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

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Representative site 3i1q:A1540, See in JSmolMgRNA representative site for type 4PO-RO-BO      Click on the image to toggle views

Site type: 4Pout·Rout·Bout

Schematic drawing for

MgRNA type 4PO-RO-BO
List of all 10 Mg2+ binding sites with the site type 4Pout·Rout·Bout 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
2qox B2938 4Pout·Rout·Bout B3180, B3181, B3182, B3183, B3184 G:B2446, G:B2447, G:B2502, C:B2501 U:B576 G:B2502
3i1q A1540 4Pout·Rout·Bout A1605, A1606, A1607, A1608, A1609 G:A557, A:A560, U:A562, G:A558 A:A559 A:A300
3ofd A2965 4Pout·Rout·Bout A3328, A3329, A3330, A3331, A3332 U:A2026, U:A2034, C:A2025, A:A2033 A:A2033 U:A2026
3ofq A2984 4Pout·Rout·Bout A3420, A3421, A3422, A3423, C477 A:A2587, G:A2588, A:A2589, A:A2600 A:A2439 A:A2589
3v2f A3434 4Pout·Rout·Bout A4652, A4653, A4654, A4655, A4656 A:A933, U:A839, C:A838, G:A818 G:A932 G:A932
4dr6 A1633 4Pout·Rout·Bout A2085, A2086, A2087, A2088 G:A557, U:A560, C:A562, G:A558 A:A559 G:A566
4dv1 A1811 4Pout·Rout·Bout A2212, A2213, A2214, A2215, A2216 U:A114, C:A307, G:A115, C:A47 G:A306 G:A31
4tp3 A3073 4Pout·Rout·Bout A3532, A3533, A3534, A3535, A3536 A:A2518, U:A2519, A:A2541, C:A2540 C:A2517 A:A2541
4tpb A3073 4Pout·Rout·Bout A3532, A3533, A3534, A3535, A3536 A:A2518, U:A2519, A:A2541, C:A2540 C:A2517 A:A2541
4tpf A3045 4Pout·Rout·Bout A3393, A3394, A3395, A3396, A3397, A3398 U:A1352, G:A1377, C:A1376, C:A1351 C:A1376 G:A1377

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>