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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 1hr2



1HR2 (2.25Å) -- RNA : Crystal structure analysis of a mutant p4-p6 domain (delc209) of tetrahymena themophila group i intron.
List of all 27 Mg2+ binding sites in the PDB structure 1hr2 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
1hr2 A11 Ob G:A188(O6) A342, A343, A344, A345, A346 U:A168, U:A182, C:A166, A:A183, C:A165 A:A183
1hr2 B12 Ob G:B188(O6) B346, B347, B348, B349, B350 U:B182, U:B168, A:B183, C:B166, C:B165 A:B183
1hr2 A5 Ob·Nb G:A163(N7), G:A164(O6) A328, A329, A330, A331 U:A162, G:A163 U:A177 A:A178, U:A177
1hr2 B6 Ob·Nb G:B163(N7), G:B164(O6) B332, B333, B334, B335 U:B162, G:B163 A:B178, U:B177
1hr2 A9 Oph·Pout A:A173(OP2) A337, A338, A339, A340, A341 A:A172 A:A171 A:A173, G:A174
1hr2 B10 Oph·Pout A:B173(OP2) B341, B342, B343, B344, B345 A:B172 A:B171 G:B174, A:B173, G:B175
1hr2 B13 Oph·Pout G:B112(OP2) B351, B352, B353, B354, B355 C:B204 A:B113, G:B112
1hr2 A7 Oph·3Pout A:A171(OP2) A332, A333, A334, A335, A336 C:A165, C:A170, U:A168 U:A167 A:A171, U:A167
1hr2 B8 Oph·3Pout A:B171(OP2) B336, B337, B338, B339, B340 C:B170, C:B165, U:B168 U:B167 A:B171, U:B167
1hr2 A1 fac-3Oph A:A183(OP1), A:A184(OP2), A:A186(OP2) A322, A323, A324 A:A184, A:A186
1hr2 B2 fac-3Oph A:B183(OP1), A:B184(OP2), A:B186(OP2) B326, B327, B328 A:B184, A:B186
1hr2 A3 mer-3Oph A:A184(OP1), A:A186(OP1), A:A187(OP2) A325, A326, A327 A:A183, G:A188
1hr2 B4 mer-3Oph A:B184(OP1), A:B186(OP1), A:B187(OP2) B329, B330, B331 A:B183, G:B188
1hr2 A27 Rout·Bout A389, A390, A391, A392, A393, A394 C:A124 G:A194
1hr2 B19 2Bout B368, B369, B370, B371, B372, B373 G:B129, G:B191
1hr2 A18 2Bout A359, A360, A361, A362, A363, A364 G:A129, G:A191
1hr2 A22 2Bout A371, A372, A373, A374, A375, A376 G:A242, U:A243
1hr2 B23 3Bout B380, B381, B382, B383, B384, B385 U:B243, G:B242, A:B230
1hr2 A24 3Bout A377, A378, A379, A380, A381, A382 G:A134, U:A135, U:A182
1hr2 A26 3Bout A383, A384, A385, A386, A387, A388 G:A111, G:A112, G:A110

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].

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