`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 2qbb



2QBB (3.54Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with gentamicin. this file contains the 30s subunit of the second 70s ribosome, with gentamicin bound. the entire crystal structure contains two 70s ribosomes and is described in
List of all 59 Mg2+ binding sites in the PDB structure 2qbb 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
2qbb A2366 Ob G:A1417(O6) A2670, A2671, A2672, A2673, A2674 G:A1416, G:A1415 G:A1482, G:A1416
2qbb A2225 Ob G:A1370(O6) A2555, A2556, A2557, A2558, A2559 U:A1351, G:A1371
2qbb A2036 Nb G:A362(N7) A2399, A2400, A2401, A2402, A2403 G:A361, G:A362 G:A361
2qbb A2250 Nb G:A324(N7) A2575, A2576, A2577, A2578, T2255 G:A324, G:A326
2qbb A2213 2Nb G:A858(N7), G:A869(N7) A2545, A2546, A2547, A2548 G:A869, G:A858, C:A868, C:A857
2qbb A2202 Oph G:A21(OP1) A2536, A2537, A2538, A2539, A2540 G:A568, G:A567 A:A573, G:A567
2qbb A2283 Oph U:A1224(OP1) A2601, A2602, A2603, A2604 C:A1223 A:A977
2qbb A2062 Oph C:A1195(OP1) A2421, A2422, A2423, A2424, A2425 U:A1194 A:A1398
2qbb A2360 Oph C:A980(OP1) A2665, A2666, A2667, A2668, A2669 G:A1221, A:A1219
2qbb A2261 Oph·Pout A:A608(OP2) A2583, A2584, A2585, A2586, A2587 A:A607 A:A630, A:A609, C:A631, U:A610
2qbb A2239 Oph·Pout A:A1433(OP2) A2566, A2567, A2568, A2569, A2570 A:A1434 G:A1432 A:A1434, G:A1435
2qbb A2196 Oph·Pout A:A572(OP1) A2531, A2532, A2533, A2534, A2535 A:A573 A:A819
2qbb A2128 Oph·Pout A:A937(OP2) A2473, A2474, A2475, A2476, A2477 A:A938 A:A937, A:A938, G:A939
2qbb A2306 Oph·Pout G:A100(OP2) A2620, A2621, A2622, A2623, A2624 A:A101 C:A99, G:A100, A:A101, G:A64
2qbb A2340 Oph·Pout G:A111(OP2) A2648, A2649, A2650, A2651, A2652 C:A110 G:A112
2qbb A2056 Oph·Pout C:A934(OP1) A2416, A2417, A2418, A2419, A2420 U:A1345
2qbb A2334 Oph·Pout C:A352(OP2) A2643, A2644, A2645, A2646, A2647 G:A354 C:A330, C:A352, G:A331 C:A330, G:A354, A:A59
2qbb A2324 Oph·2Pout C:A536(OP1) A2635, A2636, A2637, A2638, A2639 C:A504, G:A537 C:A522
2qbb A2267 Oph·2Pout A:A1110(OP2) A2588, A2589, A2590, A2591, A2592 C:A1109, A:A1111 A:A1110, A:A1111, U:A1189
2qbb A2001 Oph·2Pout U:A891(OP2) A2370, A2371, A2372, A2373, A2374 A:A892, G:A903 U:A904, U:A905, A:A906

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>