`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 2qou:A1560, See in JSmolMgRNA representative site for type NB Click on the image to toggle views


Site type: Nb

Schematic drawing for
Nb
MgRNA type NB
List of all 284 Mg2+ binding sites with the site type 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"
Page 6 of 12 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3ox0 A123 Nb G:A50(N7) A157, A158, A159, A160, A161 G:A49, A:B52 G:A49
3ox0 A125 Nb G:A62(N7) A162, A163, A164, A165, A166 U:A61, C:A39, G:A62
3oxb B112 Nb G:B62(N7) B131, B132, B133, B134, B135 C:B39, G:B62, A:B63
3oxb A131 Nb G:A50(N7) A154, A155, A156, A157, A158 G:A49, A:B52 G:A49
3oxd A130 Nb G:A50(N7) A168, A169, A170, A171, A172 G:A49, A:B52 G:A49
3oxd B113 Nb G:B62(N7) B141, B142, B143, B144, B145 C:B39, G:B62
3oxj A112 Nb G:A50(N7) A144, A145, A146, A147, A148 G:A49, A:B52 G:A49
3v23 A3354 Nb G:A974(N7) A4090, A4091, A4092, A4093, A4094 C:A971 G:A1186, G:A972
3v23 A3539 Nb G:A2857(N7) A4755, A4756, A4757, A4758, A4759 G:A2859
3v23 A3432 Nb G:A2032(N7) A4383, A4384, A4385, A4386, A4387 G:A2032 G:A2454 C:A2055, C:A2499, A:A2453, U:A2500, A:A2572, G:A2454
3v23 A3324 Nb G:A2002(N7) A3975, A3976, A3977, A3978, A3979 G:A2002 G:A2003
3v24 A1648 Nb G:A324(N7) A1741, A1742, T201, T202 G:A324
3v25 A3272 Nb G:A2032(N7) A3639, A3640, A3641, A3642, A3643 G:A2032 G:A2454 A:A2453, C:A2055, C:A2499, A:A2572, G:A2454, U:A2500
3v25 A3261 Nb G:A298(N7) A3598, A3599, A3600, Y301 C:A297, G:A298
3v26 A1708 Nb G:A362(N7) A1933, A1934, A1935, L201, L202 G:A361 G:A361
3v27 A3369 Nb G:A2640(N7) A4103, A4104, A4105, A4106 A:A2639, G:A2640 G:A2638
3v27 A3346 Nb G:A2002(N7) A4008, A4009, A4010, A4011, A4012 G:A2002 G:A2003
3v27 B214 Nb G:B103(N7) B311, B312, B313, B314, B315 A:B102, G:B103, A:B73 A:B102, G:B72
3v27 A3485 Nb G:A2032(N7) A4576, A4577, A4578, A4579, A4580 G:A2032 C:A2055, A:A2572, G:A2454, C:A2499, U:A2500, A:A2453
3v27 A3501 Nb G:A307(N7) A4646, A4647, A4648, A4649, A4650 G:A309, U:A306, G:A307
3v28 A1739 Nb G:A324(N7) A1976, A1977, A1978, T201, T202 U:A323
3v29 A3331 Nb G:A298(N7) A3750, A3751, A3752, A3753 G:A298, G:A338 C:A297
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 A3362 Nb G:A2002(N7) A3863, A3864, A3865, A3866, A3867 G:A2002 G:A1653, G:A2003
3v29 A3526 Nb G:A2375(N7) A4492, A4493, A4494, A4495, A4496 A:A2377

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>