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4UEQ
Biol. Unit 1
Info
Asym.Unit (1.7 MB)
Biol.Unit 1 (297 KB)
Biol.Unit 2 (295 KB)
Biol.Unit 3 (288 KB)
Biol.Unit 4 (288 KB)
Biol.Unit 5 (293 KB)
Biol.Unit 6 (292 KB)
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(1)
Title
:
STRUCTURE OF THE V74C LARGE SUBUNIT MUTANT OF D. FRUCTOSOVORANS NIFE-HYDROGENASE
Authors
:
A. Volbeda, L. Martin, P. -P. Liebgott, J. C. Fontecilla-Camps
Date
:
18 Dec 14 (Deposition) - 25 Mar 15 (Release) - 22 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F,Q,R,S,T,U,V
Biol. Unit 1: D,T (1x)
Biol. Unit 2: A,Q (1x)
Biol. Unit 3: C,S (1x)
Biol. Unit 4: F,V (1x)
Biol. Unit 5: B,R (1x)
Biol. Unit 6: E,U (1x)
Keywords
:
Oxidoreductase, Nife-Hydrogenase Mutant, Nickel-Carboxamido Bond, Oxygen- Tolerance
(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
]
Hetero Components
(6, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: CARBONATE ION (CO3a)
3a: S-MERCAPTOCYSTEINE (CSSa)
3b: S-MERCAPTOCYSTEINE (CSSb)
3c: S-MERCAPTOCYSTEINE (CSSc)
3d: S-MERCAPTOCYSTEINE (CSSd)
3e: S-MERCAPTOCYSTEINE (CSSe)
3f: S-MERCAPTOCYSTEINE (CSSf)
4a: FE3-S4 CLUSTER (F3Sa)
4b: FE3-S4 CLUSTER (F3Sb)
4c: FE3-S4 CLUSTER (F3Sc)
4d: FE3-S4 CLUSTER (F3Sd)
4e: FE3-S4 CLUSTER (F3Se)
4f: FE3-S4 CLUSTER (F3Sf)
5a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
5b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
5c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
5d: CARBONMONOXIDE-(DICYANO) IRON (FCOd)
5e: CARBONMONOXIDE-(DICYANO) IRON (FCOe)
5f: CARBONMONOXIDE-(DICYANO) IRON (FCOf)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
6e: GLYCEROL (GOLe)
6f: GLYCEROL (GOLf)
6g: GLYCEROL (GOLg)
6h: GLYCEROL (GOLh)
6i: GLYCEROL (GOLi)
6j: GLYCEROL (GOLj)
7a: HYDROSULFURIC ACID (H2Sa)
7b: HYDROSULFURIC ACID (H2Sb)
7c: HYDROSULFURIC ACID (H2Sc)
7d: HYDROSULFURIC ACID (H2Sd)
7e: HYDROSULFURIC ACID (H2Se)
7f: HYDROSULFURIC ACID (H2Sf)
8a: MAGNESIUM ION (MGa)
8b: MAGNESIUM ION (MGb)
8c: MAGNESIUM ION (MGc)
8d: MAGNESIUM ION (MGd)
8e: MAGNESIUM ION (MGe)
8f: MAGNESIUM ION (MGf)
8g: MAGNESIUM ION (MGg)
8h: MAGNESIUM ION (MGh)
8i: MAGNESIUM ION (MGi)
8j: MAGNESIUM ION (MGj)
9a: NICKEL (II) ION (NIa)
9b: NICKEL (II) ION (NIb)
9c: NICKEL (II) ION (NIc)
9d: NICKEL (II) ION (NId)
9e: NICKEL (II) ION (NIe)
9f: NICKEL (II) ION (NIf)
10a: IRON/SULFUR CLUSTER (SF4a)
10b: IRON/SULFUR CLUSTER (SF4b)
10c: IRON/SULFUR CLUSTER (SF4c)
10d: IRON/SULFUR CLUSTER (SF4d)
10e: IRON/SULFUR CLUSTER (SF4e)
10f: IRON/SULFUR CLUSTER (SF4f)
10g: IRON/SULFUR CLUSTER (SF4g)
10h: IRON/SULFUR CLUSTER (SF4h)
10i: IRON/SULFUR CLUSTER (SF4i)
10j: IRON/SULFUR CLUSTER (SF4j)
10k: IRON/SULFUR CLUSTER (SF4k)
10l: IRON/SULFUR CLUSTER (SF4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CO3
-1
Ligand/Ion
CARBONATE ION
3
CSS
1
Mod. Amino Acid
