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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 1vs6



1VS6 (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5a resolution. this file contains the 50s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is
List of all 108 Mg2+ binding sites in the PDB structure 1vs6 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
1vs6 B3000 Oph·2Pout A:B1938(OP2) B3451, B3452, B3453, B3454, B3455 C:B1958, C:B1957
1vs6 B2905 Oph·2Pout A:B802(OP1) B3015, B3016, B3017, B3018, B3019 G:B674, A:B675 U:B803, A:B804
1vs6 B2975 Oph·2Pout C:B2025(OP2) B3351, B3352, B3353, B3354, B3355 G:B2024, U:B2034
1vs6 B2974 Oph·2Pout G:B1776(OP2) B3346, B3347, B3348, B3349, B3350 U:B1775, A:B1981 G:B1776
1vs6 B2973 Oph·2Pout C:B1774(OP1) B3341, B3342, B3343, B3344, B3345 U:B1775, A:B1786 A:B1772 A:B1772, G:B1776
1vs6 B2949 Oph·2Pout U:B120(OP1) B3227, B3228, B3229, B3230, B3231 G:B122, G:B123 G:B123, G:B124
1vs6 B2927 Oph·2Pout A:B1970(OP2) B3125, B3126, B3127, B3128, B3129 G:B1835, A:B1900 U:B1834 G:B1835
1vs6 B2925 Oph·2Pout G:B1187(OP2) B3116, B3117, B3118, B3119, B3120 C:B816, C:B817 G:B1185 G:B1187, G:B818
1vs6 B2929 Oph·2Pout U:B1313(OP1) B3133, B3134, B3135, B3136, B3137 G:B1333, G:B1334
1vs6 B2981 Oph·2Pout A:B2270(OP2) B3377, B3378, B3379, B3380, B3381 G:B2269, A:B2267 G:B2271
1vs6 B2916 Oph·3Pout U:B2074(OP1) B3067, B3068, B3069, B3070, B3071 U:B2240, U:B2075, G:B2239 G:B2238
1vs6 B2912 Oph·3Pout A:B2518(OP2) B3049, B3050, B3051, B3052, B3053 U:B2519, A:B2541, C:B2540 A:B2541
1vs6 B2979 Oph·3Pout A:B2062(OP1) B3368, B3369, B3370, B3371, B3372 C:B2443, G:B2061, G:B2444 G:B2445, G:B2444
1vs6 B2999 Oph·3Pout G:B862(OP2) B3446, B3447, B3448, B3449, B3450 A:B861, A:B910, A:B863 G:B862, A:B863
1vs6 B2933 Oph·3Pout G:B450(OP2) B3153, B3154, B3155, B3156, B3157 U:B451, G:B452, A:B449
1vs6 B2967 Oph·3Pout A:B2005(OP1) B3311, B3312, B3313, B3314 A:B1268, A:B1269, C:B2006
1vs6 B2942 Oph·3Pout G:B1455(OP2) B3196, B3197, B3198, B3199, B3200 G:B1456, A:B1453, C:B1454 C:B1454 G:B1456, U:B1457
1vs6 B3003 Oph·3Pout G:B1828(OP2) B3466, B3467, B3468, B3469, B3470 U:B1827, G:B1972, C:B1788 G:B1828
1vs6 B2920 Oph·3Pout G:B1828(OP1) B3087, B3088, B3089, B3090, B3091 G:B1972, G:B1973, A:B1772
1vs6 B2992 Oph·4Pout C:B31(OP1) B3421, B3422, B3423, B3424, B3425 G:B1239, U:B1240, C:B1200, U:B1199

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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