`

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

Specify PDB ID or upload a structure for analysis Download the benchmark dataset in: CSV, XML, JSON

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 without 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)=1
(774)
MgRNA type OR
Or (22)
MgRNA type OB
Ob (468)
MgRNA type NB
Nb (284)
#(Ob|Nb|Or)=2
(207)
MgRNA type 2OR
2Or (6)
MgRNA type OR-OB
Or·Ob (1)
MgRNA type 2OB
2Ob (16)
MgRNA type OB-NB
Ob·Nb (26)
MgRNA type 2NB
2Nb (158)
#(Ob|Nb|Or)=3
(5)
MgRNA type 2OB-NB
2Ob·Nb (1)
MgRNA type OB-2NB
Ob·2Nb (3)
MgRNA type 2OR-NB
2Or·Nb (1)
#(Ob|Nb|Or)=4
(1)
MgRNA type 2OR-2OB
2Or·2Ob (1)
Oph=1
(5379)
#(Ob|Nb|Or)=0
(4631)
MgRNA type OP
Oph (588)
MgRNA type OP-PO
Oph·Pout (1301)
MgRNA type OP-2PO
Oph·2Pout (1607)
MgRNA type OP-3PO
Oph·3Pout (867)
MgRNA type OP-4PO
Oph·4Pout (231)
MgRNA type OP-5PO
Oph·5Pout (37)
#(Ob|Nb|Or)=1
(737)
MgRNA type OP-OR
Oph·Or (49)
MgRNA type OP-OB
Oph·Ob (554)
MgRNA type OP-NB
Oph·Nb (134)
#(Ob|Nb|Or)=2
(10)
MgRNA type OP-2OR
Oph·2Or (8)
MgRNA type OP-2OB
Oph·2Ob (2)
#(Ob|Nb|Or)=3
(1)
MgRNA type OP-OR-2OB
Oph·Or·2Ob (1)
Oph=2
(2287)
#(Ob|Nb|Or)=0
(2002)
MgRNA type cis-2OP
cis-2Oph (1720)
MgRNA type trans-2OP
trans-2Oph (282)
#(Ob|Nb|Or)=1
(252)
MgRNA type cis-2OP-OR
cis-2Oph·Or (36)
MgRNA type cis-2OP-OB
cis-2Oph·Ob (98)
MgRNA type cis-2OP-NB
cis-2Oph·Nb (118)
#(Ob|Nb|Or)=2
(33)
MgRNA type cis-2OP-2OR
cis-2Oph·2Or (2)
MgRNA type cis-2OP-OR-OB
cis-2Oph·Or·Ob (2)
MgRNA type cis-2OP-2OB
cis-2Oph·2Ob (28)
MgRNA type trans-2OP-2OB
trans-2Oph·2Ob (1)
Oph=3
(911)
#(Ob|Nb|Or)=0
(822)
MgRNA type fac-3OP
fac-3Oph (392)
MgRNA type mer-3OP
mer-3Oph (430)
#(Ob|Nb|Or)=1
(89)
MgRNA type fac-3OP-OR
fac-3Oph·Or (3)
MgRNA type mer-3OP-OR
mer-3Oph·Or (19)
MgRNA type fac-3OP-OB
fac-3Oph·Ob (64)
MgRNA type mer-3OP-OB
mer-3Oph·Ob (3)
Oph=4
(64)
#(Ob|Nb|Or)=0
(64)
MgRNA type trans,cis-4OP
trans,cis-4Oph (29)
MgRNA type trans,trans-4OP
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
(157)
MgRNA type RO
Rout (25)
MgRNA type BO
Bout (132)
#(Rout|Bout)=2
(568)
MgRNA type 2RO
2Rout (1)
MgRNA type RO-BO
Rout·Bout (12)
