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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 3orb



3ORB (3.3Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to cem-101. this file contains the 50s subunit of the first 70s ribosome bound to cem-101.
List of all 93 Mg2+ binding sites in the PDB structure 3orb 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 3 of 5 | | | 1 | 2 | 3 | 4 | 5
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3orb A2913 Oph·Ob A:A453(OP1) G:A450(O6) A3082, A3083, A3084, A3085 A:A454 A:A449
3orb A2931 Oph·Nb U:A810(OP1) A:A1253(N7) A3172, A3173, A3174, A3175 U:A811 C:A565
3orb A2989 cis-2Oph C:A1013(OP2), A:A1014(OP2) A3441, A3442, A3443, A3444
3orb A2934 cis-2Oph A:A945(OP2), C:A946(OP2) A3185, A3186, A3187, A3188 G:A822 C:A944
3orb A2941 cis-2Oph A:A1268(OP1), C:A2006(OP1) A3217, A3218, A3219, A3220 G:A2048 U:A1267
3orb A2948 cis-2Oph U:A1394(OP1), C:A1604(OP1) A3247, A3248, A3249, A3250
3orb A2954 cis-2Oph C:A1670(OP1), U:A1671(OP2) A3275, A3276, A3277, A3278 G:A2549
3orb A2977 cis-2Oph A:A2711(OP2), G:A2714(OP2) A3386, A3387, A3388, N428 U:A2713, C:A2710
3orb A2978 cis-2Oph A:A14(OP2), G:A15(OP2) A3389, A3390, A3391, A3392
3orb A2980 cis-2Oph G:A370(OP2), A:A422(OP2) A3398, A3399, A3400, A3401 U:A369 G:A370
3orb A2981 cis-2Oph G:A411(OP1), A:A2407(OP1) A3402, A3403, A3404, A3405 A:A2406, A:A412 A:A2406 A:A2407, U:A2408
3orb A2992 cis-2Oph A:A1359(OP1), G:A1360(OP2) A3455, A3456, A3457, A3458 G:A1361
3orb A3013 cis-2Oph G:A2582(OP2), G:A2583(OP2) A3548, A3549, A3550 G:A2581 U:A2584, G:A2608
3orb A3015 cis-2Oph G:A2574(OP1), C:A2575(OP2) A3553, A3554, A3555 C:A2507, C:A2573
3orb A3022 cis-2Oph C:A192(OP1), U:A2243(OP1) A3583, A3584, A3585, A3586 U:A193, A:A199
3orb A3024 cis-2Oph A:A1265(OP2), U:A2615(OP1) A3591, A3592, A3593, A3594 A:A2614 U:A1267
3orb A3032 cis-2Oph A:A1009(OP2), A:A1010(OP2) A3622, A3623, A3624, A3625 C:A1006, C:A1007 A:A1010
3orb L145 cis-2Oph A:A621(OP2), G:A622(OP2) A3130, L146, L147, L148
3orb A2970 cis-2Oph A:A2268(OP1), G:A2269(OP1) A3352, A3353, A3354, A3355 A:A2267 G:A2271, A:A2267
3orb B604 cis-2Oph A:B57(OP2), A:B58(OP2) B605, B606, B607, B608 G:B56 A:B58, A:B59, G:B23

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>