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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 |
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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]. |
I. Mg2+ sites with RNA atoms in the inner sphere (RNA-inner class) | ||||||||
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Number of inner-sphere PO4 oxygen |
Number of other inner-sphere RNA atoms |
Site types (number of instances) Click on a site type to see details |
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Oph=0 (987) | #(Ob|Nb|Or)=1 (774) |
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#(Ob|Nb|Or)=2 (207) |
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#(Ob|Nb|Or)=3 (5) |
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#(Ob|Nb|Or)=4 (1) |
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Oph=1 (5379) | #(Ob|Nb|Or)=0 (4631) |
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#(Ob|Nb|Or)=1 (737) |
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#(Ob|Nb|Or)=2 (10) |
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#(Ob|Nb|Or)=3 (1) |
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Oph=2 (2287) | #(Ob|Nb|Or)=0 (2002) |
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#(Ob|Nb|Or)=1 (252) |
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#(Ob|Nb|Or)=2 (33) |
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Oph=3 (911) | #(Ob|Nb|Or)=0 (822) |
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#(Ob|Nb|Or)=1 (89) |
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Oph=4 (64) | #(Ob|Nb|Or)=0 (64) |
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II. Mg2+ sites with RNA atoms in the outer sphere only (RNA-outer class) | ||||||||
Number of outer-sphere PO4 moiety |
Number of other outer-sphere RNA moieties |
Site types (number of instances) Click on a site type to see details |
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Pout=0 (1355) | #(Rout|Bout)=1 (157) |
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#(Rout|Bout)=2 (568) |
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#(Rout|Bout)=3 (356) |
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#(Rout|Bout)=4 (123) |
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#(Rout|Bout)=5 (54) |
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#(Rout|Bout)=6 (82) |
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#(Rout|Bout)=7 (13) |
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#(Rout|Bout)=8 (2) |
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Pout=1 (1319) | #(Rout|Bout)=0 (94) |
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#(Rout|Bout)=1 (260) |
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#(Rout|Bout)=2 (374) |
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#(Rout|Bout)=3 (384) |
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#(Rout|Bout)=4 (172) |
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#(Rout|Bout)=5 (31) |
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#(Rout|Bout)=6 (4) |
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Pout=2 (1103) | #(Rout|Bout)=0 (191) |
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#(Rout|Bout)=1 (208) |
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#(Rout|Bout)=2 (313) |
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#(Rout|Bout)=3 (235) |
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#(Rout|Bout)=4 (119) |
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#(Rout|Bout)=5 (33) |
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#(Rout|Bout)=6 (4) |
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Pout=3 (783) | #(Rout|Bout)=0 (207) |
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#(Rout|Bout)=1 (206) |
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#(Rout|Bout)=2 (178) |
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#(Rout|Bout)=3 (99) |
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#(Rout|Bout)=4 (61) |
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#(Rout|Bout)=5 (30) |
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#(Rout|Bout)=6 (2) |
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Pout=4 (412) | #(Rout|Bout)=0 (174) |
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#(Rout|Bout)=1 (176) |
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#(Rout|Bout)=2 (54) |
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#(Rout|Bout)=3 (5) |
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#(Rout|Bout)=4 (1) |
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#(Rout|Bout)=5 (2) |
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Pout=5 (54) | #(Rout|Bout)=0 (20) |
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#(Rout|Bout)=1 (18) |
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#(Rout|Bout)=2 (15) |
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#(Rout|Bout)=3 (1) |
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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]. |