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

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Representative site 2qba:B3110, See in JSmolMgRNA representative site for type 3PO-5BO        Click on the image to toggle views

Site type: 3Pout·5Bout

Schematic drawing for

MgRNA type 3PO-5BO
List of all 10 Mg2+ binding sites with the site type 3Pout·5Bout 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
2qba B3110 3Pout·5Bout B3700, B3701, B3702, B3703, B3704, B3705 U:B29, A:B28, A:B447 U:B29, G:B473, G:B30, C:B31, G:B474
2z4l B2924 3Pout·5Bout B3102, B3103, B3104, B3105, B3106, B3107 A:B28, A:B447, U:B29 U:B29, G:B473, G:B474, G:B30, C:B31
3ofd A2906 3Pout·5Bout A3044, A3045, A3046, A3047, A3048, A3049 U:A29, A:A28, A:A447 G:A473, G:A474, U:A29, G:A30, C:A31
3v27 A3633 3Pout·5Bout A5253, A5254, A5255, A5256, A5257, A5258 U:A29, A:A447, A:A28 G:A474, G:A473, U:A29, G:A30, C:A31
3v29 A3576 3Pout·5Bout A4683, A4684, A4685, A4686, A4687, A4688 U:A29, A:A28, A:A447 G:A30, C:A31, G:A474, G:A473, U:A29
4dhc A3445 3Pout·5Bout A4007, A4008, A4009, A4010, A4011 U:A29, A:A28, A:A447 U:A29, G:A30, C:A31, G:A474, G:A473
4pec A3002 3Pout·5Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 G:A473, G:A474, U:A29, G:A30, C:A31
4pec A3070 3Pout·5Bout A3519, A3520, A3521, A3522, A3523, A3524 A:A2451, A:A2453, C:A2452 A:A2453, G:A2454, A:A2497, G:A2455, C:A2496
4too A3002 3Pout·5Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 U:A29, G:A473, G:A30, C:A31, G:A474
4tpf A3081 3Pout·5Bout A3561, A3562, A3563, A3564 A:A2406, G:A411, A:A2407 G:A2410, A:A2411, A:A2407, U:A2408, G:A2409

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>