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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 3orb



3ORB (3.3Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to cem-101. this file contains the 50s subunit of the first 70s ribosome bound to cem-101.
List of all 93 Mg2+ binding sites in the PDB structure 3orb 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 5 | « Previous | | 1 | 2 | 3 | 4 | 5
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3orb A2924 Ob U:A746(O4) A3141, A3142, A3143, A3144, A3145 U:A744, C:A2611 G:A745
3orb A2974 Ob C:A2499(O2) A3372, A3373, A3374, A3375, A3376 G:A2032 G:A2454 C:A2055, U:A2500, G:A2032, G:A2454
3orb A3002 Ob U:A2419(O4) A3507, A3508, A3509, A3510, 3574 A:A2418
3orb B609 Ob U:B95(O4) B610, B611, B612, B613, B614 U:B80, G:B96
3orb A2979 Oph A:A299(OP2) A3393, A3394, A3395, A3396, A3397 U:A339, A:A299, G:A338
3orb A2911 Oph U:A419(OP1) A3072, A3073, A3074, A3075, A3076 G:A230
3orb A2929 Oph A:A800(OP1) A3162, A3163, A3164, A3165, A3166 G:A799 A:A191, C:A192, A:A800
3orb A3001 Oph·Pout U:A2022(OP1) A3502, A3503, A3504, A3505, A3506 C:A2023 A:A529 A:A529
3orb A2982 Oph·Pout A:A572(OP1) A3406, A3407, A3408, A3409, A3410 A:A983
3orb A2955 Oph·Pout A:A1678(OP2) A3279, A3280, A3281, A3282, A3283 A:A1679 A:A1678, A:A1679
3orb A2952 Oph·Pout A:A1664(OP2) A3264, A3265, A3266, A3267, A3268 G:A1992 G:A1667, A:A1664, A:A1665, G:A1992, G:A1666
3orb A2916 Oph·Pout U:A567(OP1) A3096, A3097, A3098, A3099, A3100 G:A809 G:A809, U:A810
3orb B615 Oph·Pout G:B100(OP2) B616, B617, B618, B619, B620 A:B101 A:B73 A:B101
3orb A3029 Oph·Pout A:A1676(OP2) A3608, A3609, A3610, A3611, A3612 C:A1675 A:A1677, A:A1676
3orb A2935 Oph·Pout A:A945(OP1) A3189, A3190, A3191, A3192, A3193 G:A831 G:A831, U:A832
3orb A2910 Oph·Pout G:A297(OP2) A3067, A3068, A3069, A3070, A3071 G:A338 G:A298, G:A297
3orb A2908 Oph·Pout U:A120(OP1) A3057, A3058, A3059, A3060, A3061 G:A123 G:A124, G:A123
3orb A2907 Oph·Pout U:A120(OP2) A3052, A3053, A3054, A3055, A3056 G:A121 G:A122, G:A123, G:A121
3orb A2956 Oph·2Pout C:A1774(OP1) A3284, A3285, A3286, A3287, A3288 U:A1775, A:A1786 A:A1772 A:A1772, G:A1776
3orb A2944 Oph·2Pout U:A1313(OP1) A3227, A3228, A3229, A3230, A3231 G:A1333, G:A1334

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>