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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 2qox



2QOX (3.93Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin. this file contains the 50s subunit of the second 70s ribosome. the entire crystal structure contains two 70s ribosomes.
List of all 105 Mg2+ binding sites in the PDB structure 2qox 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
2qox B2983 Ob C:B2499(O2) B3395, B3396, B3397, B3398, B3399 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454
2qox B3012 Nb G:B1190(N7) B3506, B3507, B3508, L612 A:B1189, G:B1191
2qox B2941 2Nb G:B1358(N7), G:B1371(N7) B3196, B3197, B3198, B3199 C:B1357, G:B1358, G:B1371
2qox B2921 2Nb G:B733(N7), A:B761(N7) B3095, B3096, B3097, B3098 A:B761, G:B760, C:B732, G:B733
2qox B2965 Oph U:B419(OP1) B3311, B3312, B3313, B3314, B3315
2qox B2947 Oph A:B1678(OP2) B3221, B3222, B3223, B3224, B3225 A:B1678, A:B1679
2qox B2922 Oph A:B800(OP1) B3099, B3100, B3101, B3102, B3103 G:B799 C:B192, A:B800, A:B191
2qox B2913 Oph·Pout A:B1664(OP2) B3057, B3058, B3059, B3060, B3061 G:B1992 G:B1667, G:B1992, A:B1665, G:B1666
2qox B3009 Oph·Pout A:B1676(OP2) B3492, B3493, B3494, B3495, B3496 C:B1675 A:B1677
2qox B3008 Oph·Pout G:B1332(OP1) B3489, B3490, B3491 C:B1315
2qox B2984 Oph·Pout G:B2588(OP2) B3400, B3401, B3402, B3403, B3404 A:B2589 G:B2588, A:B2589
2qox B2931 Oph·Pout A:B945(OP1) B3145, B3146, B3147, B3148, B3149 G:B831 U:B832, G:B831
2qox B2926 Oph·Pout A:B1156(OP2) B3118, B3119, B3120, B3121, B3122 A:B1155 G:B1157, C:B998
2qox B2912 Oph·2Pout G:B1776(OP2) B3052, B3053, B3054, B3055, B3056 U:B1775, A:B1981 G:B1776
2qox B2945 Oph·2Pout A:B574(OP2) B3211, B3212, B3213, B3214, B3215 U:B576, U:B573 A:B563, U:B576, G:B577
2qox B2943 Oph·2Pout G:B536(OP2) B3203, B3204, B3205, B3206, B3207 G:B537, G:B535 G:B536, G:B537
2qox B2940 Oph·2Pout A:B2270(OP2) B3191, B3192, B3193, B3194, B3195 A:B2267, G:B2271 G:B2271
2qox B2918 Oph·2Pout G:B1187(OP2) B3081, B3082, B3083, B3084, R3084 C:B816, C:B817 G:B1185 G:B818, G:B1187
2qox B2914 Oph·2Pout U:B567(OP1) B3062, B3063, B3064, B3065, B3066 G:B809, G:B808 U:B810, G:B809
2qox B2911 Oph·2Pout A:B1970(OP2) B3047, B3048, B3049, B3050, B3051 G:B1835, A:B1900 U:B1834 G:B1835, C:B1836

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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