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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qp1:B2994, See in JSmolMgRNA representative site for type OP-4PO Click on the image to toggle views


Site type: Oph·4Pout

Schematic drawing for
Oph·4Pout
MgRNA type OP-4PO
List of all 231 Mg2+ binding sites with the site type Oph·4Pout 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 5 of 10 | | | 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
3i1o A1559 Oph·4Pout G:A1198(OP1) A1713, A1714, A1715, A1716 A:A964, U:A965, C:A1054, U:A1199
3i1p A2961 Oph·4Pout G:A1828(OP1) A3304, A3305, A3306, A3307, C417 A:A1773, G:A1972, G:A1973, A:A1772
3i1p A2939 Oph·4Pout U:A963(OP1) A3204, A3205, A3206, A3207, A3208 C:A964, C:A2498, A:A2497, A:A947
3i1p A2948 Oph·4Pout G:A1333(OP2) A3242, A3243, A3244, A3245, A3246 C:A1314, G:A1332, G:A1334, U:A1313 C:A1335
3i1p A3010 Oph·4Pout C:A31(OP1) A3526, A3527, A3528, A3529, A3530 G:A1239, C:A1200, U:A1199, U:A1240 A:A1214
3i1p A3019 Oph·4Pout U:A2243(OP1) A3559, A3560, A3561, A3562 C:A192, A:A199, C:A198, U:A193
3i1s A1559 Oph·4Pout G:A1198(OP1) A1713, A1714, A1715, A1716 A:A964, U:A965, U:A1199, C:A1054
3i1t A3019 Oph·4Pout U:A2243(OP1) A3562, A3563, A3564, A3565 C:A192, A:A199, C:A198, U:A193
3i1t A3010 Oph·4Pout C:A31(OP1) A3529, A3530, A3531, A3532, A3533 G:A1239, C:A1200, U:A1199, U:A1240
3i1t A2948 Oph·4Pout G:A1333(OP2) A3245, A3246, A3247, A3248, A3249 C:A1314, G:A1332, G:A1334, U:A1313 C:A1335
3i21 A1559 Oph·4Pout G:A1198(OP1) A1713, A1714, A1715, A1716 A:A964, U:A965, C:A1054, U:A1199
3i22 A3000 Oph·4Pout U:A576(OP1) A3497, A3498, A3499, A3500 A:A2503, U:A2504, G:A577, G:A2057
3i22 A2960 Oph·4Pout G:A1828(OP1) A3306, A3307, A3308, A3309, C417 A:A1772, A:A1773, G:A1972, G:A1973
3i22 A2938 Oph·4Pout U:A963(OP1) A3205, A3206, A3207, A3208, A3209 C:A964, C:A2498, A:A2497, A:A947
3la5 A11 Oph·4Pout G:A44(OP1) A9, A191, A302, A411, A412 C:A50, G:A44, C:A51, A:A45
3oaq A1540 Oph·4Pout A:A560(OP2) A1608, A1609, A1610, A1611, A1612 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
3oar A1561 Oph·4Pout G:A1198(OP1) A1711, A1712, A1713, A1714 A:A964, U:A965, C:A1054, U:A1199
3oas A3018 Oph·4Pout U:A2243(OP1) A3561, A3562, A3563, A3564 C:A192, A:A199, C:A198, U:A193
3oas A3009 Oph·4Pout C:A31(OP1) A3528, A3529, A3530, A3531, A3532 G:A1239, C:A1200, U:A1199, U:A1240 A:A1214
3oas A3000 Oph·4Pout A:A2503(OP1) A3496, A3497, A3498, A3499 U:A2504, G:A577, U:A576, G:A2057
3oat A3011 Oph·4Pout C:A31(OP1) A3530, A3531, A3532, A3533, A3534 C:A1200, G:A1239, U:A1240, U:A1199
3oat A2997 Oph·4Pout U:A1636(OP2) A3475, A3476, A3477, A3478, A3479 G:A1299, A:A1637, A:A1635, G:A1300
3ofb A1562 Oph·4Pout G:A1198(OP1) A1711, A1712, A1713, A1714 A:A964, U:A965, C:A1054, U:A1199
3ofc A3012 Oph·4Pout C:A31(OP1) A3543, A3544, A3545, A3546, A3547 C:A1200, U:A1240, G:A1239, U:A1199
3ofd A2947 Oph·4Pout G:A1333(OP2) A3241, A3242, A3243, A3244, A3245 C:A1314, G:A1332, G:A1334, U:A1313 G:A1331 C:A1335

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>