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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 1m1k



1M1K (3.2Å) -- RIBOSOME : Co-crystal structure of azithromycin bound to the 50s ribosomal subunit of haloarcula marismortui
List of all 51 Mg2+ binding sites in the PDB structure 1m1k 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 3 | « Previous | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1m1k A8111 Nb G:A2609(N7) A3292, A3316, A5204, A5350, A9897 G:A2609 G:A2606, U:A2610
1m1k A8047 Oph·Pout A:A1098(OP2) A5872, A7476, A9730 A:A1097 G:A1099
1m1k A8039 Oph·Pout U:A115(OP2) A3560, A4701, A7403, A7404, A9508 G:A112 A:A114 A:A119, G:A118, A:A117
1m1k A8084 Oph·Pout A:A1742(OP2) A3229, A7436, A8841, A8964, A9347 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1m1k A8083 Oph·Pout A:A1754(OP2) A3302, A3749, A5957, A7435, A7485 C:A1753 A:A1755, A:A1754
1m1k A8040 Oph·2Pout U:A392(OP2) A3384, A4243, A7455, A7456, A9285 U:A391, C:A171
1m1k A8068 Oph·2Pout A:A2568(OP2) A3347, A4416, A5826, A7480, A9330 A:A2569, G:A2567 A:A2569, A:A2568
1m1k A8019 Oph·2Pout A:A2011(OP2) A3748, A6831, A7371, A7372, A7373 A:A1941, G:A1891 U:A1890 G:A1891, C:A1892
1m1k A8092 Oph·2Pout C:A1844(OP2) A3239, A3254, A7488 A:A1843, A:A1845 A:A1845
1m1k A8035 Oph·3Pout G:A1484(OP2) A3311, A7396, A7397, A7451, A7452 C:A1456, A:A1485, C:A1455 C:A1483 G:A1484, U:A1457
1m1k A8037 Oph·3Pout A:A2553(OP2) A3242, A7453, A8674, A9736, A9810 A:A2576, U:A2554, C:A2575 C:A2552 A:A2576
1m1k A8017 Oph·3Pout G:A456(OP2) A7352, A9006, E8355, E8359, E8463 A:A455, U:A457, G:A458
1m1k A8032 Oph·3Pout U:A2115(OP1) A3321, A3383, A3788, A9590, C8634 U:A2116, G:A2272, C:A2273
1m1k A8045 Oph·3Pout G:A1979(OP2) A7407, A7458, A7459, A7460 G:A1998, C:A1999, A:A1978
1m1k A8012 Oph·4Pout G:A28(OP1) A3241, A7446, A8635, A9231, A9825 C:A1305, U:A1304, C:A1343, G:A1344
1m1k A8093 Oph·Or G:A1071(OP1) A:A1070(O2') A3244, A3276, A3318, A9277 G:A627 A:A914, A:A913, G:A1071
1m1k A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3227, A3551, A5777, A8986 G:A1490, A:A1487, U:A1488 G:A1490, G:A1489
1m1k A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3520, A5002, A5635, A9100 U:A904 G:A622, A:A1356
1m1k A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3209, A7061, A7447, A9819 C:A910, U:A909 G:A1292, G:A911
1m1k A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3253, A3761, A7342, A8630 G:A2481 C:A2536, A:A2101 G:A2480, G:A2481, A:A2101

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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