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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qp1:B2994, See in JSmolMgRNA representative site for type OP-4PO Click on the image to toggle views


Site type: Oph·4Pout

Schematic drawing for
Oph·4Pout
MgRNA type OP-4PO
List of all 231 Mg2+ binding sites with the site type Oph·4Pout 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 6 of 10 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3ofd A2960 Oph·4Pout G:A1828(OP1) A3303, A3304, A3305, A3306, C338 A:A1772, A:A1773, G:A1972, G:A1973
3ofd A3018 Oph·4Pout U:A2243(OP1) A3560, A3561, A3562, A3563 C:A192, A:A199, C:A198, U:A193
3ofd A3009 Oph·4Pout C:A31(OP1) A3527, A3528, A3529, A3530, A3531 G:A1239, C:A1200, U:A1199, U:A1240 A:A1214
3ofp A1562 Oph·4Pout G:A1198(OP1) A1709, A1710, A1711, A1712 A:A964, U:A965, C:A1054, U:A1199
3ofq A2948 Oph·4Pout G:A1333(OP2) A3244, A3245, A3246, A3247, A3248 C:A1314, G:A1332, G:A1334, U:A1313 G:A1331 G:A1333
3ofq A3019 Oph·4Pout U:A2243(OP1) A3560, A3561, A3562, A3563 C:A192, A:A199, C:A198, U:A193
3ofq A3010 Oph·4Pout C:A31(OP1) A3526, A3527, A3528, A3529, A3530 G:A1239, C:A1200, U:A1199, U:A1240 A:A1214
3ofr A3013 Oph·4Pout C:A31(OP1) A3539, A3540, A3541, A3542, A3543 C:A1200, U:A1240, G:A1239, U:A1199
3ofr A2999 Oph·4Pout U:A1636(OP2) A3485, A3486, A3487, A3488, A3489 A:A1301, A:A1637, G:A1300, G:A1299
3ofx A1540 Oph·4Pout A:A560(OP2) A1607, A1608, A1609, A1610, A1611 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
3ofy A1562 Oph·4Pout G:A1198(OP1) A1711, A1712, A1713, A1714 A:A964, U:A965, C:A1054, U:A1199
3og0 A3017 Oph·4Pout U:A2243(OP1) A3559, A3560, A3561, A3562 C:A192, A:A199, C:A198, U:A193
3og0 A2959 Oph·4Pout G:A1828(OP1) A3303, A3304, A3305, A3306, C338 A:A1772, A:A1773, G:A1972, G:A1973
3og0 A2946 Oph·4Pout G:A1333(OP2) A3241, A3242, A3243, A3244, A3245 C:A1314, G:A1332, G:A1334, U:A1313 G:A1331 C:A1335
3og0 A2937 Oph·4Pout U:A963(OP1) A3203, A3204, A3205, A3206, A3207 C:A964, C:A2498, A:A2497, A:A947
3og0 A3008 Oph·4Pout C:A31(OP1) A3527, A3528, A3529, A3530, A3531 G:A1239, C:A1200, U:A1199, U:A1240 A:A1214
3or9 A1540 Oph·4Pout A:A560(OP2) A1608, A1609, A1610, A1611, A1612 U:A562, A:A563, G:A557, G:A558 G:A566
3ora A1562 Oph·4Pout G:A1198(OP1) A1717, A1718, A1719, A1720 A:A964, U:A965, C:A1054, U:A1199
3orb A3012 Oph·4Pout C:A31(OP1) A3543, A3544, A3545, A3546, A3547 C:A1200, G:A1239, U:A1240, U:A1199
3r8s A2946 Oph·4Pout G:A1333(OP2) A3291, A3292, A3293, A3294, A3295 C:A1314, G:A1334, U:A1313, G:A1332 G:A1334, G:A1333, C:A1335
3r8s A3014 Oph·4Pout C:A31(OP1) A3607, A3608, A3609, A3610, A3611 U:A1240, C:A1200, G:A1239, U:A1199
3r8s A2959 Oph·4Pout G:A1828(OP1) A3353, A3354, A3355, A3356, A3357 A:A1773, G:A1972, G:A1973, A:A1772
3r8t A2945 Oph·4Pout G:A1333(OP2) A3264, A3265, A3266, A3267, A3268 C:A1314, G:A1332, G:A1334, U:A1313 G:A1334, G:A1333, C:A1335
3v22 A1705 Oph·4Pout U:A560(OP2) A1935, A1936, A1937, A1938 C:A562, A:A563, G:A557, G:A558 A:A559 G:A566
3v25 A3267 Oph·4Pout C:A31(OP1) A3617, A3618, A3619, A3620 U:A1199, C:A1200, U:A1240, G:A1239

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>