3392, A3393 U:A2387, A:A2386 U:A2384 C:A2326, A:A2386, U:A2387
3oar A1574 2Pout·Rout·3Bout A1767, A1768, A1769, A1770, A1771 C:A352, G:A354 C:A352 C:A330, G:A354, A:A59
3ofd A2977 2Pout·Rout·3Bout A3386, A3387, A3388, A3389, A3390, A3391 U:A2387, A:A2386 C:A2385 C:A2326, A:A2386, U:A2387
3ofq A2978 2Pout·Rout·3Bout A3388, A3389, A3390, A3391, A3392, A3393 U:A2387, A:A2386 C:A2385 C:A2326, G:A2389, U:A2387
3ofr A2920 2Pout·Rout·3Bout A3117, A3118, A3119, A3120, A3121, A3122 A:A1253, A:A582 C:A1251 G:A583, C:A584, A:A582
3ofz A2919 2Pout·Rout·3Bout A3114, A3115, A3116, A3117, A3118, Q118 A:A1253, A:A582 C:A1251 G:A583, C:A584, A:A582
3og0 A2976 2Pout·Rout·3Bout A3385, A3386, A3387, A3388, A3389, A3390 U:A2387, A:A2386 C:A2385 C:A2326, G:A2389, U:A2387
3orb A2920 2Pout·Rout·3Bout A3118, A3119, A3120, A3121, A3122, A3123 A:A1253, A:A582 C:A1251 G:A583, C:A584, A:A582
3r8s A2985 2Pout·Rout·3Bout A3474, A3475, A3476, A3477, A3478, A3479 A:A574, C:A2055 A:A2054 G:A2035, A:A574, U:A2034
3r8s A2920 2Pout·Rout·3Bout A3180, A3181, A3182, A3183, A3184, A3185 A:A1253, A:A582 C:A1251 G:A583, C:A584, A:A582

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>