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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 2z4n



2Z4N (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 second 70s ribosome, with paromomycin and rrf bound. the entire crystal structure
List of all 107 Mg2+ binding sites in the PDB structure 2z4n 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
2z4n B2985 Ob C:B2499(O2) B3399, B3400, B3401, B3402, B3403 C:B2499 C:B2055, U:B2500, G:B2032, G:B2454
2z4n B2942 2Nb G:B1358(N7), G:B1371(N7) B3198, B3199, B3200, B3201 G:B1371, G:B1358, C:B1357, C:B1370
2z4n B2922 2Nb G:B733(N7), A:B761(N7) B3097, B3098, B3099, B3100 G:B733, G:B760, A:B761 C:B732
2z4n B2923 Oph A:B800(OP1) B3101, B3102, B3103, B3104, B3105 A:B802, G:B799 C:B192, A:B800
2z4n B2948 Oph A:B1678(OP2) B3223, B3224, B3225, B3226, B3227 A:B1678, A:B1679
2z4n B2967 Oph U:B419(OP1) B3315, B3316, B3317, B3318, B3319 G:B230
2z4n B2927 Oph·Pout A:B1156(OP2) B3120, B3121, B3122, B3123, B3124 A:B1155 G:B1157, C:B998
2z4n B2947 Oph·Pout U:B120(OP2) B3218, B3219, B3220, B3221, B3222 G:B121 G:B122, G:B123, G:B121
2z4n B2914 Oph·Pout A:B1664(OP2) B3059, B3060, B3061, B3062, B3063 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666
2z4n B2986 Oph·Pout G:B2588(OP2) B3404, B3405, B3406, C477, C479 A:B2589 G:B2588, A:B2589
2z4n B3011 Oph·Pout A:B1676(OP2) B3495, B3496, B3497, B3498, B3499 C:B1675 A:B1676, A:B1677
2z4n B2946 Oph·Pout A:B574(OP2) B3213, B3214, B3215, B3216, B3217 U:B576 U:B576, G:B577
2z4n B2932 Oph·Pout A:B945(OP1) B3147, B3148, B3149, B3150, B3151 G:B831 U:B832, G:B831
2z4n B2919 Oph·2Pout G:B1187(OP2) B3083, B3084, B3085, B3086, R104 C:B817, C:B816 G:B1185 G:B818, G:B1187
2z4n B2915 Oph·2Pout U:B567(OP1) B3064, B3065, B3066, B3067, B3068 G:B809, G:B808 G:B809
2z4n B2913 Oph·2Pout G:B1776(OP2) B3054, B3055, B3056, B3057, B3058 A:B1981, U:B1775 G:B1776
2z4n B2954 Oph·2Pout A:B2518(OP2) B3251, B3252, B3253, B3254, B3255 A:B2541, U:B2519 A:B2541
2z4n B2951 Oph·2Pout U:B120(OP1) B3237, B3238, B3239, B3240, B3241 G:B122, G:B123 G:B123, G:B124
2z4n B2950 Oph·2Pout G:B297(OP2) B3232, B3233, B3234, B3235, B3236 G:B338, G:B298 G:B298, G:B297
2z4n B2944 Oph·2Pout G:B536(OP2) B3205, B3206, B3207, B3208, B3209 G:B537, G:B535 G:B536, G:B537

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>