MgRNA type 2BO
2Bout (555)
#(Rout|Bout)=3
(356)
MgRNA type 2RO-BO
2Rout·Bout (3)
MgRNA type RO-2BO
Rout·2Bout (12)
MgRNA type 3BO
3Bout (341)
#(Rout|Bout)=4
(123)
MgRNA type 2RO-2BO
2Rout·2Bout (5)
MgRNA type RO-3BO
Rout·3Bout (13)
MgRNA type 4BO
4Bout (105)
#(Rout|Bout)=5
(54)
MgRNA type 2RO-3BO
2Rout·3Bout (4)
MgRNA type RO-4BO
Rout·4Bout (5)
MgRNA type 5BO
5Bout (45)
#(Rout|Bout)=6
(82)
MgRNA type 4RO-2BO
4Rout·2Bout (1)
MgRNA type 4BO-2RO
4Bout·2Rout (1)
MgRNA type RO-5BO
Rout·5Bout (2)
MgRNA type 6BO
6Bout (78)
#(Rout|Bout)=7
(13)
MgRNA type 3RO-4BO
3Rout·4Bout (1)
MgRNA type 2RO-5BO
2Rout·5Bout (3)
MgRNA type RO-6BO
Rout·6Bout (2)
MgRNA type 7BO
7Bout (7)
#(Rout|Bout)=8
(2)
MgRNA type 4RO-4BO
4Rout·4Bout (1)
MgRNA type RO-7BO
Rout·7Bout (1)
Pout=1
(1319)
#(Rout|Bout)=0
(94)
MgRNA type PO
Pout (94)
#(Rout|Bout)=1
(260)
MgRNA type PO-RO
Pout·Rout (37)
MgRNA type PO-BO
Pout·Bout (223)
#(Rout|Bout)=2
(374)
MgRNA type PO-2RO
Pout·2Rout (3)
MgRNA type PO-RO-BO
Pout·Rout·Bout (28)
MgRNA type PO-2BO
Pout·2Bout (343)
#(Rout|Bout)=3
(384)
MgRNA type PO-2RO-BO
Pout·2Rout·Bout (3)
MgRNA type PO-RO-2BO
Pout·Rout·2Bout (40)
MgRNA type PO-3BO
Pout·3Bout (341)
#(Rout|Bout)=4
(172)
MgRNA type PO-3RO-BO
Pout·3Rout·Bout (1)
MgRNA type PO-2RO-2BO
Pout·2Rout·2Bout (4)
MgRNA type PO-RO-3BO
Pout·Rout·3Bout (32)
MgRNA type PO-4BO
Pout·4Bout (135)
#(Rout|Bout)=5
(31)
MgRNA type PO-4RO-BO
Pout·4Rout·Bout (1)
MgRNA type PO-3RO-2BO
Pout·3Rout·2Bout (1)
MgRNA type PO-2RO-3BO
Pout·2Rout·3Bout (5)
MgRNA type PO-RO-4BO
Pout·Rout·4Bout (6)
MgRNA type PO-5BO
Pout·5Bout (18)
#(Rout|Bout)=6
(4)
MgRNA type PO-6BO
Pout·6Bout (4)
Pout=2
(1103)
#(Rout|Bout)=0
(191)
MgRNA type 2PO
2Pout (191)
#(Rout|Bout)=1
(208)
MgRNA type 2PO-RO
2Pout·Rout (39)
MgRNA type 2PO-BO
2Pout·Bout (169)
#(Rout|Bout)=2
(313)
MgRNA type 2PO-2RO
2Pout·2Rout (2)
MgRNA type 2PO-RO-BO
2Pout·Rout·Bout (32)
MgRNA type 2PO-2BO
2Pout·2Bout (279)
#(Rout|Bout)=3
(235)
MgRNA type 2PO-2RO-BO
2Pout·2Rout·Bout (3)
MgRNA type 2PO-RO-2BO
2Pout·Rout·2Bout (33)
MgRNA type 2PO-3BO
2Pout·3Bout (199)
#(Rout|Bout)=4
(119)
MgRNA type 2PO-2RO-2BO
2Pout·2Rout·2Bout (12)
