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

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Representative site 2i2u:A1552, See in JSmolMgRNA representative site for type 5BO            Click on the image to toggle views


Site type: 5Bout

Schematic drawing for
5Bout

MgRNA type 5BO
List of all 45 Mg2+ binding sites with the site type 5Bout 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
1vs6 B2906 5Bout B3020, B3021, B3022, B3023, B3024, B3025 U:B2074, U:B2243, U:B2075, G:B2238, G:B2242
1vs7 A1563 5Bout A1695, A1696, A1697, A1698, A1699, A1700 U:A593, U:A594, G:A592, G:A645, G:A646
1vt2 A2972 5Bout A3362, A3363, A3364, A3365, A3366, A3367 G:A2238, G:A2242, A:A2241, U:A2243, U:A2074
2aw4 B2906 5Bout B3020, B3021, B3022, B3023, B3024, B3025 U:B2074, U:B2243, U:B2075, G:B2238, G:B2242
2aw7 A1562 5Bout A1696, A1697, A1698, A1699, A1700, A1701 U:A593, U:A594, G:A645, G:A592, G:A646
2i2u A1552 5Bout A1640, A1641, A1642, A1643, A1644, A1645 U:A593, U:A594, G:A592, G:A645, G:A646
2qao B3001 5Bout B3619, B3620, B3621, B3622, B3623, B3624 G:B2238, G:B2242, A:B2241, U:B2074, U:B2243
2qbg B2905 5Bout B3016, B3017, B3018, B3019, B3020, B3021 G:B2238, G:B2242, A:B2241, U:B2074, U:B2243
2qbj A1557 5Bout A1671, A1672, A1673, A1674, A1675, A1676 G:A1050, G:A1207, U:A1205, G:A1048, C:A1051
2qoz B2906 5Bout B3516, B3517, B3518, B3519, B3520, B3521 U:B2074, U:B2243, G:B2242, U:B2075, G:B2238
2z4m A1558 5Bout A1671, A1672, A1673, A1674, A1675, A1676 G:A1050, G:A1207, C:A1051, U:A1205, G:A1048
3df4 B3001 5Bout B4002, B4003, B4004, B4005, B4006, B4007 G:B2238, G:B2242, A:B2241, U:B2243, U:B2075
3i1t A2972 5Bout A3362, A3363, A3364, A3365, A3366, A3367 A:A2077, G:A2238, G:A2242, U:A2243, A:A2241
3i22 A2971 5Bout A3361, A3362, A3363, A3364, A3365, A3366 A:A2077, G:A2238, G:A2242, U:A2243, A:A2241
3ivk M122 5Bout M138, M139, M140, M141, M142, M143 A:M97, G:M91, G:M92, U:M93, U:M94
3ivk M134 5Bout M182, M183, M184, M185, M186, M187 G:M77, U:M36, G:M37, C:M38, G:M78
3ivk C134 5Bout C183, C184, C185, C186, C187, C188 G:C77, U:C36, G:C37, C:C38, G:C78
3ofc A2967 5Bout A3339, A3340, A3341, A3342, A3343, A3344 A:A2241, G:A2242, U:A2075, U:A2074, U:A2243
3r8s A2995 5Bout A3522, A3523, A3524, A3525, A3526, A3527 U:A1411, G:A1410, A:A1591, U:A1409, A:A1590
3v23 A3490 5Bout A4607, A4608, A4609, A4610, A4611, A4612 U:A534, G:A558, G:A533, G:A559, U:A557
3v29 A3567 5Bout A4642, A4643, A4644, A4645, A4646 U:A2075, G:A2238, A:A2241, G:A2242, U:A2074
3v29 A3523 5Bout A4474, A4475, A4476, A4477, A4478, A4479 C:A540, C:A541, G:A552, G:A553, U:A554
3v2f A3306 5Bout A4277, A4278, A4279, A4280, A4281 U:A597, C:A661, C:A595, G:A596, G:A660
4bpe A5043 5Bout A2222, A2223, A2224, A2233, A2234, A2307 G:A1614, U:A1711, C:A1616, G:A1710, A:A1708
4dhc A3419 5Bout A3922, A3923, A3924, A3925, A3926 G:A2455, C:A2456, G:A2495, U:A2457, G:A2494

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>