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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 3i20



3I20 (3.71Å) -- RIBOSOME : Crystal structure of the e. coli 70s ribosome in an intermediate state of ratcheting
List of all 136 Mg2+ binding sites in the PDB structure 3i20 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 7 of 7 | | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3i20 A2920 2Pout·Rout·2Bout A3123, A3124, A3125, A3126, A3127, A3128 A:A1253, G:A583 C:A1251 G:A583, C:A584
3i20 A2921 2Pout·3Bout A3129, A3130, A3131, A3132, A3133, A3134 A:A616, A:A608 G:A617, G:A618, G:A619
3i20 A2999 2Pout·3Bout A3488, A3489, A3490, A3491, A3492, A3493 C:A1617, G:A1619 G:A1619, G:A1620, G:A1613
3i20 A2974 2Pout·4Bout A3369, A3370, A3371, A3372, A3373, A3374 A:A2453, C:A2452 A:A2497, G:A2454, G:A2455, A:A2453
3i20 A2914 3Pout A3089, A3090, A3091, A3092, A3093, A3094 G:A559, C:A560, A:A1008
3i20 A2965 3Pout A3326, A3327, A3328, A3329, A3330, A3331 A:A2051, G:A2578, C:A2050
3i20 A2918 3Pout·Rout A3111, A3112, A3113, A3114, A3115, A3116 G:A579, U:A2016, G:A578 U:A1255
3i20 A2951 3Pout·Bout A3258, A3259, A3260, A3261, A3262 G:A1455, G:A1456, A:A1453 U:A1457
3i20 A3032 3Pout·Rout·Bout A3620, A3621, A3622, A3623, A3624, A3625 G:A570, A:A973, U:A569 A:A972 A:A821
3i20 A2916 3Pout·2Bout A3100, A3101, A3102, A3103, A3104, A3105 U:A568, G:A831, C:A944 A:A945, A:A2448
3i20 A3036 3Pout·3Bout A3638, A3639, A3640, 4779, 4782, 4784 A:A2740, A:A2741, G:A2742 G:A2742, G:A2763, U:A2743
3i20 A2905 3Pout·Rout·3Bout A3046, A3047, A3048, A3049, A3050, A3051 U:A29, A:A28, A:A447 A:A447 G:A473, G:A474, U:A29
3i20 A3039 4Pout A3650, A3651, A3652, A3653, N797, N798 G:A2819, G:A2838, C:A2874, A:A2820
3i20 A2947 4Pout·Bout A3241, A3242, A3243, A3244, A3245, A3246 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377
3i20 A2954 4Pout·Bout A3273, A3274, A3275, A3276, A3277, A3278 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954
3i20 A2922 Mg2+ bound by non-RNA G:A622(OP2) A3135, A3136, L239, L240 ASN:L99(OD1) A:A621

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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