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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 3ofd



3OFD (3.19Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to chloramphenicol. this file contains the 50s subunit of the second 70s ribosome.
List of all 96 Mg2+ binding sites in the PDB structure 3ofd 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 5 | « Previous | | 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
3ofd A3013 Ob U:A1602(O4) A3540, A3541, A3542, T640 G:A1601, C:A1600, A:A1342 C:A1600
3ofd A2999 Ob U:A2419(O4) A3491, A3492, A3493, A3494, 3571
3ofd A3032 Ob U:A2593(O4) A3617, A3618, A3619, C735, C739 C:A2594, G:A2592
3ofd A2994 Ob G:A1125(O6) A3466, A3467, A3468, A3469, A3470 A:A1028
3ofd A2926 Ob U:A746(O4) A3151, A3152, A3153, A3154, A3155 U:A744, C:A2611, C:A2610 G:A745
3ofd B590 Ob U:B95(O4) B591, B592, B593, B595, V594 U:B80
3ofd A2932 Nb A:A1253(N7) A3178, A3179, A3180, A3181 U:A810, U:A811 G:A1252
3ofd A2949 2Nb G:A1358(N7), G:A1371(N7) A3252, A3253, A3254, A3255 G:A1358, C:A1357, G:A1371
3ofd A2924 2Nb G:A733(N7), A:A761(N7) A3141, A3142, A3143, A3144 A:A761, G:A733, G:A760, C:A732
3ofd A2940 Oph A:A1156(OP2) A3212, A3213, A3214, A3215, A3216 G:A1157
3ofd A2957 Oph A:A1678(OP2) A3288, A3289, A3290, A3291, A3292 A:A1679
3ofd A2909 Oph U:A120(OP2) A3061, A3062, A3063, A3064, A3065 G:A123, G:A124
3ofd A2922 Oph A:A621(OP2) A3133, A3134, L146, L147
3ofd A2986 Oph A:A299(OP2) A3429, A3430, A3431, A3432, U491 A:A299, G:A338, U:A339, A:A300
3ofd A2959 Oph·Pout G:A1776(OP2) A3298, A3299, A3300, A3301, A3302 U:A1775 G:A1776
3ofd A2956 Oph·Pout U:A1671(OP2) A3284, A3285, A3286, A3287 C:A1670
3ofd A2954 Oph·Pout A:A1664(OP2) A3273, A3274, A3275, A3276, A3277 G:A1992 G:A1667, A:A1664, A:A1665, G:A1992, G:A1666
3ofd A2946 Oph·Pout U:A1313(OP1) A3238, A3239, A3240, T255, T257 G:A1334
3ofd A2931 Oph·Pout A:A802(OP2) A3175, A3176, A3177, E204, E205 A:A675
3ofd 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
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/)
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