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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3i20:A2925, See in JSmolMgRNA representative site for type OB Click on the image to toggle views


Site type: Ob

Schematic drawing for
Ob
MgRNA type OB
List of all 468 Mg2+ binding sites with the site type 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"
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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
3i1o A3 Ob G:A362(O6) A1583, A1584, A1585, A1586, A1587 G:A361 G:A361
3i1p A3000 Ob U:A2419(O4) A3490, A3491, A3492, A3493, 3611 C:A2417
3i1p A2995 Ob G:A1125(O6) A3467, A3468, A3469, A3470, A3471 A:A1028 G:A1124
3i1p A3033 Ob U:A2593(O4) A3612, A3613, A3614, C741, C745 G:A2592 G:A2592
3i1p B119 Ob U:B95(O4) B627, B628, B629, B630, B631 U:B80
3i1p A2926 Ob U:A746(O4) A3154, A3155, A3156, D257, D259 U:A744, C:A2611, C:A2610 G:A745
3i1p A3014 Ob U:A1602(O4) A3539, A3540, A3541, T665 G:A1601, C:A1600, A:A1342
3i1q A1554 Ob G:A1417(O6) A1670, A1671, A1672, A1673, A1674 G:A1416, G:A1482
3i1q A1564 Ob G:A299(O6) A1716, A1717, A1718, A1719 G:A558, A:A560 G:A297 A:A298, G:A566
3i1r B122 Ob U:B95(O4) B656, B657, B658, B659, V660 G:B96
3i1r A2925 Ob U:A746(O4) A3145, A3146, A3147, A3148, A3149 U:A744, C:A2611, C:A2610 G:A745
3i1r A2992 Ob G:A1125(O6) A3452, A3453, A3454, A3455, A3456 A:A1028 A:A1126
3i1r A3035 Ob U:A2593(O4) A3636, A3637, A3638, C776, C778 G:A2592 G:A2592, C:A2594
3i1r A3003 Ob U:A2419(O4) A3513, A3514, 3626, 3629, 3630 A:A2418
3i1r A2975 Ob C:A2499(O2) A3375, A3376, A3377, A3378, A3379 G:A2032 C:A2055, U:A2500, G:A2032, G:A2454
3i1s A1550 Ob G:A1417(O6) A1668, A1669, A1670, A1671, A1672 G:A1482
3i1t A3032 Ob U:A2593(O4) A3614, A3615, A3616, C741, C745 G:A2592, C:A2591 C:A2594, G:A2592
3i1t A3000 Ob U:A2419(O4) A3493, A3494, A3495, A3496, 3611
3i1t A2995 Ob G:A1125(O6) A3471, A3472, A3473, A3474, A3475 A:A1028 G:A1124
3i1t A2926 Ob U:A746(O4) A3154, A3155, A3156, A3157, D259 C:A2611, C:A2610 G:A745
3i1t A3014 Ob U:A1602(O4) A3542, A3543, A3544, T665 G:A1601, C:A1600
3i1z A1554 Ob G:A1417(O6) A1672, A1673, A1674, A1675, A1676 G:A1415 G:A1416, G:A1482
3i20 A2925 Ob U:A746(O4) A3147, A3148, A3149, A3150, A3151 U:A744, C:A2611 G:A745
3i20 A2975 Ob C:A2499(O2) A3375, A3376, A3377, A3378, A3379 G:A2032 C:A2055, U:A2500, G:A2032, G:A2454
3i20 A2992 Ob G:A1125(O6) A3452, A3453, A3454, A3455, A3456 A:A1028

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>