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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 1 of 10 | « Previous | | 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
1jj2 08035 Oph·4Pout G:01484(OP2) 03243, 07356, 07357, 07411, 07412 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
1jj2 08012 Oph·4Pout G:028(OP1) 03174, 07405, 08559, 09158, 09751 C:01305, U:01304, C:01343, G:01344
1k73 A8012 Oph·4Pout G:A28(OP1) A3226, A3642, A7869, A9038, A9636 C:A1305, U:A1304, C:A1343, G:A1344
1k9m A8012 Oph·4Pout G:A28(OP1) A3220, A3638, A7868, A9039, A9630 C:A1305, U:A1304, C:A1343, G:A1344
1kc8 A8091 Oph·4Pout G:A918(OP1) A3321, A6482, A7851, A9095, A9544 C:A2294, C:A2391, A:A2465, U:A919 A:A2465
1kd1 A8012 Oph·4Pout G:A28(OP1) A3226, A3643, A7855, A9037, A9630 C:A1305, U:A1304, C:A1343, G:A1344
1kqs 08012 Oph·4Pout G:028(OP1) 03155, 07340, 08560, 09152, 09735 C:01305, U:01304, C:01343, G:01344
1m1k A8012 Oph·4Pout G:A28(OP1) A3241, A7446, A8635, A9231, A9825 C:A1305, U:A1304, C:A1343, G:A1344
1m90 A8091 Oph·4Pout G:A918(OP1) A6020, A7382, A8612, A9068, A9848 C:A2294, C:A2391, A:A2465, G:A2293 A:A2465
1m90 A8035 Oph·4Pout G:A1484(OP2) A3244, A7339, A7340, A7394, A7395 C:A1456, C:A1483, A:A1485, C:A1455 G:A1484, U:A1457
1m90 A8012 Oph·4Pout G:A28(OP1) A3176, A7388, A8558, A9157, A9752 C:A1305, U:A1304, C:A1343, G:A1344
1n8r A8012 Oph·4Pout G:A28(OP1) A3031, A3617, A4043, A8412, A9443 C:A1343, G:A1344, C:A1305, U:A1304
1nji A8035 Oph·4Pout G:A1484(OP2) A3707, A7800, A7801, A7856, A7857 C:A1456, C:A1483, A:A1485, C:A1455 G:A1484, U:A1457
1q82 A8012 Oph·4Pout G:A28(OP1) A3161, A7329, A8559, A9151, A9738 C:A1305, U:A1304, C:A1343, G:A1344
1q86 A8091 Oph·4Pout G:A918(OP1) A5999, A7354, A8614, A9072, A9845 C:A2294, C:A2391, A:A2465, U:A919 A:A2465
1qvg 08091 Oph·4Pout G:0918(OP1) 05909, 07232, 08616, 09065, 09830 C:02294, C:02391, A:02465, U:0919 A:02465
1qvg 08035 Oph·4Pout G:01484(OP2) 03221, 07189, 07190, 07243, 07244 C:01483, C:01455, C:01456, A:01485 U:01457
1s72 08012 Oph·4Pout G:028(OP1) 03169, 07360, 08559, 09156, 09747 C:01305, U:01304, C:01343, G:01344
1s72 08035 Oph·4Pout G:01484(OP2) 03238, 07311, 07312, 07367, 07368 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
1vq4 08012 Oph·4Pout G:028(OP1) 03534, 03953, 08131, 09359, 09956 C:01305, U:01304, C:01343, G:01344
1vq5 08012 Oph·4Pout G:028(OP1) 03548, 03964, 08175, 09361, 09962 C:01305, U:01304, C:01343, G:01344
1vq5 08035 Oph·4Pout G:01484(OP2) 04030, 08126, 08127, 08182, 08183 C:01483, A:01485, C:01455, C:01456 G:01484, U:01457
1vq6 08012 Oph·4Pout G:028(OP1) 03534, 03956, 08139, 09361, 09957 C:01305, U:01304, C:01343, G:01344
1vq6 08035 Oph·4Pout G:01484(OP2) 04024, 07983, 07984, 08146, 08147 C:01483, C:01455, A:01485, C:01456 U:01457
1vq7 08035 Oph·4Pout G:01484(OP2) 04039, 08122, 08123, 08177, 08178 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457

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>