Table 1 Representative motifs of the recurrent backbone topology variants of the GNRA tetraloop motif.

From: Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures

#

Topology,

#strands

PDB entry, chain ID

Residues

n1-n6

#Rfam, #BGSU

n4-n2 atom-base stacking

n4-n2 base-ribose

n2-n5 BPh

n2-n5

base pair

n1-n6

base pair

1

n1-n2-n3-n4-n5-n6

1

8VTW

1A

C2374, G2375, A2376, A2377, A2378, G2379

49

401

OP2-G

AN7-GO2′

2.7 Å

GN2-OP2

2.7 Å

G-A

tSH

C-G

cWW

2

n1-n2|n3-n4-n5-n6

2

8BTD

St

C289, G290, G275, G276, A277, G278

19

143

OP2-G

GN7-GO2′

3.9 Å

GN2-OP2

2.9 Å

G-A

tSH

C-G

cWW

3

n1-n2-n3-n4|n5-n6

2

6LNB

M

C50, G51, A52, G53, A55, G56

13

76

OP2-G

GN7-GO2′

3.7 Å

–

G-A

tSH

C-G

cWW

4

n1-n2-n3|n4-n5-n6

2

4V5H

AA

U1165, G1166, A1167, A1169, A1170, A1171

10

125

OP2-G

(U1168-n2)

AN6-GO2′

2.9 Å

GN2-OP2

3.1 Å

G-A

tSH

U-A

cWW

5

n1-n2-n3-n4|n5|n6

3

5WE4

A

C1752, G1753, A1754, A1755, U1758, G1756

6

63

OP2-G

AN7-GO2′

2.8 Å

GN2-OP2

3.2 Å

–

C-G

cWW

6

n1-n2|n3-n4-n5|n6

3

4V6W

A5

C1355, G1356, A1151, A1152, G1153, G1331

5

32

–

AN6-GO2′

3.6 Å

GN2-OP2

4.2 Å

G-G

tSH

C-G

cWW

7

n1-n2-n3-n4-n5|n6

2

1YJN

0

C1793, G1794, G1795, A1796, A1797, G1799

4

74

OP2-G

AN7-GO2′

2.8 Å

GN2-OP2

2.8 Å

G-A

tSH

C-G

cWW

8

n1-n2|n3|n4-n5-n6

3

7PAU

3

C257, G258, U245, U247, A248, G249

4

27

–

UO4-GO2′

3.2 Å

GN2-OP2

4.5 Å

G-A

tSH

C-G

cWW

9

n1-n2-n3|n4-n5|n6

3

7RQC

2A

C955, G956, A957, A959, A960, G962

4

26

AO2′-G

(n3-n2)

AN7-GO2′

3.1 Å

GN2-OP2

2.7 Å

G-A

tSH

C-G

cWW

10

n1|n2-n3-n4-n5-n6

2

8HL5

A23S

C1161, C1275, G1276, G1277, G1278, G1279

3

25

OP2-C

–

CN4-OP2

2.2 Å

–

C-G

cWW

11

n1|n2|n3-n4-n5-n6

3

9E71

4

G307, G309, G293, G294, G295, C296

3

16

OP2-G

–

GN2-OP2

3.3 Å

G-G

tSH

G-C

cWW

12

n1-n2|n3-n4|n5-n6

3

6YLX

1

C2840, G2841, U2843, C2844, A2847, G2848

3

7

OP2-G

–

–

G-A

tSH

C-G

cWW

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