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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 3v29



3V29 (3.1Å) -- RIBOSOME : Crystal structure of hpf bound to the 70s ribosome. this entry contains the 50s subunit of the 2nd molecule in the asu.
List of all 154 Mg2+ binding sites in the PDB structure 3v29 in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 1 of 8 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v29 A3330 Ob U:A2593(O4) A3747, A3748, A3749, D1 G:A2592, C:A2591 A:A1971, G:A2599, G:A2592
3v29 A3454 Ob G:A240(O6) A4234, A4235, A4236, A4237 A:A256 U:A239
3v29 A3451 Ob G:A928(O6) A4220, A4221, A4222, A4223, A4224 G:A848, U:A847, G:A927 A:A926, G:A927
3v29 A3542 Ob C:A1607(O2) A4559, A4560, A4561, A4562 G:A1619
3v29 A3434 Ob G:A2371(O6) A4157, A4158, A4159, A4160, A4161 G:A2345, G:A2372
3v29 A3563 Ob G:A1382(O6) A4627, A4628, A4629, A4630 G:A1347, G:A1380, G:A1381 G:A1381
3v29 A3365 Ob G:A530(O6) A3874, A3875, A3876, A3877 U:A2022, G:A2023
3v29 A3331 Nb G:A298(N7) A3750, A3751, A3752, A3753 G:A298, G:A338 C:A297
3v29 A3526 Nb G:A2375(N7) A4492, A4493, A4494, A4495, A4496 A:A2377
3v29 A3362 Nb G:A2002(N7) A3863, A3864, A3865, A3866, A3867 G:A2002 G:A1653, G:A2003
3v29 A3359 Nb G:A2032(N7) A3854, A3855, A3856, A3857, A3858 G:A2032 A:A2453, C:A2055, C:A2499, A:A2572, G:A2454, U:A2500
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
3v29 A3343 2Nb G:A733(N7), A:A761(N7) A3788, A3789, A3790, A3791 A:A761, G:A733, C:A732
3v29 A3369 Oph C:A574(OP1) A3890, A3891, A3892, A3893, A3894 G:A2018, G:A2035
3v29 A3507 Oph A:A311(OP2) A4423, A4424, A4425, A4426 G:A304, U:A305
3v29 A3499 Oph U:A943(OP2) A4389, P304, P305, P306
3v29 A3495 Oph A:A800(OP1) A4373, A4374, A4375, A4376, A4377 G:A799 C:A192, A:A191, A:A800
3v29 A3471 Oph A:A2598(OP1) A4295, D3, D4, D5, D6
3v29 A3379 Oph A:A1342(OP2) A3929, A3930, A3931, X101, X102 U:A1602, G:A1601
3v29 A3366 Oph G:A2035(OP1) A3878, A3879, A3880, A3881, A3882 G:A2037, G:A2024, G:A2038

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>