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

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Representative site 3r8s:A3026, See in JSmolMgRNA representative site for type cis-2OP        Click on the image to toggle views


Site type: cis-2Oph

Schematic drawing for
cis-2Oph

MgRNA type cis-2OP
List of all 1720 Mg2+ binding sites with the site type cis-2Oph 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 69 | « 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
3la5 A4 cis-2Oph A:A23(OP2), A:A24(OP2) A128, A200, A410, A416
3la5 A6 cis-2Oph G:A43(OP1), C:A51(OP1) A107, A116, A374, A418 A:A52, G:A43, G:A44, C:A51
3rer K9 cis-2Oph U:K5(OP1), U:K6(OP2) K443, K444, K445, K446 U:K4 U:K3
1pjo A31 cis-2Oph A:A9(OP1), DT:B18(OP2) A132, A133, A134, B135 G:A10, DT:B17, DG:B20, DT:B17, DT:B18
1pjo B34 cis-2Oph G:A10(OP1), DT:B18(OP1) A147, A148, A149, B146 G:A10, DT:B18, DT:B18, G:A10 DT:B19
4tra A78 cis-2Oph G:A20(OP1), A:A21(OP2) A190, A191, A192
6tna A78 cis-2Oph G:A20(OP1), A:A21(OP2) A150, A151, A152, A153
3d2g B79 cis-2Oph C:B51(OP1), A:B52(OP2) A84, B87, B88, B89 A:A50, A:B52
3d2g A80 cis-2Oph C:A51(OP1), A:A52(OP2) A96, A97, A98, B90 A:A52, A:B50
3d2g A82 cis-2Oph G:A42(OP2), C:A65(OP1) A85, A86, A87, A88 C:A67 G:A42
3q3z V85 cis-2Oph G:V46(OP1), A:A34(OP2) V175, V176, A160, A161
3q3z V87 cis-2Oph A:V34(OP2), G:A46(OP2) V178, V179, V180, A169 A:V33
3oww A101 cis-2Oph A:A34(OP1), G:A35(OP2) A131, A132, A133, A134 A:A81 G:A35, G:A36
3owz A101 cis-2Oph A:A34(OP1), G:A35(OP2) A119, A120, A121, A122 A:A81 G:A35, G:A36
3oxj A101 cis-2Oph A:A34(OP1), G:A35(OP2) A125, A126, A127, A128 A:A81 G:A35, G:A36
3owi A101 cis-2Oph A:A34(OP1), G:A35(OP2) A132, A133, A134, A135 A:A81 G:A35, G:A36
3oxm A101 cis-2Oph A:A34(OP1), G:A35(OP2) A111, A138, A139, A140 A:A81 G:A35, G:A36
4pqv A102 cis-2Oph C:A5(OP2), C:A23(OP2) A201, A202, A203, A207 A:A6 A:A6
4m30 C102 cis-2Oph A:C2(OP2), A:C3(OP2) C213, C214, C217 A:C3
3oww A104 cis-2Oph A:A75(OP1), A:A76(OP2) A142, A143, A144 C:A74 A:A76, A:A77
4oji A104 cis-2Oph U:A24(OP2), C:A26(OP1) A205, A206, A207, A208 G:A23 C:A25
3ox0 A105 cis-2Oph C:A70(OP2), A:A71(OP2) A136, A137, A138, A139 U:A69 G:A72, A:A71
3owi A105 cis-2Oph C:A70(OP2), A:A71(OP2) A146, A147, A148, A149 U:A69 G:A72, A:A71
3oww A105 cis-2Oph C:A70(OP2), A:A71(OP2) A145, A146, A147, A148 U:A69 G:A72, A:A71
3owz B110 cis-2Oph A:B34(OP1), G:B35(OP2) B126, B127, B128, B129 A:B81 G:B35, G:B36

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>