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4Y1J
Biol. Unit 1
Info
Asym.Unit (199 KB)
Biol.Unit 1 (190 KB)
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Title
:
LACTOCOCCUS LACTIS YYBP-YKOY MN RIBOSWITCH A41U BINDING SITE MUTANT IN PRESENCE OF MN2+
Authors
:
I. R. Price, A. Ke
Date
:
07 Feb 15 (Deposition) - 08 Apr 15 (Release) - 20 Jul 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.24
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Riboswitch, Manganese-Binding, Mutant, Rna
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. R. Price, A. Gaballa, F. Ding, J. D. Helmann, A. Ke
Mn(2+)-Sensing Mechanisms Of Yybp-Ykoy Orphan Riboswitches.
Mol. Cell V. 57 1110 2015
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
1b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
2m: MAGNESIUM ION (MGm)
2n: MAGNESIUM ION (MGn)
2o: MAGNESIUM ION (MGo)
2p: MAGNESIUM ION (MGp)
2q: MAGNESIUM ION (MGq)
2r: MAGNESIUM ION (MGr)
2s: MAGNESIUM ION (MGs)
2t: MAGNESIUM ION (MGt)
2u: MAGNESIUM ION (MGu)
2v: MAGNESIUM ION (MGv)
2w: MAGNESIUM ION (MGw)
2x: MAGNESIUM ION (MGx)
3a: STRONTIUM ION (SRa)
3aa: STRONTIUM ION (SRaa)
3ab: STRONTIUM ION (SRab)
3ac: STRONTIUM ION (SRac)
3ad: STRONTIUM ION (SRad)
3ae: STRONTIUM ION (SRae)
3af: STRONTIUM ION (SRaf)
3ag: STRONTIUM ION (SRag)
3ah: STRONTIUM ION (SRah)
3ai: STRONTIUM ION (SRai)
3aj: STRONTIUM ION (SRaj)
3ak: STRONTIUM ION (SRak)
3al: STRONTIUM ION (SRal)
3am: STRONTIUM ION (SRam)
3an: STRONTIUM ION (SRan)
3ao: STRONTIUM ION (SRao)
3ap: STRONTIUM ION (SRap)
3aq: STRONTIUM ION (SRaq)
3ar: STRONTIUM ION (SRar)
3as: STRONTIUM ION (SRas)
3at: STRONTIUM ION (SRat)
3au: STRONTIUM ION (SRau)
3av: STRONTIUM ION (SRav)
3aw: STRONTIUM ION (SRaw)
3ax: STRONTIUM ION (SRax)
3ay: STRONTIUM ION (SRay)
3az: STRONTIUM ION (SRaz)
3b: STRONTIUM ION (SRb)
3c: STRONTIUM ION (SRc)
3d: STRONTIUM ION (SRd)
3e: STRONTIUM ION (SRe)
3f: STRONTIUM ION (SRf)
3g: STRONTIUM ION (SRg)
3h: STRONTIUM ION (SRh)
3i: STRONTIUM ION (SRi)
3j: STRONTIUM ION (SRj)
3k: STRONTIUM ION (SRk)
3l: STRONTIUM ION (SRl)
3m: STRONTIUM ION (SRm)
3n: STRONTIUM ION (SRn)
3o: STRONTIUM ION (SRo)
3p: STRONTIUM ION (SRp)
3q: STRONTIUM ION (SRq)
3r: STRONTIUM ION (SRr)
3s: STRONTIUM ION (SRs)
3t: STRONTIUM ION (SRt)
3u: STRONTIUM ION (SRu)
3v: STRONTIUM ION (SRv)
3w: STRONTIUM ION (SRw)
3x: STRONTIUM ION (SRx)
3y: STRONTIUM ION (SRy)
3z: STRONTIUM ION (SRz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GTP
2
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
SR
-1
Ligand/Ion
STRONTIUM ION
[
close Hetero Component info
]
Sites
(72, 72)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
36: AF9 (SOFTWARE)
37: AG1 (SOFTWARE)
38: AG2 (SOFTWARE)
39: AG3 (SOFTWARE)
40: AG4 (SOFTWARE)
41: AG5 (SOFTWARE)
42: AG6 (SOFTWARE)
43: AG7 (SOFTWARE)
44: AG8 (SOFTWARE)
45: AG9 (SOFTWARE)
46: AH1 (SOFTWARE)
47: AH2 (SOFTWARE)
48: AH3 (SOFTWARE)
49: AH4 (SOFTWARE)
50: AH5 (SOFTWARE)
51: AH6 (SOFTWARE)
52: AH7 (SOFTWARE)
53: AH8 (SOFTWARE)
54: AH9 (SOFTWARE)
55: AI1 (SOFTWARE)
56: AI2 (SOFTWARE)
57: AI3 (SOFTWARE)
58: AI4 (SOFTWARE)
59: AI5 (SOFTWARE)
60: AI6 (SOFTWARE)
61: AI7 (SOFTWARE)
62: AI8 (SOFTWARE)
63: AI9 (SOFTWARE)
