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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 2aw4




2AW4 (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli at 3.5 a resolution. this file contains the 50s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in remark 400.
List of all 105 Mg2+ binding sites in the PDB structure 2aw4 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
2aw4 B2946 Ob G:B2304(O6) B3207, B3208, B3209, B3210, B3211 G:B2303
2aw4 B2939 Ob C:B2499(O2) B3180, B3181, B3182, B3183, B3184 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2aw4 B2932 2Nb G:B1358(N7), G:B1371(N7) B3146, B3147, B3148, B3149 G:B1358, G:B1371, C:B1357, C:B1370
2aw4 B2959 2Nb G:B733(N7), A:B761(N7) B3272, B3273, B3274, B3275 A:B761, G:B733, G:B760, C:B732
2aw4 B2948 Oph U:B120(OP2) B3218, B3219, B3220, B3221, B3222 G:B122, G:B123, G:B121
2aw4 B2972 Oph A:B1678(OP2) B3332, B3333, B3334, B3335, B3336 A:B1679
2aw4 B2934 Oph U:B419(OP1) B3155, B3156, B3157, B3158, B3159 G:B230
2aw4 B3010 Oph A:B1676(OP2) B3490, B3491, B3492, B3493, B3494 C:B1675 A:B1677, A:B1676
2aw4 B2962 Oph A:B800(OP1) B3286, B3287, B3288, B3289, B3290 G:B799 A:B191, C:B192, A:B800
2aw4 B2965 Oph·Pout A:B1156(OP2) B3298, B3299, B3300, B3301, B3302 A:B1155 G:B1157, G:B997
2aw4 B2954 Oph·Pout A:B574(OP2) B3246, B3247, B3248, B3249, B3250 U:B576 U:B576, G:B577
2aw4 B2951 Oph·Pout G:B536(OP2) B3232, B3233, B3234, B3235, B3236 G:B535 G:B537
2aw4 B2911 Oph·Pout U:B1647(OP2) B3041, B3042, B3043, B3044, B3045 U:B1325 C:B1646, A:B1616
2aw4 B2969 Oph·Pout A:B1664(OP2) B3317, B3318, B3319, B3320, B3321 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666
2aw4 B2930 Oph·Pout A:B945(OP1) B3135, B3136, B3137, B3138, B3139 G:B831 G:B831, U:B832
2aw4 B2927 Oph·2Pout A:B1970(OP2) B3122, B3123, B3124, B3125, B3126 A:B1900, G:B1835 U:B1834 G:B1835
2aw4 B2925 Oph·2Pout G:B1187(OP2) B3113, B3114, B3115, B3116, B3117 C:B816, C:B817 G:B1185 G:B1187, G:B818
2aw4 B2913 Oph·2Pout G:B297(OP2) B3051, B3052, B3053, B3054, B3055 G:B338, G:B298 G:B298
2aw4 B2910 Oph·2Pout G:B2588(OP2) B3036, B3037, B3038, B3039, B3040 A:B2589, A:B2587 A:B2589
2aw4 B2905 Oph·2Pout A:B802(OP1) B3015, B3016, B3017, B3018, B3019 G:B674, A:B675 U:B803, A:B804

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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