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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 2z4l



2Z4L (4.45Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with paromomycin and ribosome recycling factor (rrf). this file contains the 50s subunit of the first 70s ribosome, with paromomycin and rrf bound. the entire crystal structure
List of all 105 Mg2+ binding sites in the PDB structure 2z4l 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
2z4l B2940 Ob C:B2499(O2) B3180, B3181, B3182, B3183, B3184 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2z4l B2937 Ob U:B746(O4) B3166, B3167, B3168, B3169, D210 C:B2610, C:B2611, U:B744 G:B745
2z4l B2960 2Nb G:B733(N7), A:B761(N7) B3274, B3275, B3276, B3277 A:B761, G:B760, G:B733
2z4l B2933 2Nb G:B1358(N7), G:B1371(N7) B3147, B3148, B3149, B3150 G:B1358, G:B1371, C:B1357, C:B1370
2z4l B2977 Oph A:B2033(OP1) B3354, B3355, B3356, B3357 U:B2028
2z4l B2963 Oph A:B800(OP1) B3288, B3289, B3290, B3291, B3292 G:B799, A:B203 A:B191
2z4l B2935 Oph U:B419(OP1) B3155, B3156, B3157, B3158, B3159 G:B230
2z4l B2970 Oph·Pout A:B1664(OP2) B3319, B3320, B3321, B3322, B3323 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666
2z4l B2973 Oph·Pout A:B1678(OP2) B3334, B3335, B3336, B3337, B3338 A:B1679 A:B1678, A:B1679
2z4l B2931 Oph·Pout A:B945(OP1) B3136, B3137, B3138, B3139, B3140 G:B831 G:B831, U:B832, C:B944
2z4l B2966 Oph·Pout A:B1156(OP2) B3300, B3301, B3302, B3303, B3304 A:B1155 G:B1157, C:B998
2z4l B2952 Oph·Pout G:B536(OP2) B3232, B3233, B3234, B3235, B3236 G:B535 G:B536, G:B537
2z4l B2976 Oph·Pout C:B2025(OP2) B3349, B3350, B3351, B3352, B3353 G:B2024
2z4l B2982 Oph·Pout A:B2270(OP2) B3375, B3376, B3377, B3378, B3379 A:B2267 A:B2268 G:B2271, A:B2267
2z4l B2949 Oph·Pout U:B120(OP2) B3218, B3219, B3220, B3221, B3222 G:B121 G:B122, G:B123, G:B121
2z4l B2921 Oph·2Pout G:B1828(OP1) B3085, B3086, B3087, B3088, B3089 A:B1773, A:B1772
2z4l B2915 Oph·2Pout C:B1153(OP2) B3059, B3060, B3061, B3062 U:B999, C:B998
2z4l B2914 Oph·2Pout G:B297(OP2) B3054, B3055, B3056, B3057, B3058 U:B296, G:B298 G:B298, G:B297
2z4l B2912 Oph·2Pout U:B1647(OP2) B3044, B3045, B3046, B3047, B3048 U:B1325, A:B1272 A:B1616, C:B1646 A:B1616
2z4l B2911 Oph·2Pout G:B2588(OP2) B3041, B3042, B3043, C274, C275 A:B2589, A:B2587 G:B2588, A:B2589

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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