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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3df3:A2016, See in JSmolMgRNA representative site for type 2PO-3BO Click on the image to toggle views


Site type: 2Pout·3Bout

Schematic drawing for
2Pout·3Bout
MgRNA type 2PO-3BO
List of all 199 Mg2+ binding sites with the site type 2Pout·3Bout 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 8 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3i1n A3037 2Pout·3Bout A3638, A3639, A3640, A3641, 4779, 4784 A:A2740, A:A2741 G:A2742, G:A2763, U:A2743
3i1n A2921 2Pout·3Bout A3129, A3130, A3131, A3132, A3133, A3134 A:A616, A:A608 G:A617, G:A618, G:A619
3i1p A2921 2Pout·3Bout A3130, A3131, A3132, A3133, A3134, A3135 A:A616, A:A608 G:A617, G:A618, G:A619
3i1p A2978 2Pout·3Bout A3386, A3387, A3388, A3389, A3390, A3391 U:A2387, A:A2386 C:A2326, G:A2389, U:A2387
3i1q A1535 2Pout·3Bout A1581, A1582, A1583, A1584, A1585, A1586 A:A329, A:A315 A:A320, G:A318, G:A319
3i1r A2921 2Pout·3Bout A3128, A3129, A3130, A3131, A3132, E235 A:A616, A:A608 G:A617, G:A618, G:A619
3i1s A4 2Pout·3Bout A1588, A1589, A1590, A1591, A1592, A1593 A:A415, G:A416 G:A417, G:A425, G:A416
3i1s A2 2Pout·3Bout A1577, A1578, A1579, A1580, A1581, A1582 A:A315, A:A329 A:A320, G:A318, G:A319
3i1t A3003 2Pout·3Bout A3507, A3508, A3509, A3510, A3511 A:A2705, C:A2704 A:A2705, U:A2701, A:A2706
3i1t A2921 2Pout·3Bout A3129, A3130, A3131, A3132, A3133, A3134 A:A616, A:A608 G:A617, G:A618, G:A619
3i1z A1537 2Pout·3Bout A1593, A1594, A1595, A1596, A1597, A1598 A:A415, G:A416 G:A417, C:A418, G:A416
3i20 A2921 2Pout·3Bout A3129, A3130, A3131, A3132, A3133, A3134 A:A616, A:A608 G:A617, G:A618, G:A619
3i20 A2999 2Pout·3Bout A3488, A3489, A3490, A3491, A3492, A3493 C:A1617, G:A1619 G:A1619, G:A1620, G:A1613
3i21 A4 2Pout·3Bout A1588, A1589, A1590, A1591, A1592, A1593 A:A415, G:A416 G:A417, C:A418, G:A416
3oar A1544 2Pout·3Bout A1622, A1623, A1624, A1625, A1626, A1627 G:A803, U:A804 G:A771, U:A772, G:A773
3oar A1537 2Pout·3Bout A1588, A1589, A1590, A1591, A1592, A1593 A:A415, G:A416 G:A417, G:A425, G:A416
3oas A3002 2Pout·3Bout A3506, A3507, A3508, A3509, A3510 A:A2705, C:A2704 A:A2705, A:A2706, U:A2707
3oat A2920 2Pout·3Bout A3120, A3121, A3122, A3123, A3124, A3125 A:A616, A:A608 G:A617, G:A618, G:A619
3ofb A1544 2Pout·3Bout A1623, A1624, A1625, A1626, A1627, A1628 G:A803, U:A804 G:A771, U:A772, G:A773
3ofb A1561 2Pout·3Bout A1707, A1708, A1709, A1710, I169 U:A1348, A:A1349 G:A1371, U:A1372, G:A1370
3ofb A1537 2Pout·3Bout A1589, A1590, A1591, A1592, A1593, A1594 A:A415, G:A416 G:A417, G:A416, U:A426
3ofc A3035 2Pout·3Bout A3632, A3633, A3634, A3635, 4769, 4774 A:A2740, A:A2741 G:A2742, G:A2763, U:A2743
3ofc A3037 2Pout·3Bout A3639, A3640, A3641, A3642, A3643, A3644 A:A1650, G:A2004 G:A1651, G:A1649, A:A1650
3ofd A3002 2Pout·3Bout A3505, A3506, A3507, A3508, A3509 A:A2705, C:A2704 A:A2705, A:A2706, U:A2707
3ofp A1544 2Pout·3Bout A1623, A1624, A1625, A1626, A1627, A1628 G:A803, U:A804 G:A771, U:A772, G:A773

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>