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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 5 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
4dha A3791 Oph·Nb U:A810(OP1) A:A1253(N7) A5050, A5051, A5052, A5053 U:A811 C:A565, G:A1252
4dha A3819 Oph·Nb A:A1189(OP2) G:A1190(N7) A5153, A5154, A5155, A5156 G:A1190, U:A1188
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
4ji0 A1623 Oph·Nb A:A766(OP2) C:A812(N3) A1949, A1950, A1951, A1952 U:A813, C:A811
4ji2 A1623 Oph·Nb A:A766(OP2) C:A812(N3) A1951, A1952, A1953, A1954 U:A813, C:A811
4ji3 A1637 Oph·Nb G:A758(OP2) A1970, A1971, A1972 U:A757 G:A581
4ji8 A1619 Oph·Nb A:A766(OP2) C:A812(N3) A2042, A2043, A2044, A2045 U:A813, C:A811
4kj7 A3028 Oph·Nb U:A810(OP1) A:A1253(N7) A3330, A3331, A3332 U:A811 C:A565
4pec A3009 Oph·Nb A:A453(OP1) G:A450(N7) A3239, A3240, A3241, A3242 A:A449 A:A449
4pec A3028 Oph·Nb U:A810(OP1) A:A1253(N7) A3330, A3331, A3332, A3333 U:A811 C:A565
4qcn A3734 Oph·Nb A:A1234(OP2) G:A1235(N7) A5258, A5259, A5260, A5261 G:A1235, U:A1233
4qcr A3761 Oph·Nb A:A1234(OP2) G:A1235(N7) A5289, A5290, P310, P311 U:A1233, G:A1235
4qct A3574 Oph·Nb A:A53(OP2) G:A54(N7) A4805, A4806, A4807, A4808 A:A52
4tom A3128 Oph·Nb U:A511(OP2) G:A512(N7) A3770, A3771, A3772 C:A510
4tom A3028 Oph·Nb U:A810(OP1) A:A1253(N7) A3332, A3333, A3334, A3335 U:A566, U:A811 G:A1252
4too A3009 Oph·Nb A:A453(OP1) G:A450(N7) A3240, A3241, A3242, A3243 A:A449 A:A449
4too A3029 Oph·Nb U:A810(OP1) A:A1253(N7) A3328, A3329, A3330, A3331 U:A811 C:A565, G:A1252
4tov A3030 Oph·Nb U:A810(OP1) A:A1253(N7) A3333, A3334, A3335, A3336 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
4tox A3010 Oph·Nb A:A453(OP1) G:A450(N7) A3240, A3241, A3242, A3243 A:A449 A:A449
4tp1 A3080 Oph·Nb A:A422(OP2) G:A370(N7) A3561, A3562, A3563, A3564 G:A370, A:A423 A:A423
4tp1 A3030 Oph·Nb U:A810(OP1) A:A1253(N7) A3336, A3337, A3338, A3339 U:A811 C:A565, G:A1252
4tp3 A3079 Oph·Nb A:A422(OP2) G:A370(N7) A3553, A3554, A3555, A3556 A:A423, G:A370 A:A270, A:A423
4tp3 A3010 Oph·Nb A:A453(OP1) G:A450(N7) A3242, A3243, A3244, A3245 A:A449 U:A448 A:A449

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>