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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 1 of 7 | « Previous | | 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 A2925 Ob U:A746(O4) A3147, A3148, A3149, A3150, A3151 U:A744, C:A2611 G:A745
3i20 A2975 Ob C:A2499(O2) A3375, A3376, A3377, A3378, A3379 G:A2032 C:A2055, U:A2500, G:A2032, G:A2454
3i20 B122 Ob U:B95(O4) B656, B657, B658, B659, B660 U:B80, G:B96
3i20 A2992 Ob G:A1125(O6) A3452, A3453, A3454, A3455, A3456 A:A1028
3i20 A3035 Ob U:A2593(O4) A3635, A3636, A3637, C776, C778 G:A2592 C:A2594, G:A2599
3i20 A3003 Ob U:A2419(O4) A3513, A3514, A3515, 3626, 3629 A:A2418
3i20 A2948 2Nb G:A1358(N7), G:A1371(N7) A3247, A3248, A3249, A3250 G:A1358, G:A1371, C:A1357
3i20 A2923 2Nb G:A733(N7), A:A761(N7) A3137, A3138, A3139, A3140 G:A733, A:A761, C:A732
3i20 B123 Oph G:B100(OP2) B661, B662, B663, B664, B665 A:B73 A:B101, G:B102
3i20 A2930 Oph A:A800(OP1) A3167, A3168, A3169, A3170, A3171 G:A799, A:A802 A:A191, C:A192, A:A800
3i20 A2936 Oph A:A945(OP2) A3193, A3194, A3195, A3196, A3197 C:A944 G:A831, U:A832, C:A944
3i20 A2981 Oph A:A299(OP2) A3400, A3401, A3402, A3403, A3404 U:A339, G:A338
3i20 A2910 Oph U:A419(OP1) A3071, A3072, A3073, A3074, A3075 G:A230
3i20 A2945 Oph·Pout U:A1313(OP1) A3231, A3232, A3233, A3234, A3235 G:A1334
3i20 A2909 Oph·Pout G:A297(OP2) A3066, A3067, A3068, A3069, A3070 G:A338 G:A298
3i20 A2908 Oph·Pout A:A218(OP2) A3061, A3062, A3063, A3064, A3065 A:A217 A:A219, G:A220
3i20 A2907 Oph·Pout U:A120(OP1) A3057, A3058, A3059, A3060, 2159 G:A123 G:A123, G:A124
3i20 A3030 Oph·Pout A:A1676(OP2) A3612, A3613, A3614, A3615, A3616 C:A1675 A:A1677, A:A1676
3i20 A3002 Oph·Pout U:A2022(OP1) A3508, A3509, A3510, A3511, A3512 C:A2023 C:A2021, A:A529 A:A529
3i20 A2984 Oph·Pout A:A572(OP2) A3413, A3414, A3415, A3416, A3417 A:A983

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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