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

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Representative site 2qal:A2136, See in JSmolMgRNA representative site for type 3PO-RO         Click on the image to toggle views

Site type: 3Pout·Rout

Schematic drawing for

MgRNA type 3PO-RO
List of all 51 Mg2+ binding sites with the site type 3Pout·Rout 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
1vs6 B2955 3Pout·Rout B3256, B3257, B3258, B3259, E203, E204 U:B2017, U:B2016, G:B579 U:B1255
1vs6 B2908 3Pout·Rout B3031, B3032, B3033, B3034, B3035, B3036 C:B560, A:B1008, G:B559 C:B1007
1vt2 A3023 3Pout·Rout A3579, A3580, A3581, A3582 U:A790, C:A791, C:A787 U:A790
2aw4 B2921 3Pout·Rout B3089, B3090, B3091, B3092, B3093, B3094 A:B947, C:B965, G:B822 C:B946
2awb B2967 3Pout·Rout B3318, B3319, B3320, B3321, J424, J426 G:B559, A:B1008, C:B560 C:B1007
2i2t B2955 3Pout·Rout B3262, B3263, B3264, B3265, B3266, B3267 G:B579, U:B2016, U:B2017 U:B1255
2i2v B2936 3Pout·Rout B3179, B3180, B3181, B3182, B3183, B3184 U:B2016, U:B2017, A:B2058 U:B1255
2qal A2136 3Pout·Rout A2137, A2138, A2139, A2140, A2141, A2142 U:A854, G:A727, C:A726 C:A853
2qbc B3375 3Pout·Rout B3925, B3926, B3927, B3928, B3929, B3930 C:B560, A:B1008, G:B559 C:B1007
2qbh A1589 3Pout·Rout A1823, A1824, A1825, A1826, A1827, A1828 C:A25, U:A552, A:A553 G:A524
2qbk B2968 3Pout·Rout B3321, B3322, B3323, B3324, B3325, B3326 C:B560, A:B1008, G:B559 C:B1007
2qbk B2936 3Pout·Rout B3169, B3170, B3171, B3172, B3173, B3174 G:B579, U:B2016, G:B578 U:B1255
2qov B2968 3Pout·Rout B3315, B3316, B3317, B3318, B3319, B3320 C:B1351, G:B1377, C:B1376 U:B1352
2qoz B3004 3Pout·Rout B3959, B3960, B3961, B3962, B3963, B3964 G:B205, C:B385, U:B202 C:B253
2z4k A1566 3Pout·Rout A1712, A1713, A1714, A1715, A1716, A1717 U:A854, G:A727, C:A726 C:A853
2z4l B2956 3Pout·Rout B3252, B3253, B3254, B3255, B3256, B3257 G:B578, U:B2016, U:B2017 U:B1255
3i1m A1574 3Pout·Rout A1764, A1765, A1766, A1767, A1768, L240 C:A504, C:A536, C:A503 C:A522
3i1o A1570 3Pout·Rout A1761, A1762, A1763, A1764, A1765 A:A523, C:A536, C:A503 C:A522
3i1p A2984 3Pout·Rout A3418, A3419, A3420, A3421, C533 G:A2588, A:A2587, A:A2600 A:A2439
3i1q A1574 3Pout·Rout A1759, A1760, A1761, A1762, A1763, L240 C:A504, C:A536, C:A503 C:A522
3i1r A2918 3Pout·Rout A3111, A3112, A3113, A3114, A3115, A3116 G:A579, U:A2016, G:A578 U:A1255
3i1r A2914 3Pout·Rout A3089, A3090, A3091, A3092, A3093, A3094 G:A559, C:A560, A:A1008 C:A1007
3i1z A1574 3Pout·Rout A1762, A1763, A1764, A1765, A1766, L240 C:A504, C:A536, C:A503 C:A522
3i20 A2918 3Pout·Rout A3111, A3112, A3113, A3114, A3115, A3116 G:A579, U:A2016, G:A578 U:A1255
3oaq A1574 3Pout·Rout A1764, A1765, A1766, A1767, A1768, A1769 C:A504, C:A503, C:A536 C:A522

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>