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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 3df2:B3382, See in JSmolMgRNA representative site for type 4PO-BO         Click on the image to toggle views


Site type: 4Pout·Bout

Schematic drawing for
4Pout·Bout

MgRNA type 4PO-BO
List of all 125 Mg2+ binding sites with the site type 4Pout·Bout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
Page 5 of 5 | | Next » | 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
4too A3040 4Pout·Bout A3377, A3378, A3379, A3380 A:A2005, C:A2006, A:A1268, A:A1269 A:A1269
4too A3051 4Pout·Bout A3422, A3423, A3424, A3425, A3426, A3427 A:A1669, A:A1987, C:A2551, C:A1986 G:A1954
4tov A3058 4Pout·Bout A3457, A3458, A3459, A3460, A3461, A3462 A:A1937, A:A1936, C:A1958, G:A1959 G:A1959
4tov A3052 4Pout·Bout A3427, A3428, A3429, A3430, A3431, A3432 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954
4tov A3045 4Pout·Bout A3395, A3396, A3397, A3398, A3399, A3400 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377
4tox A3052 4Pout·Bout A3425, A3426, A3427, A3428, A3429, A3430 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954
4tox A3041 4Pout·Bout A3381, A3382, A3383, A3384 A:A2005, C:A2006, A:A1268, A:A1269 A:A1269
4tox A3058 4Pout·Bout A3455, A3456, A3457, A3458, A3459, A3460 G:A1959, A:A1936, A:A1937, C:A1958 G:A1959
4tp1 A3045 4Pout·Bout A3398, A3399, A3400, A3401, A3402, A3403 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377
4tp3 A3044 4Pout·Bout A3393, A3394, A3395, A3396, A3397, A3398 U:A1352, G:A1377, C:A1376, C:A1351 G:A1377
4tp5 A3044 4Pout·Bout A3397, A3398, A3399, A3400, A3401, A3402 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377
4tp7 A3052 4Pout·Bout A3422, A3423, A3424, A3425, A3426, A3427 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954
4tp7 A3041 4Pout·Bout A3377, A3378, A3379, A3380 A:A1269, A:A2005, C:A2006, A:A1268 A:A1269
4tp7 A3058 4Pout·Bout A3452, A3453, A3454, A3455, A3456, A3457 A:A1937, C:A1958, G:A1959, A:A1936 G:A1959
4tp7 A3045 4Pout·Bout A3390, A3391, A3392, A3393, A3394, A3395 U:A1352, G:A1377, C:A1376, C:A1351 G:A1377
4tp9 A3045 4Pout·Bout A3395, A3396, A3397, A3398, A3399, A3400 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377
4tp9 A3052 4Pout·Bout A3427, A3428, A3429, A3430, A3431, A3432 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954
4tpb A3044 4Pout·Bout A3393, A3394, A3395, A3396, A3397, A3398 U:A1352, G:A1377, C:A1376, C:A1351 G:A1377
4tpb A3051 4Pout·Bout A3425, A3426, A3427, A3428, A3429, A3430 A:A1669, C:A2551, A:A1987, C:A1986 G:A1954
4tpb A3124 4Pout·Bout A3752, A3753, A3754, A3755 U:A790, C:A787, A:A789, C:A791 U:A1781
4tpd A3044 4Pout·Bout A3397, A3398, A3399, A3400, A3401, A3402 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377
4tpf A3041 4Pout·Bout A3380, A3381, A3382, A3383 A:A1268, A:A1269, A:A2005, C:A2006 A:A1269
4tpf A3058 4Pout·Bout A3455, A3456, A3457, A3458, A3459, A3460 A:A1937, C:A1958, G:A1959, A:A1936 G:A1959
4tpf A3063 4Pout·Bout A3479, A3480, A3481, A3482, A3483, A3484 A:A2614, A:A2051, G:A2578, C:A2050 A:A2051
4tpf A3052 4Pout·Bout A3425, A3426, A3427, A3428, A3429, A3430 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954

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>