MgRNA type 2PO-RO-3BO
2Pout·Rout·3Bout (39)
MgRNA type 2PO-4BO
2Pout·4Bout (68)
#(Rout|Bout)=5
(33)
MgRNA type 2PO-3RO-2BO
2Pout·3Rout·2Bout (1)
MgRNA type 2PO-2RO-3BO
2Pout·2Rout·3Bout (11)
MgRNA type 2PO-RO-4BO
2Pout·Rout·4Bout (9)
MgRNA type 2PO-5BO
2Pout·5Bout (12)
#(Rout|Bout)=6
(4)
MgRNA type 2PO-RO-5BO
2Pout·Rout·5Bout (1)
MgRNA type 2PO-6BO
2Pout·6Bout (3)
Pout=3
(783)
#(Rout|Bout)=0
(207)
MgRNA type 3PO
3Pout (207)
#(Rout|Bout)=1
(206)
MgRNA type 3PO-RO
3Pout·Rout (51)
MgRNA type 3PO-BO
3Pout·Bout (155)
#(Rout|Bout)=2
(178)
MgRNA type 3PO-2RO
3Pout·2Rout (11)
MgRNA type 3PO-RO-BO
3Pout·Rout·Bout (36)
MgRNA type 3PO-2BO
3Pout·2Bout (131)
#(Rout|Bout)=3
(99)
MgRNA type 3PO-3RO
3Pout·3Rout (1)
MgRNA type 3PO-2RO-BO
3Pout·2Rout·Bout (6)
MgRNA type 3PO-RO-2BO
3Pout·Rout·2Bout (58)
MgRNA type 3PO-3BO
3Pout·3Bout (34)
#(Rout|Bout)=4
(61)
MgRNA type 3PO-2RO-2BO
3Pout·2Rout·2Bout (4)
MgRNA type 3PO-RO-3BO
3Pout·Rout·3Bout (33)
MgRNA type 3PO-4BO
3Pout·4Bout (24)
#(Rout|Bout)=5
(30)
MgRNA type 3PO-2RO-3BO
3Pout·2Rout·3Bout (4)
MgRNA type 3PO-RO-4BO
3Pout·Rout·4Bout (16)
MgRNA type 3PO-5BO
3Pout·5Bout (10)
#(Rout|Bout)=6
(2)
MgRNA type 3PO-RO-5BO
3Pout·Rout·5Bout (2)
Pout=4
(412)
#(Rout|Bout)=0
(174)
MgRNA type 4PO
4Pout (174)
#(Rout|Bout)=1
(176)
MgRNA type 4PO-RO
4Pout·Rout (51)
MgRNA type 4PO-BO
4Pout·Bout (125)
#(Rout|Bout)=2
(54)
MgRNA type 4PO-2RO
4Pout·2Rout (4)
MgRNA type 4PO-RO-BO
4Pout·Rout·Bout (10)
MgRNA type 4PO-2BO
4Pout·2Bout (40)
#(Rout|Bout)=3
(5)
MgRNA type 4PO-RO-2BO
4Pout·Rout·2Bout (3)
MgRNA type 4PO-3BO
4Pout·3Bout (2)
#(Rout|Bout)=4
(1)
MgRNA type 4PO-RO-3BO
4Pout·Rout·3Bout (1)
#(Rout|Bout)=5
(2)
MgRNA type 4PO-3RO-2BO
4Pout·3Rout·2Bout (1)
MgRNA type 4PO-RO-4BO
4Pout·Rout·4Bout (1)
Pout=5
(54)
#(Rout|Bout)=0
(20)
MgRNA type 5PO
5Pout (20)
#(Rout|Bout)=1
(18)
MgRNA type 5PO-RO
5Pout·Rout (12)
MgRNA type 5PO-BO
5Pout·Bout (6)
#(Rout|Bout)=2
(15)
MgRNA type 5PO-RO-BO
5Pout·Rout·Bout (5)
MgRNA type 5PO-2BO
5Pout·2Bout (10)
#(Rout|Bout)=3
(1)
MgRNA type 5PO-3RO
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].


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>