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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 3ofq




3OFQ (3.1Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to erythromycin. this file contains the 50s subunit of the second 70s ribosome.
List of all 109 Mg2+ binding sites in the PDB structure 3ofq 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 5 of 6 | | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3ofq A2943 Pout·3Bout A3225, A3226, A3227, A3228, A3229, A3230 U:A1267 A:A2009, G:A2010, U:A2011
3ofq A2937 2Pout A3199, A3200, A3201, A3202 G:A822, A:A945
3ofq A2962 2Pout A3310, A3311, A3312, A3313, A3314, A3315 A:A1916, U:A1915
3ofq A3002 2Pout·Bout A3498, A3499, A3500, A3501, A3502, A3503 C:A2047, C:A2616 G:A2048
3ofq A3029 2Pout·Bout A3600, A3601, A3602, A3603 U:A1188, A:A1189 G:A1190
3ofq A2989 2Pout·Rout·Bout A3439, A3440, A3441, A3442, A3443 A:A983, A:A572 G:A2029 U:A573
3ofq A2953 2Pout·2Bout A3266, A3267, A3268, A3269, A3270 G:A1456, A:A1453 G:A1456, U:A1457
3ofq A2992 2Pout·2Bout A3454, A3455, A3456, A3457, A3458, A3459 G:A976, G:A977 G:A977, G:A978
3ofq A2918 2Pout·2Bout A3103, A3104, A3105, A3106, A3107 A:A574, U:A576 U:A576, G:A577
3ofq A2922 2Pout·2Bout A3126, A3127, A3128, A3129, A3130, A3131 A:A616, A:A608 G:A618, G:A619
3ofq A2966 2Pout·Rout·2Bout A3331, A3332, A3333, A3334, A3335 U:A2034, C:A2025 A:A2033 U:A2026, U:A1130
3ofq A2978 2Pout·Rout·3Bout A3388, A3389, A3390, A3391, A3392, A3393 U:A2387, A:A2386 C:A2385 C:A2326, G:A2389, U:A2387
3ofq A3003 2Pout·4Bout A3504, A3505, A3506, A3507, A3508 A:A2705, C:A2704 A:A2705, A:A2706, U:A2701, U:A2707
3ofq A3037 3Pout A3637, A3638, A3639, A3640, A3641, N780 C:A2874, G:A2819, G:A2838
3ofq A2964 3Pout·Rout A3322, A3323, A3324, A3325 G:A1968, G:A2592, G:A1973 C:A1967
3ofq A3023 3Pout·Bout A3576, A3577, A3578, A3579 U:A790, C:A787, C:A791 U:A1781
3ofq A2915 3Pout·Bout A3088, A3089, A3090, A3091, A3092, A3093 A:A1008, G:A2038, C:A560 A:A1008
3ofq A2979 3Pout·Rout·Bout A3394, A3395, A3396, A3397, A3398 G:A2502, G:A2446, C:A2501 U:A576 G:A2502
3ofq A2986 3Pout·2Bout A3428, A3429, A3430, A3431 A:A217, A:A218, A:A428 A:A218, A:A219
3ofq A2968 3Pout·2Bout A3342, A3343, A3344, A3345, A3346, A3347 A:A2051, G:A2578, C:A2050 A:A2051, A:A2614

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>