S-MERCAPTOCYSTEINE
4
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
5
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
6
GOL
2
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
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: BC1 (SOFTWARE)
02: BC2 (SOFTWARE)
03: BC3 (SOFTWARE)
04: DC1 (SOFTWARE)
05: DC2 (SOFTWARE)
06: DC8 (SOFTWARE)
07: DC9 (SOFTWARE)
08: EC1 (SOFTWARE)
09: EC2 (SOFTWARE)
10: EC3 (SOFTWARE)
11: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC1
SOFTWARE
HIS D:184 , CYS D:187 , ARG D:189 , LEU D:190 , CYS D:212 , LEU D:213 , CYS D:218
BINDING SITE FOR RESIDUE SF4 D1265
02
BC2
SOFTWARE
THR D:223 , ASN D:225 , CYS D:227 , PHE D:232 , TRP D:237 , CYS D:245 , LEU D:246 , CYS D:248 , LYS T:225 , GLN T:230
BINDING SITE FOR RESIDUE F3S D1266
03
BC3
SOFTWARE
GLU D:16 , CYS D:17 , CYS D:20 , THR D:113 , CYS D:114 , GLY D:146 , CYS D:147 , PRO D:148 , ARG T:70 , HIS T:228
BINDING SITE FOR RESIDUE SF4 D1267
04
DC1
SOFTWARE
HOH B:2069 , HOH D:2231 , HOH D:2234 , HOH D:2252 , ASN R:181 , HOH R:2148
BINDING SITE FOR RESIDUE MG R1560
05
DC2
SOFTWARE
ALA B:55 , PHE D:198 , HOH D:2232 , HOH D:2252 , ASN R:181 , ALA R:182 , TYR R:183 , LEU R:185 , ARG R:529
BINDING SITE FOR RESIDUE GOL R1561
06
DC8
SOFTWARE
CYS T:75 , VAL T:78 , HIS T:79 , ALA T:474 , PRO T:475 , ARG T:476 , LEU T:479 , VAL T:497 , PRO T:498 , SER T:499 , CYS T:543 , CYS T:546 , NI T:1551 , HOH T:2078
BINDING SITE FOR RESIDUE FCO T1550
07
DC9
SOFTWARE
CYS T:72 , CYS T:75 , CYS T:543 , CYS T:546 , FCO T:1550 , HOH T:2078
BINDING SITE FOR RESIDUE NI T1551
08
EC1
SOFTWARE
GLU T:53 , LEU T:495 , HIS T:549 , HOH T:2050 , HOH T:2051 , HOH T:2290
BINDING SITE FOR RESIDUE MG T1553
09
EC2
SOFTWARE
HOH D:2089 , HOH F:2153 , HOH F:2157 , HOH F:2171 , ASN T:181 , HOH T:2177
BINDING SITE FOR RESIDUE MG T1560
10
EC3
SOFTWARE
ARG T:100 , ASN T:104 , PHE T:295 , ALA T:296 , THR T:297 , GLU T:445 , HOH T:2119 , HOH T:2402
BINDING SITE FOR RESIDUE GOL T1561
11
EC4
SOFTWARE
ALA D:55 , PHE F:198 , HOH F:2154 , HOH F:2171 , ASN T:181 , ALA T:182 , TYR T:183 , LEU T:185 , ARG T:529
BINDING SITE FOR RESIDUE GOL T1562
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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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
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)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain D
Chain T
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 PDB file:
Asym.Unit (1.7 MB)
Header - Asym.Unit
Biol.Unit 1 (297 KB)
Header - Biol.Unit 1
Biol.Unit 2 (295 KB)
Header - Biol.Unit 2
Biol.Unit 3 (288 KB)
Header - Biol.Unit 3
Biol.Unit 4 (288 KB)
Header - Biol.Unit 4
Biol.Unit 5 (293 KB)
Header - Biol.Unit 5
Biol.Unit 6 (292 KB)
Header - Biol.Unit 6
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