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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 1kc8



1KC8 (3.01Å) -- RIBOSOME : Co-crystal structure of blasticidin s bound to the 50s ribosomal subunit
List of all 41 Mg2+ binding sites in the PDB structure 1kc8 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1kc8 A8083 Oph·Pout A:A1754(OP2) A3712, A4154, A6358, A7846, A7899 C:A1753 A:A1755, A:A1754
1kc8 A8039 Oph·Pout U:A115(OP2) A3970, A5106, A7815, A7816, A9906 G:A112 A:A114 A:A119, G:A118, A:A117
1kc8 A8019 Oph·2Pout A:A2011(OP2) A4153, A7237, A7782, A7783, A7784 A:A1941, G:A1891 U:A1890 G:A1891, C:A1892
1kc8 A8068 Oph·2Pout A:A2568(OP2) A3756, A4818, A6223, A7892, G920 A:A2569, G:A2567 A:A2569, A:A2568
1kc8 A8037 Oph·3Pout A:A2553(OP2) A3131, A3208, A3654, A7864, A9081 C:A2575, A:A2576, U:A2554 C:A2552 A:A2576
1kc8 A8058 Oph·3Pout G:A2013(OP2) A3768, A7823, A7824, C8633, C8635 G:A1884, U:A1883, C:A2626
1kc8 A8021 Oph·3Pout G:A2304(OP2) A3643, A3644, A7769, A7770, A9959 A:A2301, A:A2305, A:A2303 A:A2305, G:A2304, U:A2306
1kc8 A8072 Oph·3Pout U:A954(OP1) A3230, A4000, A7420, A7836, A7893 C:A2298, G:A2299, A:A2301
1kc8 A8091 Oph·4Pout G:A918(OP1) A3321, A6482, A7851, A9095, A9544 C:A2294, C:A2391, A:A2465, U:A919 A:A2465
1kc8 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3877, A4018, A4158, N8650 G:A267, U:A268
1kc8 A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3637, A3962, A6173, A9397 G:A1490, A:A1487, U:A1488 G:A1489, G:A1490
1kc8 A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3930, A5406, A6029, A9507 U:A904 G:A622, A:A1356
1kc8 A8034 cis-2Oph A:A2302(OP1), A:A2303(OP1) A3648, A3774, A4866, A7807 A:A2301 A:A2301, G:A2304
1kc8 A8022 cis-2Oph G:A2097(OP2), G:A2540(OP1) A3874, A7774, A9113, A9458 A:A2095 A:A2096 G:A2097
1kc8 A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A4208, A4492, A7845, A7898 C:A1431 A:A1684, A:A1691, C:A1692 U:A1722, A:A1691
1kc8 A8074 cis-2Oph A:A1286(OP1), A:A1287(OP1) A7833, A7834, A7894, X7874 A:A1287
1kc8 A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A7828, A7829, A7830, A9816 A:A2649 U:A1371
1kc8 A8052 cis-2Oph U:A1125(OP1), G:B3092(OP1) A3628, A7889, A9589, B8418 C:A1126 C:A1129, G:B3090
1kc8 A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5874, A6263, A7874, A7910 C:A2745, U:A2749
1kc8 A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3218, A3617, A7469, A7858 C:A910, U:A909 G:A911, G:A1292

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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