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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 4dr5



4DR5 (3.45Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, crystallographically disordered cognate transfer rna anticodon stem-loop and streptomycin bound
List of all 69 Mg2+ binding sites in the PDB structure 4dr5 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 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4dr5 A1701 Ob G:A1370(O6) A2142, A2143, A2144 G:A1371, U:A1372
4dr5 A1681 Nb G:A362(N7) A2095, A2096, A2097, A2098 G:A362 G:A361
4dr5 A1707 Oph C:A980(OP1) A2157, A2158, A2159 G:A1220
4dr5 A1614 Oph G:A21(OP1) A1942, A1943, A1944 G:A568
4dr5 A1623 Oph A:A766(OP2) A1956, A1957, A1958, A1959 C:A811, A:A767, C:A812
4dr5 A1660 Oph·Pout C:A352(OP2) A2043, A2044, A2045, A2046, A2047 G:A354 C:A352 C:A330, A:A59, G:A354
4dr5 A1613 Oph·Pout A:A937(OP2) A1938, A1939, A1940, A1941 A:A938 G:A939, A:A937, A:A938
4dr5 A1604 Oph·Pout G:A750(OP2) A1911, A1912, A1913, A1914 C:A749 G:A752
4dr5 A1702 Oph·Pout C:A461(OP2) A2145, A2146, A2147, A2148 C:A458
4dr5 A1692 Oph·Pout A:A53(OP2) A2120, A2121, A2122 A:A353 G:A316
4dr5 A1619 Oph·2Pout A:A768(OP2) A1948, A1949, A1950, A1951 A:A767, U:A804 A:A768, G:A769
4dr5 A1671 Oph·2Pout A:A195(OP2) A2069, A2070, A2071, A2072 A:A179, C:A194 U:A180, G:A181
4dr5 A1654 Oph·2Pout A:A1110(OP2) A2030, A2031, A2032, A2033 C:A1109, A:A1111 C:A1189, A:A1111
4dr5 A1635 Oph·3Pout C:A578(OP1) A1996, A1997, A1998, A1999 U:A820, G:A576, C:A817
4dr5 A1630 Oph·3Pout G:A588(OP2) A1982, A1983, A1984, A1985 G:A644, C:A645, C:A589
4dr5 A1712 Oph·Ob A:A1238(OP2) C:A1335(O2) A2168, A2169, A2170 U:A1301
4dr5 A1690 cis-2Oph G:A558(OP1), U:A560(OP1) A2112, A2113, A2114, A2115 A:A298, G:A299, G:A566, A:A300
4dr5 A1716 cis-2Oph A:A964(OP1), U:A1199(OP1) A2179, A2180, A2181 G:A1198
4dr5 A1693 cis-2Oph C:A1054(OP2), G:A1197(OP2) A2123, A2124, A2125, A2126 G:A1197
4dr5 A1675 cis-2Oph U:A182(OP1), G:A183(OP2) A2074, A2075, A2076, A2077 G:A181 G:A183

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>