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

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Representative site 4bpp:A5063, See in JSmolMgRNA representative site for type 2PO-2RO-3BO    Click on the image to toggle views


Site type: 2Pout·2Rout·3Bout

Schematic drawing for
2Pout·2Rout·3Bout

MgRNA type 2PO-2RO-3BO
List of all 11 Mg2+ binding sites with the site type 2Pout·2Rout·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 1 of 1
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3r8t A2998 2Pout·2Rout·3Bout A3515, A3516, A3517, A3518, A3519, A3520 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
3i1n A2999 2Pout·2Rout·3Bout A3489, A3490, A3491, A3492, A3493, A3494 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
4pec A3095 2Pout·2Rout·3Bout A3637, A3638, A3639, A3640, A3641, A3642 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
4tpb A3096 2Pout·2Rout·3Bout A3636, A3637, A3638, A3639, A3640, A3641 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
4tpd A3096 2Pout·2Rout·3Bout A3646, A3647, A3648, A3649, A3650, A3651 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
4tp1 A3097 2Pout·2Rout·3Bout A3644, A3645, A3646, A3647, A3648, A3649 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
4tp7 A3097 2Pout·2Rout·3Bout A3636, A3637, A3638, A3639, A3640, A3641 A:A1608, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
4tp9 A3097 2Pout·2Rout·3Bout A3643, A3644, A3645, A3646, A3647, A3648 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
4tpf A3097 2Pout·2Rout·3Bout A3639, A3640, A3641, A3642, A3643, A3644 A:A1608, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
3v2d A3657 2Pout·2Rout·3Bout A5528, A5529, A5530, A5531, A5532 A:A1609, G:A1619 A:A1608, C:A1617 G:A1619, G:A1613, G:A1620
4bpp A5063 2Pout·2Rout·3Bout A8019, A8020, A8021, A8022, A8023, A8024 G:A1172, G:A1173 C:A1574, G:A1173 C:A1574, A:A1168, A:A1572

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>