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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3r8s:A2932, See in JSmolMgRNA representative site for type OP-NB Click on the image to toggle views


Site type: Oph·Nb

Schematic drawing for
Oph·Nb
MgRNA type OP-NB
List of all 134 Mg2+ binding sites with the site type Oph·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 4 of 6 | | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tp1 A3030 Oph·Nb U:A810(OP1) A:A1253(N7) A3336, A3337, A3338, A3339 U:A811 C:A565, G:A1252
4tox A3030 Oph·Nb U:A810(OP1) A:A1253(N7) A3332, A3333, A3334, A3335 U:A811 C:A565, G:A1252
4tp7 A3030 Oph·Nb U:A810(OP1) A:A1253(N7) A3328, A3329, A3330, A3331 U:A811 C:A565, G:A1252
4gau A3032 Oph·Nb C:A1153(OP2) G:A1154(N7) A3357, A3358, A3359, Q301 U:A999, C:A998, G:A1154
4gau A3075 Oph·Nb A:A422(OP2) G:A370(N7) A3559, A3560, A3561, A3562 G:A370, A:A423 G:A424
4tpb A3079 Oph·Nb A:A422(OP2) G:A370(N7) A3553, A3554, A3555, A3556 A:A423, G:A370 A:A270, A:A423, G:A424
4tp3 A3079 Oph·Nb A:A422(OP2) G:A370(N7) A3553, A3554, A3555, A3556 A:A423, G:A370 A:A270, A:A423
4tp9 A3080 Oph·Nb A:A422(OP2) G:A370(N7) A3560, A3561, A3562, A3563 G:A370, A:A423 U:A369 A:A423
4tp1 A3080 Oph·Nb A:A422(OP2) G:A370(N7) A3561, A3562, A3563, A3564 G:A370, A:A423 A:A423
4tom A3128 Oph·Nb U:A511(OP2) G:A512(N7) A3770, A3771, A3772 C:A510
2qao B3257 Oph·Nb U:B810(OP1) A:B1253(N7) B3830, B3831, B3832, B3833 U:B811 C:B565
2qbc B3257 Oph·Nb U:B810(OP1) A:B1253(N7) B3830, B3831, B3832, B3833 U:B811 C:B565
3df4 B3257 Oph·Nb U:B810(OP1) A:B1253(N7) B4258, B4259, B4260, B4261 U:B811 C:B565
3v27 A3314 Oph·Nb U:A511(OP2) G:A512(N7) A3876, A3877, A3878, A3879 C:A510
3v25 A3328 Oph·Nb A:A1189(OP2) G:A1190(N7) A3849, A3850, A3851, P304 G:A1190
3v23 A3336 Oph·Nb A:A2639(OP2) G:A2640(N7) A4024, A4025, A4026, A4027 G:A2640 G:A2641
3df2 B3344 Oph·Nb U:B810(OP1) A:B1253(N7) B4345, B4346, B4347, B4348 U:B811 C:B565
2qam B3344 Oph·Nb U:B810(OP1) A:B1253(N7) B3892, B3893, B3894, B3895 U:B811 C:B565
2qba B3344 Oph·Nb U:B810(OP1) A:B1253(N7) B3889, B3890, B3891, B3892 U:B811 C:B565
2qbe B3344 Oph·Nb U:B810(OP1) A:B1253(N7) B3889, B3890, B3891, B3892 U:B811 C:B565
3v23 A3352 Oph·Nb A:A981(OP1) G:A979(N7) A4083, A4084, A4085, A4086 C:A982, G:A978, G:A979
3v23 A3400 Oph·Nb U:A810(OP1) A:A1253(N7) A4270, A4271, A4272, A4273 U:A811
3v23 A3416 Oph·Nb A:A1189(OP2) G:A1190(N7) A4328, A4329, A4330, A4331 G:A1190, U:A1188
3v2f A3418 Oph·Nb A:A2639(OP2) G:A2640(N7) A4611, A4612, A4613, A4614 G:A2640 G:A2638 G:A2641
3v29 A3464 Oph·Nb A:A2639(OP2) G:A2640(N7) A4271, A4272, A4273, A4274 G:A2640 G:A2638 G:A2641

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>