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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 3oas



3OAS (3.25Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the e. coli ribosome bound to telithromycin. this file contains the 50s subunit of the second 70s ribosome.
List of all 109 Mg2+ binding sites in the PDB structure 3oas 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 6 | « Previous | | 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
3oas A3003 Or A:A2448(OP2) G:A2447(O3') A3511, A3512, A3513 U:A2449, C:A2498, C:A2499, A:A2450 A:A2497, U:A2449 G:A2447
3oas B590 Ob U:B95(O4) B591, B592, B593, B594, B595 U:B80
3oas A2926 Ob U:A746(O4) A3152, A3153, A3154, A3155, D210 U:A744, C:A2611, C:A2610 G:A745
3oas A3013 Ob U:A1602(O4) A3541, A3542, A3543, T640 G:A1601, C:A1600, A:A1342
3oas A3031 Ob U:A2593(O4) A3613, A3614, A3615, C735, C739 G:A2592 C:A2594, G:A2592
3oas A2999 Ob U:A2419(O4) A3491, A3492, A3493, A3494, A3495
3oas A2932 Nb A:A1253(N7) A3179, A3180, A3181, A3182 U:A810, U:A811 G:A1252
3oas A2924 2Nb G:A733(N7), A:A761(N7) A3142, A3143, A3144, A3145 A:A761, G:A733, G:A760, C:A732
3oas A2949 2Nb G:A1358(N7), G:A1371(N7) A3254, A3255, A3256, A3257 G:A1358, C:A1357, G:A1371
3oas A2940 Oph A:A1156(OP2) A3213, A3214, A3215, A3216, A3217 G:A1157, G:A997
3oas A2957 Oph A:A1678(OP2) A3290, A3291, A3292, A3293, A3294 A:A1679
3oas A2910 Oph U:A419(OP1) A3069, A3070, A3071, A3072, A3073 G:A230
3oas A2922 Oph A:A621(OP2) A3133, A3134, A3135, L145 G:A620
3oas A2986 Oph A:A299(OP2) A3430, A3431, A3432, A3433, U491 A:A299, G:A338, U:A339, A:A300
3oas A2913 Oph G:A536(OP2) A3082, A3083, A3084, A3085, A3086
3oas A2935 Oph·Pout A:A945(OP1) A3192, A3193, A3194, A3195, A3196 G:A831 G:A831, U:A832
3oas A2931 Oph·Pout A:A802(OP2) A3176, A3177, A3178, E204, E205 A:A675
3oas A2917 Oph·Pout A:A574(OP2) A3104, A3105, A3106, A3107, A3108 U:A576 U:A576, G:A577
3oas A2909 Oph·Pout G:A297(OP2) A3065, A3066, A3067, A3068, U3639 G:A338 G:A297
3oas A2908 Oph·Pout U:A120(OP1) A3060, A3061, A3062, A3063, A3064 G:A123 G:A123, G:A124

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>