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

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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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3df1 A2170 Oph A:A572(OP1) A4171, A4172, A4173, A4174, A4175
3df2 B3418 Oph A:B2033(OP1) B4419, B4420, B4421, B4422 G:B2027, U:B2028
3df2 B3338 Oph A:B800(OP1) B4339, B4340, B4341, B4342, B4343 G:B799 C:B192, A:B800, A:B191
3df2 B3175 Oph U:B419(OP1) B4176, B4177, B4178, B4179, B4180 G:B230
3df2 B3151 Oph A:B945(OP1) B4152, B4153, B4154, B4155, B4156 G:B831, U:B832
3df3 A2128 Oph A:A937(OP2) A4129, A4130, A4131, A4132, A4133 A:A937, A:A938, G:A939
3df4 B3364 Oph U:B419(OP1) B4365, B4366, B4367, B4368, B4369 G:B230
3df4 B3127 Oph A:B1156(OP2) B4128, B4129, B4130, B4131, B4132 G:B1157, G:B997, C:B998
3df4 B3104 Oph A:B800(OP1) B4105, B4106, B4107, B4108, B4109 A:B802, G:B799, A:B203 C:B192, A:B800
3i1m A1558 Oph G:A21(OP1) A1694, A1695, A1696, A1697, A1698 G:A568, G:A567 A:A573, G:A567
3i1m A1548 Oph A:A937(OP2) A1648, A1649, A1650, A1651, A1652 A:A937, A:A938, G:A939
3i1n A2930 Oph A:A800(OP1) A3168, A3169, A3170, A3171, A3172 G:A799 A:A191, C:A192, A:A800
3i1n A2910 Oph U:A419(OP1) A3072, A3073, A3074, A3075, A3076 G:A230
3i1n A2906 Oph U:A120(OP2) A3053, A3054, A3055, A3056, A3057 G:A122, G:A123, G:A121
3i1n A2981 Oph A:A299(OP2) A3402, A3403, A3404, A3405, A3406 U:A339, A:A299, G:A338
3i1o A1555 Oph G:A21(OP1) A1693, A1694, A1695, A1696, A1697 G:A568, G:A567 A:A563, G:A567
3i1o A1545 Oph A:A937(OP2) A1642, A1643, A1644, A1645, A1646 A:A938, G:A939
3i1o A1568 Oph G:A100(OP2) A1752, A1753, A1754, A1755, A1756 G:A64, G:A100, A:A101
3i1o A1544 Oph C:A934(OP1) A1637, A1638, A1639, A1640, A1641
3i1o A1548 Oph C:A1054(OP2) A1657, A1658, A1659, A1660 G:A1053 G:A1198, U:A1199
3i1p A2908 Oph U:A120(OP2) A3062, A3063, A3064, A3065, A3066 G:A123, G:A124
3i1p A2931 Oph A:A800(OP1) A3171, A3172, A3173, A3174, A3175 G:A799, A:A203 A:A190, A:A191
3i1p A2910 Oph U:A419(OP1) A3072, A3073, A3074, A3075, A3076 G:A230
3i1p A2987 Oph A:A299(OP2) A3430, A3431, A3432, A3433, U544 A:A299, G:A338, U:A339, A:A300
3i1p A2922 Oph A:A621(OP2) A3136, A3137, L236, L238

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>