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

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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].
[show classification tree with schematic drawings]
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)=1Or (22); Ob (468); Nb (284)
#(Ob|Nb|Or)=22Or (6); Or·Ob (1); 2Ob (16); Ob·Nb (26); 2Nb (158)
#(Ob|Nb|Or)=32Ob·Nb (1); Ob·2Nb (3); 2Or·Nb (1)
#(Ob|Nb|Or)=42Or·2Ob (1)
Oph=1
(5379)
#(Ob|Nb|Or)=0Oph (588); Oph·Pout (1301); Oph·2Pout (1607); Oph·3Pout (867); Oph·4Pout (231); Oph·5Pout (37)
#(Ob|Nb|Or)=1Oph·Or (49); Oph·Ob (554); Oph·Nb (134)
#(Ob|Nb|Or)=2Oph·2Or (8); Oph·2Ob (2)
#(Ob|Nb|Or)=3Oph·Or·2Ob (1)
Oph=2
(2287)
#(Ob|Nb|Or)=0cis-2Oph (1720); trans-2Oph (282)
#(Ob|Nb|Or)=1cis-2Oph·Or (36); cis-2Oph·Ob (98); cis-2Oph·Nb (118)
#(Ob|Nb|Or)=2cis-2Oph·2Or (2); cis-2Oph·Or·Ob (2); cis-2Oph·2Ob (28); trans-2Oph·2Ob (1)
Oph=3
(911)
#(Ob|Nb|Or)=0fac-3Oph (392); mer-3Oph (430)
#(Ob|Nb|Or)=1fac-3Oph·Or (3); mer-3Oph·Or (19); fac-3Oph·Ob (64); mer-3Oph·Ob (3)
Oph=4 (64)#(Ob|Nb|Or)=0trans,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)=1Rout (25); Bout (132)
#(Rout|Bout)=22Rout (1); Rout·Bout (12); 2Bout (555)
#(Rout|Bout)=32Rout·Bout (3); Rout·2Bout (12); 3Bout (341)
#(Rout|Bout)=42Rout·2Bout (5); Rout·3Bout (13); 4Bout (105)
#(Rout|Bout)=52Rout·3Bout (4); Rout·4Bout (5); 5Bout (45)
#(Rout|Bout)=64Rout·2Bout (1); 4Bout·2Rout (1); Rout·5Bout (2); 6Bout (78)
#(Rout|Bout)=73Rout·4Bout (1); 2Rout·5Bout (3); Rout·6Bout (2); 7Bout (7)
#(Rout|Bout)=84Rout·4Bout (1); Rout·7Bout (1)
Pout=1
(1319)
#(Rout|Bout)=0Pout (94)
#(Rout|Bout)=1Pout·Rout (37); Pout·Bout (223)
#(Rout|Bout)=2Pout·2Rout (3); Pout·Rout·Bout (28); Pout·2Bout (343)
#(Rout|Bout)=3Pout·2Rout·Bout (3); Pout·Rout·2Bout (40); Pout·3Bout (341)
#(Rout|Bout)=4Pout·3Rout·Bout (1); Pout·2Rout·2Bout (4); Pout·Rout·3Bout (32); Pout·4Bout (135)
#(Rout|Bout)=5Pout·4Rout·Bout (1); Pout·3Rout·2Bout (1); Pout·2Rout·3Bout (5); Pout·Rout·4Bout (6); Pout·5Bout (18)
#(Rout|Bout)=6Pout·6Bout (4)
Pout=2
(1103)
#(Rout|Bout)=02Pout (191)
#(Rout|Bout)=12Pout·Rout (39); 2Pout·Bout (169)
#(Rout|Bout)=22Pout·2Rout (2); 2Pout·Rout·Bout (32); 2Pout·2Bout (279)
#(Rout|Bout)=32Pout·2Rout·Bout (3); 2Pout·Rout·2Bout (33); 2Pout·3Bout (199)
#(Rout|Bout)=42Pout·2Rout·2Bout (12); 2Pout·Rout·3Bout (39); 2Pout·4Bout (68)
#(Rout|Bout)=52Pout·3Rout·2Bout (1); 2Pout·2Rout·3Bout (11); 2Pout·Rout·4Bout (9); 2Pout·5Bout (12)
#(Rout|Bout)=62Pout·Rout·5Bout (1); 2Pout·6Bout (3)
Pout=3
(783)
#(Rout|Bout)=03Pout (207)
#(Rout|Bout)=13Pout·Rout (51); 3Pout·Bout (155)
#(Rout|Bout)=23Pout·2Rout (11); 3Pout·Rout·Bout (36); 3Pout·2Bout (131)
#(Rout|Bout)=33Pout·3Rout (1); 3Pout·2Rout·Bout (6); 3Pout·Rout·2Bout (58); 3Pout·3Bout (34)
#(Rout|Bout)=43Pout·2Rout·2Bout (4); 3Pout·Rout·3Bout (33); 3Pout·4Bout (24)
#(Rout|Bout)=53Pout·2Rout·3Bout (4); 3Pout·Rout·4Bout (16); 3Pout·5Bout (10)
#(Rout|Bout)=63Pout·Rout·5Bout (2)
Pout=4
(412)
#(Rout|Bout)=04Pout (174)
#(Rout|Bout)=14Pout·Rout (51); 4Pout·Bout (125)
#(Rout|Bout)=24Pout·2Rout (4); 4Pout·Rout·Bout (10); 4Pout·2Bout (40)
#(Rout|Bout)=34Pout·Rout·2Bout (3); 4Pout·3Bout (2)
#(Rout|Bout)=44Pout·Rout·3Bout (1)
#(Rout|Bout)=54Pout·3Rout·2Bout (1); 4Pout·Rout·4Bout (1)
Pout=5
(54)
#(Rout|Bout)=05Pout (20)
#(Rout|Bout)=15Pout·Rout (12); 5Pout·Bout (6)
#(Rout|Bout)=25Pout·Rout·Bout (5); 5Pout·2Bout (10)
#(Rout|Bout)=35Pout·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].


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>