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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 2qbk



2QBK (4Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with gentamicin and ribosome recycling factor (rrf). this file contains the 50s subunit of the second 70s ribosome, with gentamicin and rrf bound. the entire crystal structure
List of all 108 Mg2+ binding sites in the PDB structure 2qbk 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
2qbk B2984 Ob C:B2499(O2) B3398, B3399, B3400, B3401, B3402 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qbk B2972 Ob U:B746(O4) B3345, B3346, B3347, B3348, B3349 C:B2610, C:B2611, U:B744 G:B745
2qbk B2941 2Nb G:B1358(N7), G:B1371(N7) B3195, B3196, B3197, B3198 G:B1371, G:B1358, C:B1357, C:B1370
2qbk B2947 Oph A:B1678(OP2) B3220, B3221, B3222, B3223, B3224 A:B1678, A:B1679
2qbk B2922 Oph A:B800(OP1) B3101, B3102, B3103, B3104, B3105 G:B799, A:B203 C:B192, A:B800
2qbk B2966 Oph U:B419(OP1) B3312, B3313, B3314, B3315, B3316 G:B230
2qbk B2913 Oph·Pout A:B1664(OP2) B3059, B3060, B3061, B3062, B3063 G:B1992 G:B1667, A:B1665, G:B1992, G:B1666
2qbk B3010 Oph·Pout A:B1676(OP2) B3490, B3491, B3492, B3493, B3494 C:B1675 A:B1677
2qbk B2974 Oph·Pout A:B802(OP1) B3353, B3354, B3355, B3356, B3357 A:B675 U:B803, A:B804
2qbk B2946 Oph·Pout U:B120(OP2) B3215, B3216, B3217, B3218, B3219 G:B121 G:B121, G:B122, G:B123
2qbk B2945 Oph·Pout A:B574(OP2) B3210, B3211, B3212, B3213, B3214 U:B576 U:B576, G:B577
2qbk B2943 Oph·Pout G:B536(OP2) B3202, B3203, B3204, B3205, B3206 G:B535 G:B536, G:B537
2qbk B2931 Oph·Pout A:B945(OP1) B3147, B3148, B3149, B3150, B3151 G:B831 C:B944 U:B832, G:B831
2qbk B2926 Oph·Pout A:B1156(OP2) B3120, B3121, B3122, B3123, B3124 A:B1155 G:B1157, C:B998
2qbk B2940 Oph·Pout A:B2270(OP2) B3190, B3191, B3192, B3193, B3194 A:B2267 A:B2266 G:B2271
2qbk B2914 Oph·2Pout U:B567(OP1) B3064, B3065, B3066, B3067, B3068 G:B809, G:B808 G:B809
2qbk B2950 Oph·2Pout U:B120(OP1) B3234, B3235, B3236, B3237, B3238 G:B122, G:B123 G:B124
2qbk B2949 Oph·2Pout G:B297(OP2) B3229, B3230, B3231, B3232, B3233 G:B338, G:B298 G:B298, G:B297
2qbk B2928 Oph·2Pout C:B2025(OP2) B3131, B3132, B3133, B3134, B3135 G:B2024, U:B2034 U:B1130
2qbk B2924 Oph·2Pout G:B2502(OP2) B3112, B3113, B3114, B3115 G:B2061, G:B2446 C:B2501, A:B2060 G:B2446

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>