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 1 of 6 | « Previous | | 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 A2927 Ob U:A746(O4) A3150, A3151, A3152, A3153, A3154 U:A2580, C:A2611, C:A2610, U:A744 G:A745
3ofq A3032 Ob U:A2593(O4) A3615, A3616, A3617, C735, C739 G:A2592, C:A2591 G:A2592
3ofq B590 Ob U:B95(O4) B591, B592, B593, V594, V595 U:B80
3ofq A3000 Ob U:A2419(O4) A3492, A3493, 3568, 3570, 3571
3ofq A2933 Nb A:A1253(N7) A3181, A3182, A3183, A3184 U:A810, U:A811 G:A1252
3ofq A3014 Ob·Nb G:A1601(N7), U:A1602(O4) A3539, A3540, A3541, A3542 G:A1601, C:A1600, A:A1342
3ofq A2925 2Nb G:A733(N7), A:A761(N7) A3140, A3141, A3142, A3143 A:A761, G:A733, G:A760, C:A732 G:A760
3ofq A2950 2Nb G:A1358(N7), G:A1371(N7) A3255, A3256, A3257, A3258 G:A1358, C:A1357, G:A1371
3ofq A2941 Oph A:A1156(OP2) A3215, A3216, A3217, A3218, A3219 C:A998, G:A1157, G:A997
3ofq A2958 Oph A:A1678(OP2) A3291, A3292, A3293, A3294, A3295 A:A1678, A:A1679
3ofq A2911 Oph U:A419(OP1) A3070, A3071, A3072, A3073, A3074 G:A230
3ofq A2923 Oph A:A621(OP2) A3132, A3133, L147, L148
3ofq A2914 Oph G:A536(OP2) A3083, A3084, A3085, A3086, A3087
3ofq A2987 Oph A:A299(OP2) A3432, A3433, A3434, U491, U495 A:A299, G:A338, U:A339, A:A300
3ofq A2939 Oph·Pout U:A963(OP1) A3206, A3207, A3208, A3209, A3210 A:A947 C:A2498
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 A2931 Oph·Pout A:A800(OP1) A3171, A3172, A3173, A3174, A3175 A:A204 G:A799, A:A203 U:A206, A:A191
3ofq A2909 Oph·Pout U:A120(OP2) A3061, A3062, A3063, A3064, A3065 G:A123 G:A123, G:A124
3ofq A2908 Oph·Pout U:A120(OP2) A3056, A3057, A3058, A3059, A3060 G:A121 A:A119 G:A122, G:A123

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>