64: AJ1 (SOFTWARE)
65: AJ2 (SOFTWARE)
66: AJ3 (SOFTWARE)
67: AJ4 (SOFTWARE)
68: AJ5 (SOFTWARE)
69: AJ6 (SOFTWARE)
70: AJ7 (SOFTWARE)
71: AJ8 (SOFTWARE)
72: AJ9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
A A:3 , C A:101 , HOH A:303 , C B:101 , C B:102 , GTP B:202
binding site for residue GTP A 201
02
AC2
SOFTWARE
G A:8 , HOH A:349 , HOH A:366 , HOH A:367 , HOH A:368 , HOH A:369 , HOH A:370
binding site for residue SR A 202
03
AC3
SOFTWARE
G A:21 , HOH A:333 , HOH A:334 , HOH A:381 , HOH A:383 , HOH A:384
binding site for residue SR A 203
04
AC4
SOFTWARE
G A:8 , G A:9 , A A:10 , U A:39 , C A:45 , HOH A:372
binding site for residue SR A 204
05
AC5
SOFTWARE
G A:85 , U A:86 , SR A:211 , SR A:224
binding site for residue SR A 206
06
AC6
SOFTWARE
C A:45
binding site for residue SR A 207
07
AC7
SOFTWARE
U A:68 , HOH A:346 , HOH A:355 , HOH A:387 , HOH A:396 , HOH A:397 , HOH A:398
binding site for residue SR A 208
08
AC8
SOFTWARE
G A:21 , HOH A:333 , HOH A:334 , HOH A:337 , HOH A:354
binding site for residue SR A 209
09
AC9
SOFTWARE
G A:9 , U A:39 , C A:40 , U A:41 , C A:45 , HOH A:330
binding site for residue SR A 210
10
AD1
SOFTWARE
SR A:206
binding site for residue SR A 211
11
AD2
SOFTWARE
HOH A:364 , HOH A:365
binding site for residue SR A 212
12
AD3
SOFTWARE
SR A:225
binding site for residue SR A 213
13
AD4
SOFTWARE
G A:35 , U A:36 , SR A:218
binding site for residue SR A 214
14
AD5
SOFTWARE
G A:70
binding site for residue SR A 215
15
AD6
SOFTWARE
G A:77 , HOH A:301
binding site for residue SR A 216
16
AD7
SOFTWARE
HOH A:358
binding site for residue SR A 217
17
AD8
SOFTWARE
G A:35 , U A:36 , G A:61 , G A:62 , SR A:214
binding site for residue SR A 218
18
AD9
SOFTWARE
U A:88
binding site for residue SR A 219
19
AE1
SOFTWARE
A A:13 , HOH A:360 , HOH A:361 , HOH A:419
binding site for residue SR A 220
20
AE2
SOFTWARE
A A:13
binding site for residue SR A 221
21
AE3
SOFTWARE
G A:51 , MG A:238
binding site for residue SR A 222
22
AE4
SOFTWARE
G A:11 , A A:92
binding site for residue SR A 223
23
AE5
SOFTWARE
U A:86 , U A:87 , SR A:206
binding site for residue SR A 224
24
AE6
SOFTWARE
SR A:213 , HOH A:329
binding site for residue SR A 225
25
AE7
SOFTWARE
HOH A:417
binding site for residue SR A 226
26
AE8
SOFTWARE
U A:36
binding site for residue SR A 227
27
AE9
SOFTWARE
A A:71
binding site for residue SR A 230
28
AF1
SOFTWARE
A A:79
binding site for residue SR A 231
29
AF2
SOFTWARE
G A:19
binding site for residue MG A 232
30
AF3
SOFTWARE
U A:69 , G A:70 , U A:82
binding site for residue MG A 233
31
AF4
SOFTWARE
G A:94 , A A:95
binding site for residue MG A 234
32
AF5
SOFTWARE
A A:93 , G A:94
binding site for residue MG A 235
33
AF6
SOFTWARE
G A:9 , A A:10 , G A:11
binding site for residue MG A 236
34
AF7
SOFTWARE
U A:68 , U A:69 , G B:81 , U B:82
binding site for residue MG A 237
35
AF8
SOFTWARE
G A:48 , SR A:222
binding site for residue MG A 238
36
AF9
SOFTWARE
C A:91
binding site for residue MG A 239
37
AG1
SOFTWARE
C A:91 , HOH A:375
binding site for residue MG A 240
38
AG2
SOFTWARE
G A:90 , C A:91 , U B:47
binding site for residue MG A 241
39
AG3
SOFTWARE
A A:10 , G A:11 , U A:12 , G A:62 , C A:63
binding site for residue MG A 242
