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4UQP
Biol. Unit 1
Info
Asym.Unit (590 KB)
Biol.Unit 1 (296 KB)
Biol.Unit 2 (292 KB)
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(1)
Title
:
HIGH-RESOLUTION STRUCTURE OF THE D. FRUCTOSOVORANS NIFE-HYDROGENASE L122A MUTANT AFTER EXPOSURE TO AIR
Authors
:
A. Volbeda, L. Martin, E. Barbier, O. Gutierrez-Sanz, A. L. Delacey, P. P. Liebgott, S. Dementin, M. Rousset, J. C. Fontecilla-Camps
Date
:
24 Jun 14 (Deposition) - 29 Oct 14 (Release) - 21 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.42
Chains
:
Asym. Unit : A,B,Q,R
Biol. Unit 1: B,R (1x)
Biol. Unit 2: A,Q (1x)
Keywords
:
Oxidoreductase, Nife-Site, Ni-A State, Sulfenate, Ni-Sox State, Persulfide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, L. Martin, E. Barbier, O. Gutierrez-Sanz, A. L. De Lacey, P. Liebgott, S. Dementin, M. Rousset, J. C. Fontecilla-Camps
Crystallographic Studies Of [Nife]-Hydrogenase Mutants: Towards Consensus Structures For The Elusive Unready Oxidized States.
J. Biol. Inorg. Chem. V. 20 11 2015
(for further references see the
PDB file header
)
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Hetero Components
(9, 14)
Info
All Hetero Components
1a: S-MERCAPTOCYSTEINE (CSSa)
1b: S-MERCAPTOCYSTEINE (CSSb)
2a: S-OXY CYSTEINE (CSXa)
2b: S-OXY CYSTEINE (CSXb)
3a: FE3-S4 CLUSTER (F3Sa)
3b: FE3-S4 CLUSTER (F3Sb)
4a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
4b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
5a: GLYCINE (GLYa)
5b: GLYCINE (GLYb)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
6e: GLYCEROL (GOLe)
6f: GLYCEROL (GOLf)
6g: GLYCEROL (GOLg)
6h: GLYCEROL (GOLh)
7a: HYDROSULFURIC ACID (H2Sa)
8a: MAGNESIUM ION (MGa)
8b: MAGNESIUM ION (MGb)
9a: NICKEL (II) ION (NIa)
9b: NICKEL (II) ION (NIb)
10a: IRON/SULFUR CLUSTER (SF4a)
10b: IRON/SULFUR CLUSTER (SF4b)
10c: IRON/SULFUR CLUSTER (SF4c)
10d: IRON/SULFUR CLUSTER (SF4d)
11a: MORPHOLINE-4-SULFONIC ACID (SOTa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSS
1
Mod. Amino Acid
S-MERCAPTOCYSTEINE
2
CSX
1
Mod. Amino Acid
S-OXY CYSTEINE
3
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
4
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
5
GLY
1
Mod. Amino Acid
GLYCINE
6
GOL
5
Ligand/Ion
GLYCEROL
7
H2S
1
Ligand/Ion
HYDROSULFURIC ACID
8
MG
-1
Ligand/Ion
MAGNESIUM ION
9
NI
-1
Ligand/Ion
NICKEL (II) ION
10
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
11
SOT
1
Ligand/Ion
MORPHOLINE-4-SULFONIC ACID
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Sites
(15, 15)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC8 (SOFTWARE)
09: BC9 (SOFTWARE)
10: CC1 (SOFTWARE)
11: CC2 (SOFTWARE)
12: CC3 (SOFTWARE)
13: CC4 (SOFTWARE)
14: CC5 (SOFTWARE)
15: CC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
ASP A:82 , GLN A:85 , HOH A:2459 , HOH A:2468 , HOH A:2477 , GLN B:129 , LYS B:131 , THR Q:360 , HOH Q:2794
BINDING SITE FOR RESIDUE GOL A1268
02
AC5
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
03
AC6
SOFTWARE
THR B:223 , ASN B:225 , CYS B:227 , PHE B:232 , TRP B:237 , CYS B:245 , LEU B:246 , CYS B:248 , LYS R:225 , GLN R:230
BINDING SITE FOR RESIDUE F3S B1266
04
AC7
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
05
AC8
SOFTWARE
TYR B:214 , PRO B:221
BINDING SITE FOR RESIDUE SOT B1268
06
AC9
SOFTWARE
HIS B:5 , ASP B:68 , HOH B:2483 , HOH B:2491 , HOH B:2546 , GLN R:175
BINDING SITE FOR RESIDUE H2S B1269
07
BC7
SOFTWARE
ARG R:100 , ASN R:104 , PHE R:295 , ALA R:296 , THR R:297 , GLU R:445 , GOL R:1552 , HOH R:2782 , HOH R:2803
BINDING SITE FOR RESIDUE GOL R1550
08
BC8
SOFTWARE
SER R:313 , ASN R:326 , LYS R:395 , HOH R:2821 , HOH R:2984 , HOH R:2994 , HOH R:3008
BINDING SITE FOR RESIDUE GOL R1551
09
BC9
SOFTWARE
GLN R:310 , TRP R:442 , GLU R:445 , GOL R:1550 , HOH R:2990 , HOH R:3042 , HOH R:3260
BINDING SITE FOR RESIDUE GOL R1552
10
CC1
SOFTWARE
ASN R:454 , HOH R:2765 , HOH R:2813 , HOH R:2946 , HOH R:3011
BINDING SITE FOR RESIDUE GOL R1553
11
CC2
SOFTWARE
PRO R:15 , VAL R:17 , GLU R:33 , TRP R:43 , LYS R:365 , HOH R:3246
BINDING SITE FOR RESIDUE GOL R1554
12
CC3
SOFTWARE
CSX 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 , CYS R:546 , NI R:1556 , HOH R:2701
BINDING SITE FOR RESIDUE FCO R1555
13
CC4
SOFTWARE
CYS R:72 , CSX R:75 , CSS R:543 , CYS R:546 , FCO R:1555 , HOH R:2701
BINDING SITE FOR RESIDUE NI R1556
14
CC5
SOFTWARE
GLU R:53 , LEU R:495 , HIS R:549 , HOH R:2702 , HOH R:2703 , HOH R:2704
BINDING SITE FOR RESIDUE MG R1557
15
CC6
SOFTWARE
ILE R:24 , GLU R:25 , HIS R:118 , ARG R:476 , ASP R:541 , HOH R:2705 , HOH R:2706 , HOH R:2707 , HOH R:2708 , HOH R:2792
BINDING SITE FOR RESIDUE GLY R1558
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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)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
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CATH Domains
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Pfam Domains
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Chain B
Chain R
Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (590 KB)
Header - Asym.Unit
Biol.Unit 1 (296 KB)
Header - Biol.Unit 1
Biol.Unit 2 (292 KB)
Header - Biol.Unit 2
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