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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 2 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 A2951 Oph·Pout C:A1604(OP1) A3259, A3260, A3261, A3262 U:A1394
3ofq A2947 Oph·Pout U:A1313(OP1) A3241, A3242, A3243, T255, T257 G:A1334
3ofq A2939 Oph·Pout U:A963(OP1) A3206, A3207, A3208, A3209, A3210 A:A947 C:A2498
3ofq A2909 Oph·Pout U:A120(OP2) A3061, A3062, A3063, A3064, A3065 G:A123 G:A123, G:A124
3ofq A2936 Oph·Pout A:A945(OP1) A3194, A3195, A3196, A3197, A3198 G:A831 G:A831, U:A832, C:A944
3ofq A2932 Oph·Pout A:A802(OP2) A3176, A3177, A3178, A3179, A3180 A:A675
3ofq A2957 Oph·Pout U:A1671(OP2) A3287, A3288, A3289, A3290 C:A1670
3ofq A2931 Oph·Pout A:A800(OP1) A3171, A3172, A3173, A3174, A3175 A:A204 G:A799, A:A203 U:A206, A:A191
3ofq A3035 Oph·Pout A:A943(OP2) A3626, A3627, A3628, A3629, A3630 U:A832
3ofq A2954 Oph·2Pout U:A1647(OP2) A3271, A3272, A3273, A3274, A3275 A:A1272, C:A1617 C:A1646, A:A1616 G:A1271
3ofq A2916 Oph·2Pout U:A567(OP1) A3094, A3095, A3096, A3097, L145 G:A809, G:A808 U:A810, G:A809
3ofq A2913 Oph·2Pout A:A526(OP1) A3079, A3080, A3081, A3082 A:A528, C:A527
3ofq A2910 Oph·2Pout G:A297(OP2) A3066, A3067, A3068, A3069, A3642 G:A338, G:A298 G:A297
3ofq A2976 Oph·2Pout A:A2270(OP2) A3378, A3379, A3380, A3381, A3382 A:A2267, G:A2271 A:A2266 G:A2271, U:A2272
3ofq A2999 Oph·2Pout C:A1658(OP1) A3488, A3489, A3490, A3491, D564 G:A1659, U:A744 A:A743
3ofq A2960 Oph·2Pout G:A1776(OP2) A3301, A3302, A3303, A3304, A3305 U:A1775, A:A1981 G:A1776
3ofq A2965 Oph·2Pout A:A1970(OP2) A3326, A3327, A3328, A3329, A3330 A:A1900, G:A1835 U:A1834 G:A1835, C:A1836
3ofq A3017 Oph·2Pout G:A862(OP2) A3550, A3551, A3552, A3553, A3554 A:A861, A:A910 G:A862, A:A863
3ofq A2961 Oph·2Pout G:A1828(OP1) A3306, A3307, A3308, A3309, C338 G:A1973, A:A1772
3ofq A2959 Oph·2Pout C:A1774(OP1) A3296, A3297, A3298, A3299, A3300 U:A1775, A:A1786 A:A1772 A:A1789, G:A1776

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>