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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"
Page 4 of 24 | | | 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
2qb9 A2213 Oph A:A1433(OP2) A2530, A2531, A2532, A2533, A2534 A:A1434, G:A1435
2qb9 A2288 Oph G:A100(OP2) A2591, A2592, A2593, A2594, A2595 G:A64, G:A100, A:A101
2qb9 A2064 Oph A:A937(OP2) A2411, A2412, A2413, A2414, A2415 A:A938, G:A939
2qba B3253 Oph U:B120(OP2) B3818, B3819, B3820, B3821, B3822 G:B122, G:B123, G:B121
2qba B3270 Oph G:B536(OP2) B3832, B3833, B3834, B3835, B3836 G:B536, G:B537
2qba B3338 Oph A:B800(OP1) B3884, B3885, B3886, B3887, B3888 G:B799 C:B192, A:B800, A:B191
2qba B3418 Oph A:B2033(OP1) B3950, B3951, B3952, B3953 G:B2027, U:B2028
2qba B3175 Oph U:B419(OP1) B3754, B3755, B3756, B3757, B3758 G:B230
2qba B3394 Oph A:B1678(OP2) B3930, B3931, B3932, B3933, B3934 A:B1678, A:B1679
2qbb A2283 Oph U:A1224(OP1) A2601, A2602, A2603, A2604 C:A1223 A:A977
2qbb A2360 Oph C:A980(OP1) A2665, A2666, A2667, A2668, A2669 G:A1221, A:A1219
2qbb A2202 Oph G:A21(OP1) A2536, A2537, A2538, A2539, A2540 G:A568, G:A567 A:A573, G:A567
2qbb A2062 Oph C:A1195(OP1) A2421, A2422, A2423, A2424, A2425 U:A1194 A:A1398
2qbc B3104 Oph A:B800(OP1) B3705, B3706, B3707, B3708, B3709 G:B799 C:B192, A:B800, A:B191
2qbc B3251 Oph A:B1678(OP2) B3825, B3826, B3827, B3828, B3829 A:B1678, A:B1679
2qbc B3364 Oph U:B419(OP1) B3916, B3917, B3918, B3919, B3920 G:B230
2qbd A2176 Oph G:A21(OP1) A2177, A2178, A2179, A2180, A2181 G:A568, G:A567 A:A573, G:A567
2qbd A2288 Oph G:A100(OP2) A2289, A2290, A2291, A2292, A2293 G:A100, A:A101, G:A64
2qbd A2064 Oph A:A937(OP2) A2065, A2066, A2067, A2068, A2069 A:A938, G:A939
2qbd A2213 Oph A:A1433(OP2) A2214, A2215, A2216, A2217, A2218 G:A1432 A:A1434, G:A1435
2qbe B3253 Oph U:B120(OP2) B3817, B3818, B3819, B3820, B3821 G:B122, G:B123
2qbe B3353 Oph A:B1156(OP2) B3896, B3897, B3898, B3899, B3900 A:B1155 G:B1157, C:B998
2qbe B3175 Oph U:B419(OP1) B3754, B3755, B3756, B3757, B3758 G:B230
2qbe B3338 Oph A:B800(OP1) B3884, B3885, B3886, B3887, B3888 G:B799 A:B191, C:B192, A:B800
2qbf A1574 Oph G:A21(OP1) A1768, A1769, A1770, A1771, A1772 G:A568, G:A567 A:A573, G:A567

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>