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3V7E
Asym. Unit
Info
Asym.Unit (141 KB)
Biol.Unit 1 (69 KB)
Biol.Unit 2 (67 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF YBXF BOUND TO THE SAM-I RIBOSWITCH APTAMER
Authors
:
N. J. Baird, J. Zhang, T. Hamma, A. R. Ferre-D'Amare
Date
:
21 Dec 11 (Deposition) - 07 Mar 12 (Release) - 18 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Rna-Protein Complex, Riboswitch, K-Turn, L7Ae-Like, A Member Of The L7Ae/L30E Superfamily, Unknown Function, K-Turn Motif, Ribosomal Protein-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. J. Baird, J. Zhang, T. Hamma, A. R. Ferre-D'Amare
Ybxf And Ylxq Are Bacterial Homologs Of L7Ae And Bind K-Turns But Not K-Loops.
Rna V. 18 759 2012
[
close entry info
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Hetero Components
(3, 42)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
1i: MAGNESIUM ION (MGi)
1j: MAGNESIUM ION (MGj)
1k: MAGNESIUM ION (MGk)
1l: MAGNESIUM ION (MGl)
1m: MAGNESIUM ION (MGm)
1n: MAGNESIUM ION (MGn)
1o: MAGNESIUM ION (MGo)
1p: MAGNESIUM ION (MGp)
1q: MAGNESIUM ION (MGq)
1r: MAGNESIUM ION (MGr)
1s: MAGNESIUM ION (MGs)
1t: MAGNESIUM ION (MGt)
1u: MAGNESIUM ION (MGu)
1v: MAGNESIUM ION (MGv)
2a: COBALT HEXAMMINE(III) (NCOa)
2b: COBALT HEXAMMINE(III) (NCOb)
2c: COBALT HEXAMMINE(III) (NCOc)
2d: COBALT HEXAMMINE(III) (NCOd)
2e: COBALT HEXAMMINE(III) (NCOe)
2f: COBALT HEXAMMINE(III) (NCOf)
2g: COBALT HEXAMMINE(III) (NCOg)
2h: COBALT HEXAMMINE(III) (NCOh)
2i: COBALT HEXAMMINE(III) (NCOi)
2j: COBALT HEXAMMINE(III) (NCOj)
2k: COBALT HEXAMMINE(III) (NCOk)
2l: COBALT HEXAMMINE(III) (NCOl)
2m: COBALT HEXAMMINE(III) (NCOm)
2n: COBALT HEXAMMINE(III) (NCOn)
2o: COBALT HEXAMMINE(III) (NCOo)
2p: COBALT HEXAMMINE(III) (NCOp)
2q: COBALT HEXAMMINE(III) (NCOq)
2r: COBALT HEXAMMINE(III) (NCOr)
3a: S-ADENOSYLMETHIONINE (SAMa)
3b: S-ADENOSYLMETHIONINE (SAMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
22
Ligand/Ion
MAGNESIUM ION
2
NCO
18
Ligand/Ion
COBALT HEXAMMINE(III)
3
SAM
2
Ligand/Ion
S-ADENOSYLMETHIONINE
[
close Hetero Component info
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Sites
(38, 38)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
U C:4 , U C:5 , A C:6 , A C:119 , U C:120 , G C:121 , A C:122
BINDING SITE FOR RESIDUE NCO C 901
02
AC2
SOFTWARE
G C:23 , C C:25 , U C:26 , G C:27 , G C:28
BINDING SITE FOR RESIDUE NCO C 902
03
AC3
SOFTWARE
C C:59 , G C:60 , U C:61 , G C:73 , A C:74 , NCO C:909
BINDING SITE FOR RESIDUE NCO C 903
04
AC4
SOFTWARE
A C:45 , A C:46 , G C:87 , G C:88
BINDING SITE FOR RESIDUE NCO C 904
05
AC5
SOFTWARE
A C:10 , G C:11 , A C:12 , A C:94 , U C:95 , U C:96
BINDING SITE FOR RESIDUE NCO C 905
06
AC6
SOFTWARE
U C:113 , G C:114 , A C:115
BINDING SITE FOR RESIDUE NCO C 906
07
AC7
SOFTWARE
A C:24 , C C:25 , U C:96 , C C:98 , U C:99 , G C:100 , A C:116 , A C:117
BINDING SITE FOR RESIDUE NCO C 907
08
AC8
SOFTWARE
C C:41 , G C:42 , G C:43
BINDING SITE FOR RESIDUE NCO C 908
