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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 2qov




2QOV (3.93Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin. this file contains the 50s subunit of the first 70s ribosome. the entire crystal structure contains two 70s ribosomes.
List of all 101 Mg2+ binding sites in the PDB structure 2qov 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
2qov B2939 Ob C:B2499(O2) B3182, B3183, B3184, B3185, B3186 G:B2032 C:B2055, U:B2500, G:B2454, G:B2032
2qov B2936 Ob U:B746(O4) B3167, B3168, B3169, B3170, B3171 U:B744, C:B2610, C:B2611
2qov B2932 Ob·Nb G:B1371(N7) B3148, B3149, B3150, B3151 G:B1358, C:B1357, G:B1371 G:B1358
2qov B2962 Oph A:B800(OP1) B3290, B3291, B3292, B3293, B3294 G:B799 A:B191
2qov B2930 Oph A:B945(OP1) B3137, B3138, B3139, B3140, B3141 G:B831
2qov B2934 Oph U:B419(OP1) B3156, B3157, B3158, B3159, B3160 C:B418 G:B230
2qov B2910 Oph·Pout G:B2588(OP2) B3041, B3042, B3043, B3044, C273 A:B2589 A:B2589
2qov B3010 Oph·Pout A:B1676(OP2) B3492, B3493, B3494, B3495, B3496 C:B1675 A:B1677, A:B1676
2qov B2972 Oph·Pout A:B1678(OP2) B3336, B3337, B3338, B3339, B3340 A:B1679 A:B1678, A:B1679
2qov B2969 Oph·Pout A:B1664(OP2) B3321, B3322, B3323, B3324, B3325 G:B1992 G:B1667, A:B1665, G:B1992, G:B1666
2qov B2965 Oph·Pout A:B1156(OP2) B3302, B3303, B3304, B3305, B3306 A:B1155 G:B1157, C:B998
2qov B2951 Oph·Pout G:B536(OP2) B3234, B3235, B3236, B3237, B3238 G:B535 G:B536, G:B537
2qov B2948 Oph·Pout U:B120(OP2) B3220, B3221, B3222, B3223, B3224 G:B121 G:B122, G:B123, G:B121
2qov B2913 Oph·Pout G:B297(OP2) B3055, B3056, B3057, B3058, B3059 U:B296 G:B298, G:B297
2qov B2912 Oph·2Pout A:B2518(OP2) B3050, B3051, B3052, B3053, B3054 U:B2519, A:B2541 A:B2541
2qov B2949 Oph·2Pout U:B120(OP1) B3225, B3226, B3227, B3228, B3229 G:B122, G:B123 G:B123, G:B124
2qov B2942 Oph·2Pout G:B1455(OP2) B3194, B3195, B3196, B3197, B3198 A:B1453, C:B1454 C:B1454 G:B1456, U:B1457
2qov B2929 Oph·2Pout U:B1313(OP1) B3132, B3133, B3134, B3135, B3136 G:B1333, G:B1334
2qov B2927 Oph·2Pout A:B1970(OP2) B3124, B3125, B3126, B3127, B3128 G:B1835, A:B1900 G:B1835
2qov B2925 Oph·2Pout G:B1187(OP2) B3115, B3116, B3117, B3118, B3119 C:B816, C:B817 G:B818, G:B1187

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>