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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 2 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
1vq7 08035 Oph·4Pout G:01484(OP2) 04039, 08122, 08123, 08177, 08178 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
1vq8 08012 Oph·4Pout G:028(OP1) 03256, 03828, 04240, 08380, 09665 C:01343, G:01344, C:01305, U:01304
1vqk 08012 Oph·4Pout G:028(OP1) 03264, 03837, 04251, 08418, 09665 C:01343, G:01344, C:01305, U:01304
1vql 08012 Oph·4Pout G:028(OP1) 03256, 03827, 04239, 08384, 09664 C:01343, G:01344, C:01305, U:01304
1vqm 08012 Oph·4Pout G:028(OP1) 03258, 03833, 04246, 08385, 09664 C:01343, G:01344, C:01305, U:01304
1vqn 08012 Oph·4Pout G:028(OP1) 03258, 03830, 04243, 08377, 09665 C:01343, G:01344, C:01305, U:01304
1vqo 08012 Oph·4Pout G:028(OP1) 03269, 03849, 04264, 08433, 09664 C:01343, G:01344, C:01305, U:01304
1vqp 08012 Oph·4Pout G:028(OP1) 03265, 03841, 04259, 08405, 09664 C:01343, G:01344, C:01305, U:01304
1vs6 B2917 Oph·4Pout G:B1333(OP2) B3072, B3073, B3074, B3075, B3076 C:B1314, G:B1332, G:B1334, U:B1313 G:B1334, G:B1333
1vs6 B2992 Oph·4Pout C:B31(OP1) B3421, B3422, B3423, B3424, B3425 G:B1239, U:B1240, C:B1200, U:B1199
1vt2 A3019 Oph·4Pout U:A2243(OP1) A3564, A3565, A3566, A3567 C:A192, A:A199, C:A198, U:A193
1vt2 A2961 Oph·4Pout G:A1828(OP1) A3306, A3307, A3308, A3309, A3310 A:A1773, G:A1972, G:A1973, A:A1772
1vt2 A3010 Oph·4Pout C:A31(OP1) A3531, A3532, A3533, A3534, A3535 G:A1239, C:A1200, U:A1199, U:A1240
1yhq 08008 Oph·4Pout G:028(OP1) 03139, 03729, 04144, 08368, 09537 C:01343, G:01344, C:01305, U:01304
1yhq 08070 Oph·4Pout G:0918(OP1) 03049, 03824, 06950, 08362, 09588 A:02465, G:02293, C:02294, C:02391 A:02465
1yi2 08091 Oph·4Pout G:0918(OP1) 03325, 06465, 07809, 09091, 09549 G:02293, C:02294, A:02465, U:0919 A:02465
1yi2 08035 Oph·4Pout G:01484(OP2) 03713, 07767, 07768, 07822, 07823 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
1yi2 08012 Oph·4Pout G:028(OP1) 03229, 03645, 07815, 09037, 09639 C:01305, U:01304, C:01343, G:01344
1yij 08012 Oph·4Pout G:028(OP1) 03236, 03657, 07828, 09038, 09640 C:01305, U:01304, C:01343, G:01344
1yj9 08035 Oph·4Pout G:01484(OP2) 03530, 07589, 07590, 07644 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
1yjn 08035 Oph·4Pout G:01484(OP2) 03729, 07792, 07793, 07848, 07849 C:01483, C:01455, C:01456, A:01485 U:01457
1yjw 78091 Oph·4Pout G:0918(OP1) 06150, 08660, 08668, 09021, 09022 C:02294, A:02465, C:02391, U:0919 G:02397, A:02465
2aw4 B2917 Oph·4Pout G:B1333(OP2) B3069, B3070, B3071, B3072, B3073 C:B1314, G:B1332, G:B1334, U:B1313 G:B1334, G:B1333
2aw4 B2992 Oph·4Pout C:B31(OP1) B3417, B3418, B3419, B3420, B3421 G:B1239, U:B1240, C:B1200, U:B1199
2awb B3014 Oph·4Pout U:B963(OP1) B3509, B3510, B3511, B3512, B3513 A:B947, A:B2497, C:B964, C:B2498

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>