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

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Representative site 1hr2:A5, See in JSmolMgRNA representative site for type OB-NB          Click on the image to toggle views

Site type: Ob·Nb

Schematic drawing for

MgRNA type OB-NB
List of all 26 Mg2+ binding sites with the site type Ob·Nb 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
1hr2 A5 Ob·Nb G:A163(N7), G:A164(O6) A328, A329, A330, A331 U:A162, G:A163 U:A177 A:A178, U:A177
1hr2 B6 Ob·Nb G:B163(N7), G:B164(O6) B332, B333, B334, B335 U:B162, G:B163 A:B178, U:B177
3zgz B1078 Ob·Nb G:B45(O6) B2063, B2064, B2065, B2066 G:B45 G:B46, G:B21
4kj8 A1631 Ob·Nb G:A324(O6) A1839, A1842 G:A324
4ji5 A1636 Ob·Nb G:A324(N7) A1865, A1866, A1867, T201
4duz A1665 Ob·Nb G:A362(N7) A2018, A2019, A2020, A2021 G:A361
4nxm A1685 Ob·Nb G:A362(N7) A2040, A2041, A2042, A2043
4ji2 A1685 Ob·Nb G:A362(O6) A2038, A2039, A2040, A2041 G:A361
4ji4 A1706 Ob·Nb G:A1370(O6) A2073, A2074, A2075 U:A1372
2qov B2932 Ob·Nb G:B1371(N7) B3148, B3149, B3150, B3151 G:B1358, C:B1357, G:B1371 G:B1358
3ofq A3014 Ob·Nb G:A1601(N7), U:A1602(O4) A3539, A3540, A3541, A3542 G:A1601, C:A1600, A:A1342
4too A3045 Ob·Nb G:A1358(O6) A3396, A3397, A3398, A3399 G:A1358, G:A1371 G:A1371
3v2d A3124 Ob·Nb G:A2303(O6) A4025, A4026, A4027, A4028 G:A2302
4qcq A3163 Ob·Nb G:A1432(O6) A4138, A4139, A4140, A4141 C:A1466 G:A1467
4nvy A3187 Ob·Nb G:A1432(O6) A4092, A4093, A4094, A4095 C:A1466 G:A1467
3v2f A3232 Ob·Nb A:A1632(N7), G:A1633(O6) A4037, A4038, A4039, A4040 A:A1632, A:A1631 A:A1631, A:A1762
3v25 A3284 Ob·Nb A:A1632(N7), G:A1633(O6) A3689, A3690, A3691, A3692 A:A1631, A:A1632 G:A1682 C:A1631
4dhc A3375 Ob·Nb G:A2592(N7), U:A2593(O4) A3787, A3788, A3789, A3790 C:A2591, G:A2592
3v29 A3381 Ob·Nb A:A1632(N7), G:A1633(O6) A3936, A3937, A3938, A3939 A:A1632, A:A1631 G:A1682, C:A1631 A:A1631, C:A1631, G:A1635
4qcp A3464 Ob·Nb A:A1632(N7), G:A1633(O6) A4584, A4585, A4586, A4587 A:A1632, A:A1631 C:A1631, A:A1631, A:A1762
4qct A3472 Ob·Nb A:A1632(N7), G:A1633(O6) A4593, A4594, A4595, A4596 A:A1632, A:A1631 C:A1631, A:A1631, A:A1762
4dha A3507 Ob·Nb G:A2303(O6) A4088, A4089, A4090, A4091 G:A2302
4qcn A3574 Ob·Nb A:A1679(N7), G:A1680(O6) A4923, A4924, A4925, A4926 A:A1679, A:A1678 C:A1677, A:A1678, A:A1793
4qcr A3596 Ob·Nb A:A1679(N7), G:A1680(O6) A4941, A4942, A4943, A4944 A:A1679, A:A1678 C:A1677, G:A1682, A:A1678, A:A1793
4dha A3677 Ob·Nb G:A2685(N7) A4663, A4664, A4665, A4666 G:A2686, U:A2684

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>