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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2z4n:B3007, See in JSmolMgRNA representative site for type cis-2OP-OR Click on the image to toggle views


Site type: cis-2Oph·Or

Schematic drawing for
cis-2Oph·Or
MgRNA type cis-2OP-OR
List of all 36 Mg2+ binding sites with the site type cis-2Oph·Or 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
1vs6 B3006 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B3481, B3482, B3483 G:B1380
1vs7 A1556 cis-2Oph·Or C:A1054(OP1), A:A1197(OP1) A:A1196(O2') A1664, A1665, A1666 G:A1198
1vs8 B3004 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B3474, B3475, B3476 G:B1380
2aw4 B3006 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B3477, B3478, B3479 G:B1380
2aw7 A1555 cis-2Oph·Or C:A1054(OP1), A:A1197(OP1) A:A1196(O2') A1664, A1665, A1666 G:A1198
2qam B3573 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B4077, B4078, B4079
2qao B3575 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B4084, B4085, B4086 G:B1380
2qbc B3575 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B4084, B4085, B4086 G:B1380
2qbe B3573 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B4073, B4074, B4075 A:B1347
2qbg B3006 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B3484, B3485, B3486 G:B1380
2qbi B3006 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B3474, B3475, B3476 G:B1380
2qbk B2988 cis-2Oph·Or A:B2448(OP2), C:B2499(OP2) G:B2447(O2') B3415, B3416, B3417 U:B2449, C:B2498 A:B2497
2qox B2996 cis-2Oph·Or C:B2573(OP1), C:B2575(OP2) G:B2574(O5') B3442, B3443, B3444 G:B2574, C:B2507
2qox B3005 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B3479, B3480, B3481 G:B1380
2qoz B3006 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B3969, B3970, B3971 G:B1380
2z4n B3007 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B3482, B3483, B3484 G:B1380
3df1 A2060 cis-2Oph·Or C:A1054(OP1), A:A1197(OP1) A:A1196(O2') A4061, A4062, A4063 G:A1198
3df2 B3573 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B4574, B4575, B4576
3df4 B3575 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B4576, B4577, B4578 G:B1380
3df4 B3528 cis-2Oph·Or C:B2573(OP1), C:B2575(OP2) G:B2574(O5') B4529, B4530, B4531 G:B2574, C:B2507
3i1o A1567 cis-2Oph·Or A:A1500(OP2), G:A1505(OP2) G:A1504(O2') A1749, A1750, A1751 A:A1499 A:A1500
3i20 A3007 cis-2Oph·Or A:A2448(OP2), C:A2499(OP2) G:A2447(O2') A3531, A3532, A3533 U:A2449, C:A2498 A:A2497
3oar A1569 cis-2Oph·Or A:A1500(OP2), G:A1505(OP2) G:A1504(O2') A1747, A1748, A1749 A:A1499 U:A1498 C:A1501, A:A1500
3ofb A1570 cis-2Oph·Or A:A1500(OP2), G:A1505(OP2) G:A1504(O2') A1747, A1748, A1749 A:A1499 U:A1498 C:A1501, A:A1500
3ofy A1570 cis-2Oph·Or A:A1500(OP2), G:A1505(OP2) G:A1504(O2') A1747, A1748, A1749 A:A1499 U:A1498 A:A1500

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>