09
AC9
SOFTWARE
C C:59 , NCO C:903
BINDING SITE FOR RESIDUE NCO C 909
10
BC1
SOFTWARE
A C:46 , A C:84 , G C:85
BINDING SITE FOR RESIDUE NCO C 910
11
BC2
SOFTWARE
G C:53 , U C:54 , A C:79 , G C:80 , G C:81
BINDING SITE FOR RESIDUE NCO C 911
12
BC3
SOFTWARE
C C:62 , A C:63 , G C:64
BINDING SITE FOR RESIDUE NCO C 912
13
BC4
SOFTWARE
U C:7 , G C:11 , A C:45 , C C:47 , U C:89 , G C:90 , U C:120 , G C:121
BINDING SITE FOR RESIDUE SAM C 913
14
BC5
SOFTWARE
G C:13 , G C:42 , C C:92 , HOH C:1007
BINDING SITE FOR RESIDUE MG C 914
15
BC6
SOFTWARE
A C:36
BINDING SITE FOR RESIDUE MG C 917
16
BC7
SOFTWARE
G C:100 , C C:101 , A C:102
BINDING SITE FOR RESIDUE MG C 918
17
BC8
SOFTWARE
G C:1 , HOH C:1003 , HOH D:501 , HOH D:502
BINDING SITE FOR RESIDUE MG C 919
18
BC9
SOFTWARE
G C:19
BINDING SITE FOR RESIDUE MG C 920
19
CC1
SOFTWARE
U C:83 , A C:84
BINDING SITE FOR RESIDUE MG C 921
20
CC2
SOFTWARE
C C:104 , G C:105
BINDING SITE FOR RESIDUE MG C 922
21
CC3
SOFTWARE
HOH C:1001 , HOH C:1004 , HOH C:1005
BINDING SITE FOR RESIDUE MG C 923
22
CC4
SOFTWARE
G C:18 , G C:19 , G C:35 , HOH C:1002
BINDING SITE FOR RESIDUE MG C 924
23
CC5
SOFTWARE
C C:3 , HOH C:1006
BINDING SITE FOR RESIDUE MG C 926
24
CC6
SOFTWARE
U D:204 , U D:205 , A D:319 , U D:320 , G D:321
BINDING SITE FOR RESIDUE NCO D 401
25
CC7
SOFTWARE
A D:210 , G D:211 , A D:294 , U D:295 , U D:296
BINDING SITE FOR RESIDUE NCO D 402
26
CC8
SOFTWARE
A D:245 , A D:246 , U D:286 , G D:287 , G D:288 , U D:289
BINDING SITE FOR RESIDUE NCO D 403
27
CC9
SOFTWARE
G D:223 , C D:225 , U D:226 , G D:227 , G D:228 , C D:229 , HOH D:502
BINDING SITE FOR RESIDUE NCO D 404
28
DC1
SOFTWARE
U D:313 , G D:314 , A D:315
BINDING SITE FOR RESIDUE NCO D 405
29
DC2
SOFTWARE
C D:259 , G D:260 , U D:261 , G D:273
BINDING SITE FOR RESIDUE NCO D 406
30
DC3
SOFTWARE
U D:207 , C D:208 , G D:211 , A D:245 , A D:246 , C D:247 , U D:289 , G D:290 , C D:291 , U D:320 , G D:321
BINDING SITE FOR RESIDUE SAM D 407
31
DC4
SOFTWARE
U D:299 , G D:300 , HOH D:506 , HOH D:507
BINDING SITE FOR RESIDUE MG D 408
32
DC5
SOFTWARE
G D:201
BINDING SITE FOR RESIDUE MG D 409
33
DC6
SOFTWARE
G D:300
BINDING SITE FOR RESIDUE MG D 410
34
DC7
SOFTWARE
G D:213 , G D:242
BINDING SITE FOR RESIDUE MG D 412
35
DC8
SOFTWARE
C D:203 , C D:324
BINDING SITE FOR RESIDUE MG D 413
36
DC9
SOFTWARE
HOH D:503 , HOH D:504
BINDING SITE FOR RESIDUE MG D 414
37
EC1
SOFTWARE
U D:217 , G D:218 , HOH D:505
BINDING SITE FOR RESIDUE MG D 415
38
EC2
SOFTWARE
A D:316
BINDING SITE FOR RESIDUE MG D 416
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
[
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Atom Selection
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Protein
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Backbone
Sidechain
Hetero
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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show bonds with a radius of 100 units (=0.4Å)
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