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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 2awb



2AWB (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli at 3.5 a resolution. this file contains the 50s subunit of the second 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in remark 400.
List of all 104 Mg2+ binding sites in the PDB structure 2awb 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2awb B2906 Oph·2Pout C:B1774(OP1) B3021, B3022, B3023, B3024, B3025 U:B1775, A:B1786 A:B1772 A:B1772
2awb B2953 Oph·2Pout A:B2518(OP2) B3249, B3250, B3251, B3252, B3253 A:B2541, U:B2519 A:B2541
2awb B2949 Oph·2Pout G:B297(OP2) B3229, B3230, B3231, B3232, B3233 U:B296, G:B338 G:B298
2awb B2945 Oph·2Pout A:B574(OP2) B3210, B3211, B3212, B3213, B3214 U:B573, U:B576 U:B576, G:B577
2awb B2928 Oph·2Pout C:B2025(OP2) B3131, B3132, B3133, B3134, D231 G:B2024, U:B2034
2awb B2981 Oph·2Pout U:B2074(OP1) B3383, B3384, B3385, B3386, B3387 G:B2239, U:B2240
2awb B2914 Oph·2Pout U:B567(OP1) B3063, B3064, B3065, B3066, B3067 G:B808, G:B809 G:B809, U:B810
2awb B2911 Oph·2Pout A:B1970(OP2) B3048, B3049, B3050, B3051, B3052 G:B1835, A:B1900 U:B1834 G:B1835
2awb B2912 Oph·2Pout G:B1776(OP2) B3053, B3054, B3055, B3056, B3057 U:B1775, A:B1981 G:B1776
2awb B3003 Oph·2Pout G:B1828(OP2) B3466, B3467, B3468, B3469, B3470 U:B1827, G:B1972 G:B1828
2awb B2918 Oph·2Pout G:B1187(OP2) B3082, B3083, B3084, B3085, B3086 C:B817, C:B816 G:B1185 G:B818, G:B1187
2awb B2938 Oph·3Pout G:B2447(OP2) B3179, B3180, B3181, B3182, B3183 G:B2502, G:B2446, C:B2501 G:B2502
2awb B3000 Oph·3Pout G:B862(OP2) B3452, B3453, B3454, B3455, B3456 A:B863, A:B861, A:B910 G:B862, A:B863
2awb B2929 Oph·3Pout A:B2062(OP2) B3135, B3136, B3137, B3138, B3139 G:B2061, C:B2443, G:B2444 G:B2444
2awb B2993 Oph·3Pout C:B31(OP1) B3429, B3430, B3431, B3432, B3433 C:B1200, G:B1239, U:B1199
2awb B2979 Oph·3Pout G:B1828(OP1) B3374, B3375, B3376, B3377, B3378 G:B1972, G:B1973, A:B1772
2awb B2954 Oph·3Pout G:B1455(OP2) B3254, B3255, B3256, B3257, B3258 G:B1456, A:B1453, C:B1454 C:B1454 G:B1456
2awb B3014 Oph·4Pout U:B963(OP1) B3509, B3510, B3511, B3512, B3513 A:B947, A:B2497, C:B964, C:B2498
2awb B3005 Oph·Or U:B1379(OP2) A:B1378(O2') B3475, B3476, B3477 G:B1380 G:B1380
2awb B2982 Oph·Ob C:B2248(OP2) U:B2249(O4) B3388, B3389, B3390, B3391 C:B2066, G:B2253 A:B2247

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].

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