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4UD2
Asym. Unit
Info
Asym.Unit (793 KB)
Biol.Unit 1 (264 KB)
Biol.Unit 2 (268 KB)
Biol.Unit 3 (267 KB)
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(1)
Title
:
STRUCTURE OF ANAEROBICALLY PURIFIED D. FRUCTOSOVORANS NIFE-HYDROGENASE
Authors
:
A. Volbeda, L. Martin, P. -P. Liebgott, J. C. Fontecilla-Camps
Date
:
05 Dec 14 (Deposition) - 25 Mar 15 (Release) - 22 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,Q,R,S
Biol. Unit 1: A,Q (1x)
Biol. Unit 2: C,S (1x)
Biol. Unit 3: B,R (1x)
Keywords
:
Oxidoreductase, Ni-Sib State, Ni-C State
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, L. Martin, P. -P. Liebgott, A. L. De Lacey, J. C. Fontecilla-Camps
[Nife]-Hydrogenases Revisited: Nickel-Carboxamido Bond Formation In A Variant With Accrued O2-Tolerance And A Tentative Re-Interpretation Of Ni-Si States.
Metallomics V. 7 710 2015
[
close entry info
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Hetero Components
(7, 35)
Info
All Hetero Components
1a: S-HYDROXYCYSTEINE (CSOa)
1b: S-HYDROXYCYSTEINE (CSOb)
1c: S-HYDROXYCYSTEINE (CSOc)
2a: FE3-S4 CLUSTER (F3Sa)
2b: FE3-S4 CLUSTER (F3Sb)
2c: FE3-S4 CLUSTER (F3Sc)
3a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
3b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
3c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
4l: GLYCEROL (GOLl)
4m: GLYCEROL (GOLm)
4n: GLYCEROL (GOLn)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
6a: NICKEL (II) ION (NIa)
6b: NICKEL (II) ION (NIb)
6c: NICKEL (II) ION (NIc)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
7c: IRON/SULFUR CLUSTER (SF4c)
7d: IRON/SULFUR CLUSTER (SF4d)
7e: IRON/SULFUR CLUSTER (SF4e)
7f: IRON/SULFUR CLUSTER (SF4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSO
3
Mod. Amino Acid
S-HYDROXYCYSTEINE
2
F3S
3
Ligand/Ion
FE3-S4 CLUSTER
3
FCO
3
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
4
GOL
14
Ligand/Ion
GLYCEROL
5
MG
3
Ligand/Ion
MAGNESIUM ION
6
NI
3
Ligand/Ion
NICKEL (II) ION
7
SF4
6
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(32, 32)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:184 , CYS A:187 , ARG A:189 , LEU A:190 , CYS A:212 , LEU A:213 , CYS A:218
BINDING SITE FOR RESIDUE SF4 A1265
02
AC2
SOFTWARE
ASN A:225 , CYS A:227 , PHE A:232 , CYS A:245 , LEU A:246 , CYS A:248 , GLN Q:230
BINDING SITE FOR RESIDUE F3S A1266
03
AC3
SOFTWARE
GLU A:16 , CYS A:17 , CYS A:20 , THR A:113 , CYS A:114 , GLY A:146 , CYS A:147 , PRO A:148 , ARG Q:70 , HIS Q:228
BINDING SITE FOR RESIDUE SF4 A1267
04
AC4
SOFTWARE
HIS B:184 , CYS B:187 , ARG B:189 , LEU B:190 , CYS B:212 , LEU B:213 , CYS B:218 , PRO B:221
BINDING SITE FOR RESIDUE SF4 B1265
05
AC5
SOFTWARE
ASN B:225 , CYS B:227 , PHE B:232 , CYS B:245 , LEU B:246 , CYS B:248 , GLN R:230
BINDING SITE FOR RESIDUE F3S B1266
06
AC6
SOFTWARE
GLU B:16 , CYS B:17 , CYS B:20 , THR B:113 , CYS B:114 , GLY B:146 , CYS B:147 , PRO B:148 , ARG R:70
BINDING SITE FOR RESIDUE SF4 B1267
07
AC7
SOFTWARE
HIS C:184 , CYS C:187 , ARG C:189 , LEU C:190 , CYS C:212 , LEU C:213 , CYS C:218
BINDING SITE FOR RESIDUE SF4 C1265
08
AC8
SOFTWARE
ASN C:225 , CYS C:227 , PHE C:232 , CYS C:245 , LEU C:246 , CYS C:248 , GLN S:230
BINDING SITE FOR RESIDUE F3S C1266
09
AC9
SOFTWARE
GLU C:16 , CYS C:17 , CYS C:20 , THR C:113 , CYS C:114 , GLY C:146 , CYS C:147 , PRO C:148 , ARG S:70 , HIS S:228
BINDING SITE FOR RESIDUE SF4 C1267
10
BC1
SOFTWARE
CYS Q:75 , VAL Q:78 , HIS Q:79 , ALA Q:474 , PRO Q:475 , ARG Q:476 , LEU Q:479 , VAL Q:497 , PRO Q:498 , SER Q:499 , CSO Q:543 , CYS Q:546 , NI Q:1551
