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

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Representative site 3r8s:A2999, See in JSmolMgRNA representative site for type 2PO-2RO-2BO    Click on the image to toggle views

Site type: 2Pout·2Rout·2Bout

Schematic drawing for

MgRNA type 2PO-2RO-2BO
List of all 12 Mg2+ binding sites with the site type 2Pout·2Rout·2Bout 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
1vt2 A2978 2Pout·2Rout·2Bout A3390, A3391, A3392, A3393, A3394, A3395 U:A2387, A:A2386 C:A2385, U:A2384 C:A2326, U:A2387
3oas A2977 2Pout·2Rout·2Bout A3387, A3388, A3389, A3390, A3391, A3392 U:A2387, A:A2386 C:A2385, U:A2384 C:A2326, U:A2387
3orb A2997 2Pout·2Rout·2Bout A3481, A3482, A3483, A3484, A3485, A3486 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613
3r8s A2999 2Pout·2Rout·2Bout A3544, A3545, A3546, A3547, A3548, A3549 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613
3v2f A3328 2Pout·2Rout·2Bout A4350, A4351, A4352, A4353 C:A1617, A:A1609 C:A1617, A:A1608 G:A1613, G:A1619
4dha A3658 2Pout·2Rout·2Bout A4580, A4581, A4582, A4583, A4584, A4585 G:A570, A:A973 G:A972, U:A569 A:A820, A:A821
4gar A3094 2Pout·2Rout·2Bout A3642, A3643, A3644, A3645, A3646, A3647 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613
4nvx A3350 2Pout·2Rout·2Bout A4285, A4286, A4287, A4288 A:A1609, C:A1617 A:A1608, C:A1617 G:A1613, G:A1619
4peb A3095 2Pout·2Rout·2Bout A3646, A3647, A3648, A3649, A3650, A3651 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613
4pec A3026 2Pout·2Rout·2Bout A3320, A3321, A3322, A3323, A3324 A:A204, A:A800 G:A799, A:A203 A:A191, C:A192
4tov A3097 2Pout·2Rout·2Bout A3644, A3645, A3646, A3647, A3648, A3649 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613
4tp3 A3027 2Pout·2Rout·2Bout A3323, A3324, A3325, A3326, A3327 A:A204, A:A800 G:A799, A:A203 A:A190, A:A191

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>