`

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

Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 4dr7




4DR7 (3.75Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the second codon position, and streptomycin bound
List of all 34 Mg2+ binding sites in the PDB structure 4dr7 in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 1 of 2 | « Previous | | 1 | 2
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4dr7 A1701 Ob G:A1370(O6) A2251, A2252, A2253 U:A1372
4dr7 A1616 Oph G:A21(OP1) A2044, A2045, A2046 G:A568 A:A563, A:A573
4dr7 A1623 Oph A:A766(OP2) A2058, A2059, A2060, A2061 U:A813, C:A811, C:A812
4dr7 A1690 Oph G:A1094(OP1) A2218, A2219, A2220, A2221 A:A1067, G:A1068, G:A1387, C:A1388
4dr7 A1615 Oph A:A937(OP2) A2040, A2041, A2042, A2043 G:A939, A:A938
4dr7 A1662 Oph·Pout C:A352(OP2) A2154, A2155, A2156, A2157, A2158 G:A354 G:A331, C:A352 A:A59, C:A330, G:A354
4dr7 A1713 Oph·2Pout A:A794(OP1) A2278, A2279, A2280, A2281 A:A782, C:A783 G:A1521 C:A1515
4dr7 A1633 Oph·2Pout G:A588(OP2) A2090, A2091, A2092, A2093 G:A644, C:A589
4dr7 A1672 Oph·3Pout A:A195(OP2) A2176, A2177, A2178, A2179 C:A178, A:A179, C:A194 U:A180, G:A181
4dr7 A1638 Oph·3Pout C:A578(OP1) A2104, A2105, A2106, A2107 U:A820, G:A576, C:A817
4dr7 A1716 cis-2Oph A:A964(OP1), U:A1199(OP1) A2286, A2287, A2288 G:A1198
4dr7 A1654 cis-2Oph U:A1095(OP2), C:A1096(OP2) A2136, A2137, A2138 G:A1108
4dr7 A1692 cis-2Oph C:A1054(OP2), G:A1197(OP2) A2225, A2226, A2227 G:A1053 G:A1197
4dr7 A1635 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A2097, A2098 U:A571
4dr7 A1878 3Bout A2831, A2832, A2833, A2834, A2835, A2836 C:A1264, G:A1265, G:A1266
4dr7 A1788 4Bout A2302, A2303, A2304, A2305, A2306, A2307 G:A593, G:A594, G:A592, U:A646
4dr7 A1697 Rout·4Bout A2236, A2237, A2238, A2239 C:A1359 C:A980, C:A979, A:A1360, G:A1361
4dr7 A1698 Pout·Bout A2240, A2241, A2242, A2243 U:A1450 G:A700
4dr7 A1805 Pout·3Bout A2400, A2401, A2402, A2403, A2404, A2405 A:A414 G:A424, G:A425, G:A426
4dr7 A1872 Pout·2Rout·2Bout A2796, A2797, A2798, A2799, A2800, A2801 A:A702 C:A1452, C:A701 C:A701, G:A703

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>