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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 4peb



4PEB (2.95Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to quinupristin. this file contains the 50s subunit of the first 70s ribosome with quinupristin bound.
List of all 104 Mg2+ binding sites in the PDB structure 4peb 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
4peb A3132 Ob U:A2593(O4) A3793, A3794, A3795, C306, C307 G:A2592 G:A2592, C:A2594, G:A2599, A:A2600
4peb B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, A:B94
4peb A3088 Ob G:A1125(O6) A3610, A3611, A3612, A3613, A3614 A:A1028 G:A1124
4peb A3071 Ob C:A2499(O2) A3533, A3534, A3535, A3536, A3537 G:A2032 G:A2454 C:A2055, U:A2500, G:A2032, G:A2454
4peb A3044 2Nb G:A1358(N7), G:A1371(N7) A3404, A3405, A3406, A3407 G:A1358, G:A1371, C:A1357, C:A1370
4peb A3077 Oph A:A299(OP2) A3558, A3559, A3560, A3561, A3562 U:A339, A:A299, G:A338
4peb A3007 Oph U:A419(OP1) A3233, A3234, A3235, A3236, A3237 G:A230
4peb A3026 Oph A:A800(OP1) A3325, A3326, A3327, A3328, A3329 A:A191, C:A192, A:A800
4peb A3049 Oph·Pout A:A1664(OP2) A3425, A3426, A3427, A3428, A3429 G:A1992 G:A1667, A:A1664, G:A1992, A:A1665, G:A1666
4peb A3032 Oph·Pout A:A945(OP1) A3352, A3353, A3354, A3355, A3356 G:A831 G:A831, U:A832
4peb A3014 Oph·Pout A:A574(OP2) A3266, A3267, A3268, A3269, A3270 U:A573 U:A576, G:A577, A:A563
4peb A3012 Oph·Pout U:A567(OP1) A3256, A3257, A3258, A3259, A3260 G:A809 U:A810, G:A809
4peb B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B101 A:B73 A:B101, G:B102
4peb A3052 Oph·Pout A:A1678(OP2) A3440, A3441, A3442, A3443, A3444 A:A1679 A:A1678, A:A1679
4peb A3006 Oph·Pout G:A297(OP2) A3228, A3229, A3230, A3231, A3232 G:A338 G:A298, G:A297
4peb A3134 Oph·Pout A:A943(OP2) A3800, A3801, A3802, L304, L305 U:A832
4peb A3085 Oph·Pout A:A981(OP1) A3598, A3599, A3600, A3601, A3602 G:A978
4peb A3080 Oph·Pout A:A572(OP1) A3571, A3572, A3573, A3574, A3575 A:A983 A:A572
4peb A3076 Oph·Pout G:A15(OP2) A3554, A3555, A3556, A3557 A:A14
4peb A3004 Oph·Pout U:A120(OP1) A3218, A3219, A3220, A3221, A3222 G:A123 G:A124, G:A123

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>