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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 2qb9




2QB9 (3.54Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with gentamicin. this file contains the 30s subunit of the first 70s ribosome, with gentamicin bound. the entire crystal structure contains two 70s ribosomes and is described in
List of all 57 Mg2+ binding sites in the PDB structure 2qb9 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
2qb9 A2109 Ob G:A1050(O6) A2446, A2447, A2448, A2449, A2450
2qb9 A2355 Ob G:A1417(O6) A2647, A2648, A2649, A2650, A2651 G:A1416, G:A1415 G:A1416, G:A1482
2qb9 A2199 Ob G:A1370(O6) A2519, A2520, A2521, A2522, A2523 G:A1371, U:A1351
2qb9 A2231 Nb G:A324(N7) A2545, A2546, A2547, A2548, T2236 U:A323, G:A324
2qb9 A2103 Nb G:A362(N7) A2443, A2444, A2445, L2107, L2108 G:A362, A:A364
2qb9 A2187 2Nb G:A858(N7), G:A869(N7) A2509, A2510, A2511, A2512 G:A858, G:A869, C:A868
2qb9 A2176 Oph G:A21(OP1) A2500, A2501, A2502, A2503, A2504 G:A567, A:A573, A:A563
2qb9 A2064 Oph A:A937(OP2) A2411, A2412, A2413, A2414, A2415 A:A938, G:A939
2qb9 A2288 Oph G:A100(OP2) A2591, A2592, A2593, A2594, A2595 G:A64, G:A100, A:A101
2qb9 A2213 Oph A:A1433(OP2) A2530, A2531, A2532, A2533, A2534 A:A1434, G:A1435
2qb9 A2242 Oph·Pout A:A608(OP2) A2553, A2554, A2555, A2556, A2557 A:A609 A:A630, A:A609, U:A610
2qb9 A2316 Oph·Pout C:A352(OP2) A2614, A2615, A2616, A2617, A2618 G:A354 G:A331, C:A352, C:A330 C:A330, A:A59
2qb9 A2025 Oph·Pout C:A934(OP1) A2379, A2380, A2381, A2382, A2383 U:A1345
2qb9 A2322 Oph·Pout G:A111(OP2) A2619, A2620, A2621, A2622, A2623 C:A110 G:A112, G:A111
2qb9 A2170 Oph·Pout A:A572(OP1) A2495, A2496, A2497, A2498, A2499 A:A573
2qb9 A2306 Oph·2Pout C:A536(OP1) A2606, A2607, A2608, A2609, A2610 C:A504, G:A537 C:A522
2qb9 A2248 Oph·2Pout A:A1110(OP2) A2558, A2559, A2560, A2561, A2562 C:A1109, A:A1111 A:A1110, A:A1111, U:A1189
2qb9 A2264 Oph·2Pout U:A1224(OP1) A2571, A2572, A2573, A2574, A2575 G:A951, U:A952 A:A977
2qb9 A2001 Oph·3Pout C:A578(OP1) A2359, A2360, A2361, A2362, A2363 C:A817, C:A576, U:A820 G:A575
2qb9 A2038 Oph·3Pout A:A560(OP2) A2390, A2391, A2392, A2393, A2394 U:A562, A:A563, G:A557 A:A559 G:A566

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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