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

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Representative site 3r8s:A3000, See in JSmolMgRNA representative site for type OP-5PO         Click on the image to toggle views


Site type: Oph·5Pout

Schematic drawing for
Oph·5Pout

MgRNA type OP-5PO
List of all 37 Mg2+ binding sites with the site type Oph·5Pout 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 1 of 2 | « Previous | | 1 | 2
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1jj2 08060 Oph·5Pout G:0175(OP2) 07373, 07374, 07375, 08687 C:0173, G:0225, U:0172, G:0393, U:0392
1k9m A8060 Oph·5Pout G:A175(OP2) A7836, A7837, A7838, A9172 C:A173, G:A225, U:A172, G:A393, U:A392
1m90 A8060 Oph·5Pout G:A175(OP2) A7356, A7357, A7358, A8690 C:A173, U:A172, G:A225, G:A393, U:A392
1nji A8060 Oph·5Pout G:A175(OP2) A7818, A7819, A7820, A9167 C:A173, G:A225, U:A172, G:A393, U:A392
1nji A8091 Oph·5Pout G:A918(OP1) A3321, A6484, A7844, A9093, A9539 G:A2293, C:A2294, C:A2391, A:A2465, U:A919 A:A2465
1s72 08060 Oph·5Pout G:0175(OP2) 07328, 07329, 07330, 08687 C:0173, G:0225, U:0172, G:0393, U:0392
1vq4 08091 Oph·5Pout G:0918(OP1) 03631, 06732, 08125, 09411, 09867 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
1vq5 08091 Oph·5Pout G:0918(OP1) 03644, 06749, 08169, 09413, 09872 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
1vq5 08060 Oph·5Pout G:0175(OP2) 08143, 08144, 08145, 09493 C:0173, G:0225, U:0172, G:0393, U:0392
1vq6 08091 Oph·5Pout G:0918(OP1) 03631, 06713, 08133, 09414, 09870 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
1vq7 08060 Oph·5Pout G:0175(OP2) 08139, 08140, 08141, 09498 C:0173, G:0225, U:0172, G:0393, U:0392
1vq7 08091 Oph·5Pout G:0918(OP1) 03645, 06741, 08164, 09414, 09872 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
1yij 08091 Oph·5Pout G:0918(OP1) 03334, 06483, 07822, 09093, 09549 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
1yjw 78035 Oph·5Pout G:01484(OP2) 07233, 07235, 07237, 07289, 07290 C:01455, C:01456, U:01457, A:01485, C:01483 U:01457, G:01484
2otj 08060 Oph·5Pout G:0175(OP2) 07820, 07821, 07822, 09172 C:0173, G:0225, U:0172, G:0393, U:0392
2otl 08091 Oph·5Pout G:0918(OP1) 03333, 06486, 07832, 09092, 09550 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
2qex 08060 Oph·5Pout G:0175(OP2) 07658, 07659, 07660, 08990 C:0173, G:0225, U:0172, U:0392, G:0393
3cc2 08091 Oph·5Pout G:0918(OP1) 06058, 07412, 08614, 09082, 09869 C:02294, C:02391, A:02465, U:0919, G:02293 A:02465
3cc2 08060 Oph·5Pout G:0175(OP2) 07386, 07387, 07388, 08694 C:0173, G:0225, U:0172, G:0393, U:0392
3i1r A3000 Oph·5Pout U:A1636(OP2) A3494, A3495, A3496, A3497, A3498 A:A1301, G:A1300, A:A1637, A:A1635, G:A1299
3i20 A3000 Oph·5Pout U:A1636(OP2) A3494, A3495, A3496, A3497, A3498 A:A1301, A:A1637, A:A1635, G:A1299, G:A1300
3ofc A2998 Oph·5Pout U:A1636(OP2) A3488, A3489, A3490, A3491, A3492 G:A1300, A:A1637, A:A1301, A:A1635, G:A1299
3ofz A2997 Oph·5Pout U:A1636(OP2) A3477, A3478, A3479, A3480, A3481 A:A1637, A:A1301, A:A1635, G:A1299, G:A1300
3r8s A3000 Oph·5Pout U:A1636(OP2) A3550, A3551, A3552, A3553, A3554 A:A1301, A:A1637, A:A1635, G:A1299, G:A1300
3r8t A2999 Oph·5Pout U:A1636(OP2) A3521, A3522, A3523, A3524, A3525 A:A1301, A:A1637, A:A1635, G:A1299, G:A1300

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>