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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 4 of 10 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qox B2975 Oph·4Pout G:B1333(OP2) B3361, B3362, B3363, B3364, B3365 C:B1314, G:B1334, U:B1313, G:B1332 G:B1334, G:B1333
2qoy A1549 Oph·4Pout A:A560(OP2) A1930, A1931, A1932, A1933, A1934 U:A562, A:A563, G:A557, G:A558 A:A559
2qoz B2920 Oph·4Pout G:B1828(OP1) B3580, B3581, B3582, B3583, B3584 A:B1773, G:B1972, G:B1973, A:B1772
2qp0 A1576 Oph·4Pout C:A536(OP1) A2047, A2048, A2049, A2050, A2051 C:A504, G:A537, A:A523, C:A503 C:A522
2qp1 B2976 Oph·4Pout G:B1333(OP2) B3870, B3871, B3872, B3873, B3874 C:B1314, G:B1332, G:B1334, U:B1313 G:B1334, G:B1333
2qp1 B2994 Oph·4Pout C:B31(OP1) B3940, B3941, B3942, B3943, B3944 C:B1200, U:B1199, G:B1239, U:B1240
2z4k A1550 Oph·4Pout A:A560(OP2) A1635, A1636, A1637, A1638, A1639 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
2z4l B2993 Oph·4Pout C:B31(OP1) B3419, B3420, B3421, B3422, B3423 G:B1239, C:B1200, U:B1199, U:B1240
2z4m A1548 Oph·4Pout A:A560(OP2) A1623, A1624, A1625, A1626, A1627 U:A562, A:A563, G:A558, G:A557 A:A559
2z4n B3016 Oph·4Pout U:B963(OP1) B3515, B3516, B3517, B3518, B3519 A:B947, C:B964, C:B2498, A:B2497
3cc2 08035 Oph·4Pout G:01484(OP2) 03269, 07369, 07370, 07425, 07426 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
3cc2 08012 Oph·4Pout G:028(OP1) 03201, 07418, 08560, 09173, 09772 C:01305, U:01304, C:01343, G:01344
3ccm 08008 Oph·4Pout G:028(OP1) 03251, 03676, 07889, 09047, 09660 C:01305, U:01304, G:01344, C:01343
3ccq 08008 Oph·4Pout G:028(OP1) 03250, 03669, 07906, 09049, 09653 G:01344, C:01305, U:01304, C:01343
3ccr 08008 Oph·4Pout G:028(OP1) 03131, 03657, 07849, 09047, 09654 C:01305, U:01304, G:01344, C:01343
3ccs 08008 Oph·4Pout G:028(OP1) 03228, 03648, 07858, 09046, 09646 C:01305, U:01304, C:01343, G:01344 A:01318
3ccv 08008 Oph·4Pout G:028(OP1) 03236, 03657, 07864, 09044, 09645 C:01305, U:01304, C:01343, G:01344
3cpw 08008 Oph·4Pout G:028(OP1) 03101, 03678, 04085, 08282, 09535 C:01343, G:01344, C:01305, U:01304
3cxc 08035 Oph·4Pout G:01484(OP2) 04664, 08702, 08703, 08756, 08757 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
3cxc 08012 Oph·4Pout G:028(OP1) 03037, 03617, 04190, 04596, 08750 U:01304, C:01305, C:01343, G:01344
3df1 A2038 Oph·4Pout A:A560(OP2) A4039, A4040, A4041, A4042, A4043 A:A563, U:A562, G:A557, G:A558 G:A566
3df2 B3072 Oph·4Pout G:B1333(OP2) B4073, B4074, B4075, B4076, B4077 C:B1314, G:B1334, U:B1313, G:B1332 G:B1334, C:B1335
3df2 B3499 Oph·4Pout C:B31(OP1) B4500, B4501, B4502, B4503, B4504 G:B1239, U:B1240, C:B1200, U:B1199
3df3 A2023 Oph·4Pout A:A560(OP2) A4024, A4025, A4026, A4027, A4028 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
3i1m A1540 Oph·4Pout A:A560(OP2) A1608, A1609, A1610, A1611, A1612 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566

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>