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

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Representative site 2qow:A1583, See in JSmolMgRNA representative site for type OR             Click on the image to toggle views

Site type: Or

Schematic drawing for

MgRNA type OR
List of all 22 Mg2+ binding sites with the site type Or 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
2qou A1547 Or C:A934(O5') A1917, A1918, A1919, A1920, A1921 U:A1345, C:A934
2qow A1583 Or C:A934(O5') A2083, A2084, A2085, A2086, A2087 C:A934, U:A1345
3df1 A2025 Or C:A934(O5') A4026, A4027, A4028, A4029, A4030 C:A934, U:A1345
3df3 A2056 Or C:A934(O5') A4057, A4058, A4059, A4060, A4061 C:A934, U:A1345
3oas A3003 Or A:A2448(OP2) G:A2447(O3') A3511, A3512, A3513 U:A2449, C:A2498, C:A2499, A:A2450 A:A2497, U:A2449 G:A2447
3ofr A3002 Or U:A2022(O5') A3499, A3500, A3501, A3502, A3503 U:A2022, C:A2023 C:A2021 A:A529
3ucu R1 Or A:R48(O5') R673, R674, R675, R676, A3 A:R47 A:R91, G:R14, G:A2
3v23 A3407 Or U:A2406(O5') A4296, A4297, A4298, A4299, A4300 G:A2407, U:A2408, U:A2406 G:A2410, U:A2408, G:A2409
3v23 A3404 Or A:A528(O2') A4285, A4286, A4287, A4288, A4289 A:A529
3v27 A3458 Or A:A536(O2') A4462, A4463, A4464, A4465, N201
3v27 A3358 Or U:A2849(O2') A4060, A4061, A4062, A4063 A:A2850 G:A2864, U:A2865
3v2e A1747 Or U:A1364(O2') A2159, A2160, A2161, A2162 A:A949, G:A1233, G:A1365 G:A971, U:A1364, A:A949, G:A1233
3v7e C919 Or G:C1(O5') C1003, D501, D502 G:D223, C:D225 G:D222
4dha A3800 Or A:A670(O2') A5086, A5087, A5088, A5089 C:A671, G:A666 U:A667, G:A668
4dv6 A1687 Or C:A1054(O5') A2047, A2048, A2049 G:A1198, C:A1054, G:A1197 U:A1196
4gaq A1630 Or G:A1053(O2') A1847, A1848, A1849, A1850 C:A1054, A:A1197, G:A1198
4gar A3021 Or A:A750(O3') A3312, A3313, A3314, A3315 A:A1614, A:A752 G:A1613, C:A1617
4gar A3027 Or G:A1252(O2') A3337, A3338, A3339, L303 C:A812, U:A810 C:A1251 A:A1253
4pec A3063 Or G:A2061(O5') A3486, A3487, A3488, A3489 G:A2061, G:A2502 C:A2501, A:A2060 G:A2446, G:A2445
4qcz A3516 Or A:A70(O3') A4671, A4672, A4673, A4674 G:A111
4tox A3065 Or G:A2061(O5') A3489, A3490, A3491, A3492 G:A2502 C:A2501, A:A2060 G:A2446, G:A2445
4tp7 A3065 Or G:A2061(O5') A3486, A3487, A3488, A3489 A:A2062, G:A2502, G:A2061 C:A2501, A:A2060 G:A2446, G:A2445

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/)
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