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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 3 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 A3026 Oph·2Pout A:A1676(OP2) A3586, A3587, A3588, A3589, A3590 C:A1675, A:A1677 A:A1677
3ofq A3020 Oph·3Pout G:A1828(OP2) A3564, A3565, A3566, A3567, A3568 U:A1827, G:A1972, C:A1788 G:A1828
3ofq A2945 Oph·3Pout A:A2005(OP1) A3235, A3236, A3237, A3238 A:A1268, A:A1269, C:A2006 A:A1269
3ofq A2981 Oph·3Pout A:A2518(OP2) A3405, A3406, A3407, A3408, A3409 C:A2540, A:A2541, U:A2519 A:A2541
3ofq A3018 Oph·3Pout A:A1938(OP2) A3555, A3556, A3557, A3558, A3559 A:A1937, C:A1957, C:A1958 G:A1770
3ofq A3019 Oph·4Pout U:A2243(OP1) A3560, A3561, A3562, A3563 C:A192, A:A199, C:A198, U:A193
3ofq A2948 Oph·4Pout G:A1333(OP2) A3244, A3245, A3246, A3247, A3248 C:A1314, G:A1332, G:A1334, U:A1313 G:A1331 G:A1333
3ofq A3010 Oph·4Pout C:A31(OP1) A3526, A3527, A3528, A3529, A3530 G:A1239, C:A1200, U:A1199, U:A1240 A:A1214
3ofq A2974 Oph·Ob C:A2248(OP2) U:A2249(O4) A3370, A3371, A3372, A3373 A:A2247, C:A2066
3ofq A2990 Oph·Ob G:A818(OP2) G:A1187(O6) A3444, A3445, A3446, A3447 C:A817, G:A1186
3ofq A2997 Oph·Ob A:A1439(OP2) U:A1440(O4) A3478, A3479, A3480, A3481
3ofq A2912 Oph·Nb A:A453(OP1) G:A450(N7) A3075, A3076, A3077, A3078 A:A449 A:A449
3ofq A3001 cis-2Oph U:A576(OP1), A:A2503(OP1) A3494, A3495, A3496, A3497 U:A2504, G:A577, G:A2057
3ofq A2940 cis-2Oph U:A999(OP2), C:A1153(OP2) A3211, A3212, A3213, A3214 C:A998, C:A1152 G:A1154
3ofq A2969 cis-2Oph G:A2056(OP2), G:A2057(OP2) A3348, A3349, A3350, A3351 A:A2503, U:A2504 A:A2058
3ofq A2975 cis-2Oph A:A2268(OP1), G:A2269(OP1) A3374, A3375, A3376, A3377 G:A2271
3ofq A2983 cis-2Oph C:A2579(OP1), C:A2611(OP2) A3416, A3417, A3418, A3419 C:A2612 C:A2610, G:A2576
3ofq A2985 cis-2Oph A:A2711(OP2), G:A2714(OP2) A3424, A3425, A3426, A3427 U:A2713, C:A2710
3ofq A3007 cis-2Oph A:A730(OP2), C:A731(OP2) A3518, A3519, A3520 U:A762, A:A761
3ofq A3021 cis-2Oph A:A1265(OP2), U:A2615(OP2) A3569, A3570, A3571, A3572

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>