40
AG4
SOFTWARE
C A:18 , G A:19 , HOH A:383
binding site for residue MG A 243
41
AG5
SOFTWARE
G A:19 , A A:54 , C A:72
binding site for residue MG A 244
42
AG6
SOFTWARE
G A:21 , A A:24
binding site for residue MG A 245
43
AG7
SOFTWARE
U A:65 , U A:66 , HOH A:397
binding site for residue MG A 246
44
AG8
SOFTWARE
G A:77 , A A:78
binding site for residue MG A 247
45
AG9
SOFTWARE
G A:81 , U A:82 , U B:68 , U B:69
binding site for residue MG B 201
46
AH1
SOFTWARE
C A:101 , C A:102 , GTP A:201 , A B:3 , C B:101 , HOH B:302
binding site for residue GTP B 202
47
AH2
SOFTWARE
U B:68 , HOH B:322 , HOH B:367 , HOH B:368 , HOH B:370 , HOH B:376 , HOH B:377
binding site for residue SR B 203
48
AH3
SOFTWARE
SR B:223
binding site for residue SR B 204
49
AH4
SOFTWARE
G B:21 , HOH B:306 , HOH B:334 , HOH B:339 , HOH B:382 , HOH B:383 , HOH B:384
binding site for residue SR B 205
50
AH5
SOFTWARE
G B:21 , HOH B:318 , HOH B:339 , HOH B:356 , HOH B:381
binding site for residue SR B 206
51
AH6
SOFTWARE
G B:8 , HOH B:317 , HOH B:332 , HOH B:348 , HOH B:352
binding site for residue SR B 207
52
AH7
SOFTWARE
G B:9 , U B:39 , C B:40 , U B:41 , C B:45 , HOH B:353
binding site for residue SR B 208
53
AH8
SOFTWARE
HOH B:307 , HOH B:316 , HOH B:358
binding site for residue SR B 209
54
AH9
SOFTWARE
HOH B:332 , HOH B:350 , HOH B:351
binding site for residue SR B 210
55
AI1
SOFTWARE
G B:8 , G B:9 , A B:10 , U B:39 , C B:45 , HOH B:324
binding site for residue SR B 211
56
AI2
SOFTWARE
G B:70
binding site for residue SR B 212
57
AI3
SOFTWARE
U B:12 , A B:13 , HOH B:362 , HOH B:387
binding site for residue SR B 213
58
AI4
SOFTWARE
G B:51
binding site for residue SR B 214
59
AI5
SOFTWARE
G B:35 , U B:36 , G B:61 , G B:62 , SR B:219
binding site for residue SR B 215
60
AI6
SOFTWARE
G B:11 , A B:92
binding site for residue SR B 216
61
AI7
SOFTWARE
U B:88
binding site for residue SR B 217
62
AI8
SOFTWARE
G B:77 , HOH B:328 , HOH B:385
binding site for residue SR B 218
63
AI9
SOFTWARE
G B:35 , U B:36 , SR B:215
binding site for residue SR B 219
64
AJ1
SOFTWARE
A B:29 , U B:87 , HOH B:376
binding site for residue SR B 221
65
AJ2
SOFTWARE
SR B:204
binding site for residue SR B 223
66
AJ3
SOFTWARE
G B:38 , G B:46 , C B:59
binding site for residue SR B 224
67
AJ4
SOFTWARE
G B:8 , G B:9 , C B:40 , HOH B:354
binding site for residue MG B 226
68
AJ5
SOFTWARE
A B:73 , U B:74
binding site for residue MG B 227
69
AJ6
SOFTWARE
C B:55 , A B:73
binding site for residue MG B 228
70
AJ7
SOFTWARE
G B:8 , A B:10
binding site for residue MG B 229
71
AJ8
SOFTWARE
U B:56 , C B:57
binding site for residue MG B 230
72
AJ9
SOFTWARE
A B:95
binding site for residue MG B 231
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
Info
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
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CATH Domains
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all CATH domains
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Pfam Domains
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Asym.Unit (199 KB)
Header - Asym.Unit
Biol.Unit 1 (190 KB)
Header - Biol.Unit 1
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