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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 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 B590 Ob U:B95(O4) B591, B592, B593, V594, V595 U:B80
3ofq C722 Mg2+ bound by non-RNA A3607, A3608, C723, C724 HIS:C52(ND1) G:A1824
3ofq A2905 2Bout A3038, A3039, A3040, A3041, A3042, A3043 U:A521, G:A17
3ofq A2906 3Pout·Rout·3Bout A3044, A3045, A3046, A3047, A3048, A3049 U:A29, A:A28, A:A447 A:A447 G:A473, U:A29, G:A30
3ofq A2907 Pout A3050, A3051, A3052, A3053, A3054, A3055 C:A41
3ofq A2908 Oph·Pout U:A120(OP2) A3056, A3057, A3058, A3059, A3060 G:A121 A:A119 G:A122, G:A123
3ofq A2909 Oph·Pout U:A120(OP2) A3061, A3062, A3063, A3064, A3065 G:A123 G:A123, G:A124
3ofq A2910 Oph·2Pout G:A297(OP2) A3066, A3067, A3068, A3069, A3642 G:A338, G:A298 G:A297
3ofq A2911 Oph U:A419(OP1) A3070, A3071, A3072, A3073, A3074 G:A230
3ofq A2912 Oph·Nb A:A453(OP1) G:A450(N7) A3075, A3076, A3077, A3078 A:A449 A:A449
3ofq A2913 Oph·2Pout A:A526(OP1) A3079, A3080, A3081, A3082 A:A528, C:A527
3ofq A2914 Oph G:A536(OP2) A3083, A3084, A3085, A3086, A3087
3ofq A2915 3Pout·Bout A3088, A3089, A3090, A3091, A3092, A3093 A:A1008, G:A2038, C:A560 A:A1008
3ofq A2916 Oph·2Pout U:A567(OP1) A3094, A3095, A3096, A3097, L145 G:A809, G:A808 U:A810, G:A809
3ofq A2918 2Pout·2Bout A3103, A3104, A3105, A3106, A3107 A:A574, U:A576 U:A576, G:A577
3ofq A2920 3Bout A3114, A3115, A3116, A3117, A3118, A3119 C:A581, G:A1259, U:A1258
3ofq A2921 3Pout·Rout·3Bout A3120, A3121, A3122, A3123, A3124, A3125 A:A582, A:A1253, G:A583 C:A1251 G:A583, G:A585, A:A582
3ofq A2922 2Pout·2Bout A3126, A3127, A3128, A3129, A3130, A3131 A:A616, A:A608 G:A618, G:A619
3ofq A2923 Oph A:A621(OP2) A3132, A3133, L147, L148
3ofq A2924 Bout A3134, A3135, A3136, A3137, A3138, A3139 G:A651

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>