`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 3r8s:A2930, See in JSmolMgRNA representative site for type OP             Click on the image to toggle views


Site type: Oph

Schematic drawing for
Oph

MgRNA type OP
List of all 588 Mg2+ binding sites with the site type Oph 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 8 of 24 | | | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3i1p A2941 Oph A:A1156(OP2) A3213, A3214, A3215, A3216, A3217 G:A1157, G:A997
3i1p A2913 Oph G:A536(OP2) A3085, A3086, A3087, A3088, A3089
3i1p A2987 Oph A:A299(OP2) A3430, A3431, A3432, A3433, U544 A:A299, G:A338, U:A339, A:A300
3i1r A2910 Oph U:A419(OP1) A3071, A3072, A3073, A3074, A3075 G:A230
3i1r A2930 Oph A:A800(OP1) A3165, A3166, A3167, A3168, A3169 G:A799 A:A191, C:A192, A:A800
3i1r A2981 Oph A:A299(OP2) A3400, A3401, A3402, A3403, A3404 U:A339, G:A338
3i1r A2964 Oph A:A2033(OP1) A3322, A3323, A3324, A3325 G:A2027, G:A2029
3i1s A1560 Oph A:A1433(OP2) A1717, A1718, A1719, A1720, A1721 G:A1435, C:A1466, A:A1434
3i1s A1545 Oph A:A937(OP2) A1642, A1643, A1644, A1645, A1646 A:A938, G:A939
3i1s A1544 Oph C:A934(OP1) A1637, A1638, A1639, A1640, A1641
3i1s A1555 Oph G:A21(OP1) A1693, A1694, A1695, A1696, A1697 G:A568, G:A567 G:A567
3i1s A1561 Oph G:A558(OP1) A1722, A1723, A1724, A1725 G:A299
3i1s A1568 Oph G:A100(OP2) A1752, A1753, A1754, A1755, A1756 G:A64, C:A99, G:A100, A:A101
3i1t A2910 Oph U:A419(OP1) A3071, A3072, A3073, A3074, A3075 G:A230
3i1t A2987 Oph A:A299(OP2) A3434, A3435, A3436, A3437, U544 A:A299, G:A338, U:A339, A:A300
3i1t A2958 Oph A:A1678(OP2) A3292, A3293, A3294, A3295, A3296 A:A1678, A:A1679
3i1t A2922 Oph A:A621(OP2) A3135, A3136, A3137, L238
3i1t A2913 Oph G:A536(OP2) A3084, A3085, A3086, A3087, A3088
3i1z A1548 Oph A:A937(OP2) A1648, A1649, A1650, A1651, A1652 A:A937, A:A938, G:A939
3i1z A1558 Oph G:A21(OP1) A1692, A1693, A1694, A1695, A1696 G:A567 G:A567, A:A573
3i20 A2910 Oph U:A419(OP1) A3071, A3072, A3073, A3074, A3075 G:A230
3i20 A2930 Oph A:A800(OP1) A3167, A3168, A3169, A3170, A3171 G:A799, A:A802 A:A191, C:A192, A:A800
3i20 B123 Oph G:B100(OP2) B661, B662, B663, B664, B665 A:B73 A:B101, G:B102
3i20 A2981 Oph A:A299(OP2) A3400, A3401, A3402, A3403, A3404 U:A339, G:A338
3i20 A2936 Oph A:A945(OP2) A3193, A3194, A3195, A3196, A3197 C:A944 G:A831, U:A832, C:A944

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>