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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"
Page 5 of 6 | | | 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
1vs6 B2998 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3444, B3445 C:B2551
1vs6 B2991 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3419, B3420 U:B827
1vs6 B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3205, B3206
1vs6 B2907 2Bout B3026, B3027, B3028, B3029, B3030, E202 U:B580, G:B1259
1vs6 B2961 2Bout B3284, B3285, B3286, B3287, B3288, B3289 G:B798, G:B797
1vs6 B2924 3Bout B3110, B3111, B3112, B3113, B3114, B3115 A:B756, A:B739, G:B757
1vs6 B2984 3Bout B3394, B3395, B3396, B3397, B3398, B3399 G:B2550, G:B2557, C:B2558
1vs6 B2918 3Bout B3077, B3078, B3079, B3080, B3081, B3082 U:B521, G:B17, U:B18
1vs6 B2947 3Bout B3216, B3217, B3218, B3219, B3220, B3221 G:B43, U:B434, A:B42
1vs6 B2906 5Bout B3020, B3021, B3022, B3023, B3024, B3025 U:B2074, U:B2243, U:B2075, G:B2238, G:B2242
1vs6 B2997 Pout·2Bout B3438, B3439, B3440, B3441, B3442, B3443 U:B686 G:B770, G:B771
1vs6 B2921 2Pout B3092, B3093, B3094, B3095, B3096, B3097 A:B947, G:B822
1vs6 B2968 2Pout·Rout·Bout B3315, B3316, B3317, B3318, B3319, B3320 C:B1376, C:B1351 U:B1352 G:B1377
1vs6 B2937 2Pout·2Bout B3174, B3175, B3176, B3177, B3178, B3179 G:B649, C:B650 C:B650, G:B651
1vs6 B2957 2Pout·2Bout B3266, B3267, B3268, B3269, B3270, B3271 A:B616, G:B617 G:B617, G:B618
1vs6 B3001 2Pout·2Bout B3456, B3457, B3458, B3459, B3460, B3461 A:B1000, A:B1001 G:B1003, G:B1002
1vs6 B2923 2Pout·3Bout B3104, B3105, B3106, B3107, B3108, B3109 U:B29, A:B447 G:B474, U:B29, G:B30
1vs6 B2956 2Pout·Rout·3Bout B3260, B3261, B3262, B3263, B3264, B3265 A:B1253, A:B582 C:B1251 G:B583, C:B584, A:B582
1vs6 B2982 2Pout·Rout·3Bout B3382, B3383, B3384, B3385, B3386, B3387 A:B2386, G:B2325 U:B2384 C:B2326, A:B2386, U:B2387
1vs6 B2922 2Pout·4Bout B3098, B3099, B3100, B3101, B3102, B3103 A:B2009, U:B1267 G:B2010, U:B2011, G:B2012, A:B2009

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>