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

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Representative site 1vs6:B2970, See in JSmolMgRNA representative site for type 3PO-RO-BO      Click on the image to toggle views

Site type: 3Pout·Rout·Bout

Schematic drawing for

MgRNA type 3PO-RO-BO
List of all 36 Mg2+ binding sites with the site type 3Pout·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
1vs6 B2970 3Pout·Rout·Bout B3326, B3327, B3328, B3329, B3330, B3331 A:B1669, C:B1986, A:B1987 G:B2550 G:B1954
2i2v B2938 3Pout·Rout·Bout B3189, B3190, B3191, B3192, B3193 G:B2446, G:B2447, G:B2502 U:B576 G:B2502
2qbk B2938 3Pout·Rout·Bout B3179, B3180, B3181, B3182, B3183 G:B2446, G:B2447, G:B2502 U:B576 G:B2502
2qox B2963 3Pout·Rout·Bout B3300, B3301, B3302, B3303, B3304 C:B2310, G:B2308, A:B2311 G:B2307 G:B2304
2qp1 B2964 3Pout·Rout·Bout B3809, B3810, B3811, B3812, B3813 C:B2310, G:B2308, A:B2311 G:B2307 G:B2304
2z4n B2939 3Pout·Rout·Bout B3182, B3183, B3184, B3185, B3186 G:B2446, G:B2447, G:B2502 U:B576 G:B2502
3df4 B3201 3Pout·Rout·Bout B4202, B4203, B4204, B4205, B4206 G:B2446, G:B2447, G:B2502 U:B576 G:B2502
3i1t A2979 3Pout·Rout·Bout A3395, A3396, A3397, A3398, A3399 G:A2447, G:A2502, C:A2501 U:A576 G:A2502
3i1z A1540 3Pout·Rout·Bout A1608, A1609, A1610, A1611, A1612 G:A557, A:A560, U:A562 A:A559 G:A566
3i20 A3032 3Pout·Rout·Bout A3620, A3621, A3622, A3623, A3624, A3625 G:A570, A:A973, U:A569 A:A972 A:A821
3i22 A3027 3Pout·Rout·Bout A3595, A3596, A3597, A3598, A3599, A3600 G:A570, A:A973, U:A569 A:A972 A:A820
3i22 A2955 3Pout·Rout·Bout A3281, A3282, A3283, A3284, A3285, A3286 A:A1669, C:A1986, A:A1987 G:A2550 G:A1954
3la5 A2 3Pout·Rout·Bout A111, A112, A117, A118, A395, A442 A:A55, U:A41, U:A40 A:A45 A:A45
3oas A2983 3Pout·Rout·Bout A3419, A3420, A3421, C477, C479 A:A2587, G:A2588, A:A2600 A:A2439 A:A2589
3ofd A2983 3Pout·Rout·Bout A3418, A3419, A3420, C477, C479 A:A2587, G:A2588, A:A2600 A:A2439 G:A2588
3ofq A2979 3Pout·Rout·Bout A3394, A3395, A3396, A3397, A3398 G:A2502, G:A2446, C:A2501 U:A576 G:A2502
3og0 A2982 3Pout·Rout·Bout A3417, A3418, A3419, A3420, A3421 A:A2587, G:A2588, A:A2600 A:A2439 A:A2589
3v29 A3575 3Pout·Rout·Bout A4679, A4680, A4681, A4682 G:A570, A:A973, U:A569 G:A972 A:A820
3v2d A3512 3Pout·Rout·Bout A5167, A5168, A5169, A5170, A5171 C:A698, G:A1555, C:A697 A:A1554 A:A1554
4bpe A5015 3Pout·Rout·Bout A2132, A2133, A2134, A2135, A2206, A2207 C:A608, A:A609, G:A1072 U:A1071 C:A1068
4bpn A5015 3Pout·Rout·Bout A6372, A6373, A6374, A6375, A6376, A6377 G:A1072, C:A608, A:A609 U:A1071 C:A1068
4bpn A5002 3Pout·Rout·Bout A6012, A6013, A6014, A6015, A6016, A6017 G:A920, A:A1005, A:A919 G:A1742 A:A1003
4bpo A5015 3Pout·Rout·Bout A2130, A2131, A2132, A2133, A2210, A2212 C:A608, A:A609, G:A1072 U:A1071 C:A1068
4bpp A5002 3Pout·Rout·Bout A7043, A7044, A7045, A7046, A7047, A7048 G:A920, A:A1005, A:A919 G:A1742 A:A1003
4dr4 A1658 3Pout·Rout·Bout A2088, A2089, A2090, A2091 A:A563, U:A560, C:A562 A:A559 G:A566

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>