BINDING SITE FOR RESIDUE FCO Q1550
11
BC2
SOFTWARE
CYS Q:72 , CYS Q:75 , CSO Q:543 , CYS Q:546 , FCO Q:1550
BINDING SITE FOR RESIDUE NI Q1551
12
BC3
SOFTWARE
GLU Q:53 , LEU Q:495 , HIS Q:549 , HOH Q:2026 , HOH Q:2027 , HOH Q:2173
BINDING SITE FOR RESIDUE MG Q1553
13
BC4
SOFTWARE
CYS R:75 , VAL R:78 , HIS R:79 , ALA R:474 , PRO R:475 , ARG R:476 , LEU R:479 , VAL R:497 , PRO R:498 , SER R:499 , CSO R:543 , CYS R:546 , NI R:1551
BINDING SITE FOR RESIDUE FCO R1550
14
BC5
SOFTWARE
GLU R:53 , LEU R:495 , HIS R:549 , HOH R:2025 , HOH R:2026 , HOH R:2141
BINDING SITE FOR RESIDUE MG R1553
15
BC6
SOFTWARE
CYS S:75 , VAL S:78 , HIS S:79 , ALA S:474 , PRO S:475 , ARG S:476 , LEU S:479 , VAL S:497 , PRO S:498 , SER S:499 , CSO S:543 , CYS S:546 , NI S:1551
BINDING SITE FOR RESIDUE FCO S1550
16
BC7
SOFTWARE
CYS S:72 , CYS S:75 , CSO S:543 , CYS S:546 , FCO S:1550
BINDING SITE FOR RESIDUE NI S1551
17
BC8
SOFTWARE
GLU S:53 , LEU S:495 , HIS S:549 , HOH S:2013 , HOH S:2014 , HOH S:2076
BINDING SITE FOR RESIDUE MG S1553
18
BC9
SOFTWARE
LEU A:169 , LYS A:176 , GOL A:305 , HOH A:2107 , HOH A:2184
BINDING SITE FOR RESIDUE GOL A 304
19
CC1
SOFTWARE
LYS A:140 , LEU A:169 , ASP A:170 , GOL A:304
BINDING SITE FOR RESIDUE GOL A 305
20
CC2
SOFTWARE
ALA A:90 , HOH A:2044 , VAL Q:17 , ARG Q:29
BINDING SITE FOR RESIDUE GOL A 306
21
CC3
SOFTWARE
ARG A:6 , LEU A:37 , ALA Q:169 , PHE Q:170 , SER Q:173
BINDING SITE FOR RESIDUE GOL A 307
22
CC4
SOFTWARE
ARG Q:100 , ASN Q:104 , PHE Q:295 , ALA Q:296 , GLU Q:445 , HOH Q:2063 , HOH Q:2239
BINDING SITE FOR RESIDUE GOL Q 604
23
CC5
SOFTWARE
ALA A:55 , ASN Q:181 , ALA Q:182 , LEU Q:185 , ARG Q:529 , HOH Q:2238
BINDING SITE FOR RESIDUE GOL Q 605
24
CC6
SOFTWARE
GLY Q:281 , GLY Q:282 , ILE Q:283 , GLY Q:285 , ARG Q:319 , HIS Q:419
BINDING SITE FOR RESIDUE GOL Q 606
25
CC7
SOFTWARE
LYS Q:245 , LYS Q:337 , TYR Q:338 , ASP Q:366
BINDING SITE FOR RESIDUE GOL Q 607
26
CC8
SOFTWARE
ALA B:55 , ASN R:181 , ALA R:182 , TYR R:183 , LEU R:185 , ARG R:529
BINDING SITE FOR RESIDUE GOL R 604
27
CC9
SOFTWARE
ALA B:136 , LEU B:137 , GLY B:138 , GLY R:409 , LYS R:410 , HOH R:2176
BINDING SITE FOR RESIDUE GOL R 605
28
DC1
SOFTWARE
ARG R:100 , ASN R:104 , PHE R:295 , ALA R:296 , THR R:297 , TRP R:442 , GLU R:445 , HOH R:2206
BINDING SITE FOR RESIDUE GOL R 606
29
DC2
SOFTWARE
GLU R:465 , SER R:466 , ARG R:484 , ILE R:485
BINDING SITE FOR RESIDUE GOL R 607
30
DC3
SOFTWARE
ARG S:100 , ASN S:104 , PHE S:295 , ALA S:296 , TRP S:442 , GLU S:445 , HOH S:2073 , HOH S:2216
BINDING SITE FOR RESIDUE GOL S 604
31
DC4
SOFTWARE
HOH C:2121 , GLY S:450 , ALA S:451 , ASP S:453 , ASN S:454
BINDING SITE FOR RESIDUE GOL S 605
32
DC5
SOFTWARE
CYS R:72 , CYS R:75 , CSO R:543 , CYS R:546 , FCO R:1550
BINDING SITE FOR RESIDUE NI R1551
[
close Site info
]
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
;
View:
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Label:
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
View:
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Label:
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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Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
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)
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Hetero
Ligand
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All Atoms
Protein & NOT Variant
Protein & NOT Site
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Chain S
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