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

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Representative site 3df3:A2121, See in JSmolMgRNA representative site for type 2PO-RO-2BO     Click on the image to toggle views

Site type: 2Pout·Rout·2Bout

Schematic drawing for

MgRNA type 2PO-RO-2BO
List of all 33 Mg2+ binding sites with the site type 2Pout·Rout·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
1vq5 08108 2Pout·Rout·2Bout 06380, 07720, 08200, 08201, 08202 U:01977, A:01978 U:01977 G:01986, G:02000
1yhq 08085 2Pout·Rout·2Bout 06570, 07939, 08395, 08396, 08397 U:01977, A:01978 U:01977 G:01986, G:02000
1yjn 08107 2Pout·Rout·2Bout 06114, 07485, 07867, 07868, 07869 U:01977, A:01978 U:01977 G:01986, G:02000
3df3 A2121 2Pout·Rout·2Bout A4122, A4123, A4124, A4125, A4126, A4127 A:A329, A:A315 C:A328 G:A319, A:A320
3i1r A2936 2Pout·Rout·2Bout A3192, A3193, A3194, A3195, A3196 G:A831, A:A945 C:A944 G:A831, U:A832
3i20 A2920 2Pout·Rout·2Bout A3123, A3124, A3125, A3126, A3127, A3128 A:A1253, G:A583 C:A1251 G:A583, C:A584
3i20 A2960 2Pout·Rout·2Bout A3303, A3304, A3305, A3306, A3307, A3308 A:A1936, G:A1959 A:A1936 A:A1960, G:A1959
3i22 A2988 2Pout·Rout·2Bout A3441, A3442, A3443, A3444, A3445 A:A572, A:A983 G:A2029 A:A572, U:A573
3i8g A1 2Pout·Rout·2Bout A2, A2293, A2294, A2295, A2296, 14 U:145, U:146 U:A789 A:A790, G:A791
3oas A2967 2Pout·Rout·2Bout A3341, A3342, A3343, A3344, A3345, A3346 A:A2051, G:A2578 C:A2050 A:A2051, A:A2614
3ofq A2966 2Pout·Rout·2Bout A3331, A3332, A3333, A3334, A3335 U:A2034, C:A2025 A:A2033 U:A2026, U:A1130
3r8s A2951 2Pout·Rout·2Bout A3313, A3314, A3315, A3316, A3317 G:A1455, A:A1453 C:A1454 G:A1456, U:A1457
4bpe A5019 2Pout·Rout·2Bout A2031, A2032, A2033, A2060, A2061, A2268 A:A99, G:A347 A:A99 G:A348, G:A347
4bpo A5019 2Pout·Rout·2Bout A2032, A2033, A2034, A2058, A2059, A2355 A:A99, G:A347 A:A99 G:A348, G:A347
4bpp A5019 2Pout·Rout·2Bout A7315, A7316, A7317, A7318, A7319, A7320 A:A99, G:A347 A:A99 G:A347, G:A348
4dha A3647 2Pout·Rout·2Bout A4532, A4533, A4534, A4535, A4536, A4537 G:A1332, C:A1333 U:A1313 U:A1335, G:A1334
4duz A1841 2Pout·Rout·2Bout A2223, A2224, A2225, A2226, A2227 C:A1303, U:A1301 G:A1331 G:A1305, G:A1304
4dv3 A1850 2Pout·Rout·2Bout A2224, A2225, A2226, A2227, A2228 C:A1303, U:A1301 G:A1331 G:A1305, G:A1304
4dv7 A1864 2Pout·Rout·2Bout A2240, A2241, A2242, A2243, A2244 C:A1303, U:A1301 G:A1331 G:A1304, G:A1305
4gaq A1615 2Pout·Rout·2Bout A1764, A1765, A1766, A1767 A:A533, G:A515 A:A532 G:A515, U:A516
4gar A3046 2Pout·Rout·2Bout A3416, A3417, A3418, A3419, A3420 G:A1455, A:A1453 C:A1454 G:A1456, U:A1457
4nw1 A3335 2Pout·Rout·2Bout A4263, A4264, A4265, A4266, A4267 A:A945, G:A831 G:A944 G:A944, G:A831
4qcn A3690 2Pout·Rout·2Bout A5161, A5162, A5163, A5164, A5165 G:A733, C:A734 A:A732 U:A735, G:A737
4qcq A3169 2Pout·Rout·2Bout A4154, A4155, A4156, V101 C:A1496, G:A1497 U:V17 G:A1497, U:A1498
4qct A3564 2Pout·Rout·2Bout A4775, A4776, A4777, A4778 G:A686, C:A687 A:A685 U:A688, A:A689

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>