`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 3v27



3V27 (3.1Å) -- RIBOSOME : Crystal structure of hpf bound to the 70s ribosome. this pdb entry contains coordinates for the 50s subunit of the 1st ribosome in the asu
List of all 256 Mg2+ binding sites in the PDB structure 3v27 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 13 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v27 A3458 Or A:A536(O2') A4462, A4463, A4464, A4465, N201
3v27 A3358 Or U:A2849(O2') A4060, A4061, A4062, A4063 A:A2850 G:A2864, U:A2865
3v27 A3491 Ob G:A2685(O6) A4605, A4606, A4607, A4608, A4609 G:A2686, U:A2684
3v27 A3547 Ob G:A2345(O6) A4858, A4859, A4860, A4861 G:A2371, G:A2372, G:A2370
3v27 A3344 Ob G:A1822(O6) A3998, A3999, A4000, A4001, A4002 U:A1796, A:A1821, G:A1823
3v27 A3336 Ob G:A82(O6) A3965, A3966, A3967, A3968, A3969 G:A81 G:A83
3v27 A3519 Ob U:A2419(O4) A4724, A4725, A4726, A4727, A4728 A:A2418
3v27 A3337 Ob G:A58(O6) A3970, A3971, A3972, A3973, A3974 G:A68, U:A59, U:A67
3v27 A3343 Ob G:A1814(O6) A3993, A3994, A3995, A3996, A3997 A:A1812, G:A1813 A:A1815, A:A1812, G:A1813
3v27 A3555 Ob G:A271(O6) A4894, A4895, A4896, A4897, A4898 A:A270 G:A271, G:A271, G:A271
3v27 A3509 Ob U:A2593(O4) A4683, A4684, A4685, D416, D417 G:A2592, C:A2591 G:A2592, A:A1971, G:A2599
3v27 A3596 Ob G:A1425(O6) A5052, A5053, A5054, A5055 G:A1424 G:A1426
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 A3369 Nb G:A2640(N7) A4103, A4104, A4105, A4106 A:A2639, G:A2640 G:A2638
3v27 A3501 Nb G:A307(N7) A4646, A4647, A4648, A4649, A4650 G:A309, U:A306, G:A307
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 A3312 2Nb G:A733(N7), A:A761(N7) A3869, A3870, A3871, A3872 C:A732, G:A733, G:A760, A:A761
3v27 A3348 Oph U:A1518(OP2) A4018, A4019, A4020, A4021 G:A1470, G:A1519, A:A1469
3v27 A3327 Oph G:A399(OP2) A3932, A3933, A3934, A3935 G:A372, G:A400

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>