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

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Representative site 2qou:A1560, See in JSmolMgRNA representative site for type NB             Click on the image to toggle views


Site type: Nb

Schematic drawing for
Nb

MgRNA type NB
List of all 284 Mg2+ binding sites with the site type Nb 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"
Page 7 of 12 | | | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v2d A3207 Nb G:A2002(N7) A4261, A4262, A4263, A4264, A4265 G:A2002, A:A2001 G:A2003
3v2d A3120 Nb G:A298(N7) A4011, A4012, A4013, A4014, A4015 C:A297, G:A298, G:A338
3v2d A3407 Nb G:A2032(N7) A4852, A4853, A4854, A4855, A4856 G:A2032 C:A2055, A:A2572, G:A2454, C:A2499, U:A2500, A:A2453
3v2e A1764 Nb G:A362(N7) A2201, A2202, A2203, A2204 G:A361, G:A362 G:A361
3v2e A1741 Nb G:A324(N7) A2143, A2144, T201, T202 U:A323
3v2f A3201 Nb G:A2032(N7) A3920, A3921, A3922, A3923, A3924 G:A2032 A:A2453, C:A2055, C:A2499, A:A2572, G:A2454, U:A2500
3v2f A3205 Nb G:A2002(N7) A3939, A3940, A3941, A3942, A3943 G:A2002, A:A2001 G:A2003
4dh9 A1918 Nb G:A251(N7) A2231, A2232, A2233, A2234 A:A270, C:A271 G:A266, C:A271
4dha A3674 Nb G:A2032(N7) A4646, A4647, A4648, A4649, A4650 G:A2032 C:A2055, A:A2572, G:A2454, C:A2499, U:A2500, A:A2453
4dha A3721 Nb G:A2353(N7) A4794, A4795, A4796, A4797 A:A2352 G:A2354
4dha A3554 Nb G:A2002(N7) A4221, A4222, A4223, A4224 A:A2001, G:A2003
4dha A3683 Nb G:A307(N7) A4684, A4685, A4686, A4687 G:A309, U:A306, G:A307
4dhb A1789 Nb G:A362(N7) A2107, A2108, A2109, A2110 G:A362 G:A361
4dhb A1778 Nb G:A324(N7) A2084, A2085, T301, T302 U:A323
4dhc A3625 Nb G:A2375(N7) A4487, A4488, A4489, A4490 A:A2377
4dhc A3412 Nb G:A2002(N7) A3895, A3896, A3897, A3898, A3899 G:A2002 G:A2004
4dhc A3410 Nb G:A2032(N7) A3888, A3889, A3890, A3891, A3892 G:A2032 G:A2454 C:A2055, C:A2499, A:A2572, U:A2500
4dr1 A1688 Nb G:A362(N7) A2044, A2045, A2046, L301
4dr1 A1695 Nb G:A324(N7) A2054, A2055, T201, T202
4dr2 A1726 Nb G:A362(N7) A2299, A2300, A2301, A2302
4dr2 A1734 Nb G:A324(N7) A2324, A2325, A2326, A2327, A2328 G:A324, G:A326
4dr3 A1681 Nb G:A362(N7) A2047, A2048, A2049, A2050 G:A361, G:A362
4dr4 A1737 Nb G:A324(N7) A2259, A2260, A2261, A2262 G:A324
4dr4 A1729 Nb G:A362(N7) A2244, A2245, A2246, L302 G:A361, G:A362
4dr5 A1681 Nb G:A362(N7) A2095, A2096, A2097, A2098 G:A362 G:A361

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
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>