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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]. |
I. Mg2+ sites with RNA atoms in the inner sphere (RNA-inner class) | ||
---|---|---|
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 |
Oph=0 (987) | #(Ob|Nb|Or)=1 | Or (22); Ob (468); Nb (284) |
#(Ob|Nb|Or)=2 | 2Or (6); Or·Ob (1); 2Ob (16); Ob·Nb (26); 2Nb (158) | |
#(Ob|Nb|Or)=3 | 2Ob·Nb (1); Ob·2Nb (3); 2Or·Nb (1) | |
#(Ob|Nb|Or)=4 | 2Or·2Ob (1) | |
Oph=1 (5379) | #(Ob|Nb|Or)=0 | Oph (588); Oph·Pout (1301); Oph·2Pout (1607); Oph·3Pout (867); Oph·4Pout (231); Oph·5Pout (37) |
#(Ob|Nb|Or)=1 | Oph·Or (49); Oph·Ob (554); Oph·Nb (134) | |
#(Ob|Nb|Or)=2 | Oph·2Or (8); Oph·2Ob (2) | |
#(Ob|Nb|Or)=3 | Oph·Or·2Ob (1) | |
Oph=2 (2287) | #(Ob|Nb|Or)=0 | cis-2Oph (1720); trans-2Oph (282) |
#(Ob|Nb|Or)=1 | cis-2Oph·Or (36); cis-2Oph·Ob (98); cis-2Oph·Nb (118) | |
#(Ob|Nb|Or)=2 | cis-2Oph·2Or (2); cis-2Oph·Or·Ob (2); cis-2Oph·2Ob (28); trans-2Oph·2Ob (1) | |
Oph=3 (911) | #(Ob|Nb|Or)=0 | fac-3Oph (392); mer-3Oph (430) |
#(Ob|Nb|Or)=1 | fac-3Oph·Or (3); mer-3Oph·Or (19); fac-3Oph·Ob (64); mer-3Oph·Ob (3) | |
Oph=4 (64) | #(Ob|Nb|Or)=0 | trans,cis-4Oph (29); trans,trans-4Oph(35) |
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 |
Pout=0 (1355) | #(Rout|Bout)=1 | Rout (25); Bout (132) |
#(Rout|Bout)=2 | 2Rout (1); Rout·Bout (12); 2Bout (555) | |
#(Rout|Bout)=3 | 2Rout·Bout (3); Rout·2Bout (12); 3Bout (341) | |
#(Rout|Bout)=4 | 2Rout·2Bout (5); Rout·3Bout (13); 4Bout (105) | |
#(Rout|Bout)=5 | 2Rout·3Bout (4); Rout·4Bout (5); 5Bout (45) | |
#(Rout|Bout)=6 | 4Rout·2Bout (1); 4Bout·2Rout (1); Rout·5Bout (2); 6Bout (78) | |
#(Rout|Bout)=7 | 3Rout·4Bout (1); 2Rout·5Bout (3); Rout·6Bout (2); 7Bout (7) | |
#(Rout|Bout)=8 | 4Rout·4Bout (1); Rout·7Bout (1) | |
Pout=1 (1319) | #(Rout|Bout)=0 | Pout (94) |
#(Rout|Bout)=1 | Pout·Rout (37); Pout·Bout (223) | |
#(Rout|Bout)=2 | Pout·2Rout (3); Pout·Rout·Bout (28); Pout·2Bout (343) | |
#(Rout|Bout)=3 | Pout·2Rout·Bout (3); Pout·Rout·2Bout (40); Pout·3Bout (341) | |
#(Rout|Bout)=4 | Pout·3Rout·Bout (1); Pout·2Rout·2Bout (4); Pout·Rout·3Bout (32); Pout·4Bout (135) | |
#(Rout|Bout)=5 | Pout·4Rout·Bout (1); Pout·3Rout·2Bout (1); Pout·2Rout·3Bout (5); Pout·Rout·4Bout (6); Pout·5Bout (18) | |
#(Rout|Bout)=6 | Pout·6Bout (4) | |
Pout=2 (1103) | #(Rout|Bout)=0 | 2Pout (191) |
#(Rout|Bout)=1 | 2Pout·Rout (39); 2Pout·Bout (169) | |
#(Rout|Bout)=2 | 2Pout·2Rout (2); 2Pout·Rout·Bout (32); 2Pout·2Bout (279) | |
#(Rout|Bout)=3 | 2Pout·2Rout·Bout (3); 2Pout·Rout·2Bout (33); 2Pout·3Bout (199) | |
#(Rout|Bout)=4 | 2Pout·2Rout·2Bout (12); 2Pout·Rout·3Bout (39); 2Pout·4Bout (68) | |
#(Rout|Bout)=5 | 2Pout·3Rout·2Bout (1); 2Pout·2Rout·3Bout (11); 2Pout·Rout·4Bout (9); 2Pout·5Bout (12) | |
#(Rout|Bout)=6 | 2Pout·Rout·5Bout (1); 2Pout·6Bout (3) | |
Pout=3 (783) | #(Rout|Bout)=0 | 3Pout (207) |
#(Rout|Bout)=1 | 3Pout·Rout (51); 3Pout·Bout (155) | |
#(Rout|Bout)=2 | 3Pout·2Rout (11); 3Pout·Rout·Bout (36); 3Pout·2Bout (131) | |
#(Rout|Bout)=3 | 3Pout·3Rout (1); 3Pout·2Rout·Bout (6); 3Pout·Rout·2Bout (58); 3Pout·3Bout (34) | |
#(Rout|Bout)=4 | 3Pout·2Rout·2Bout (4); 3Pout·Rout·3Bout (33); 3Pout·4Bout (24) | |
#(Rout|Bout)=5 | 3Pout·2Rout·3Bout (4); 3Pout·Rout·4Bout (16); 3Pout·5Bout (10) | |
#(Rout|Bout)=6 | 3Pout·Rout·5Bout (2) | |
Pout=4 (412) | #(Rout|Bout)=0 | 4Pout (174) |
#(Rout|Bout)=1 | 4Pout·Rout (51); 4Pout·Bout (125) | |
#(Rout|Bout)=2 | 4Pout·2Rout (4); 4Pout·Rout·Bout (10); 4Pout·2Bout (40) | |
#(Rout|Bout)=3 | 4Pout·Rout·2Bout (3); 4Pout·3Bout (2) | |
#(Rout|Bout)=4 | 4Pout·Rout·3Bout (1) | |
#(Rout|Bout)=5 | 4Pout·3Rout·2Bout (1); 4Pout·Rout·4Bout (1) | |
Pout=5 (54) | #(Rout|Bout)=0 | 5Pout (20) |
#(Rout|Bout)=1 | 5Pout·Rout (12); 5Pout·Bout (6) | |
#(Rout|Bout)=2 | 5Pout·Rout·Bout (5); 5Pout·2Bout (10) | |
#(Rout|Bout)=3 | 5Pout·3Rout (1) |
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]. |