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4UPE
Asym. Unit
Info
Asym.Unit (841 KB)
Biol.Unit 1 (283 KB)
Biol.Unit 2 (282 KB)
Biol.Unit 3 (283 KB)
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(1)
Title
:
STRUCTURE OF THE UNREADY NI-A STATE OF THE S499C MUTANT OF D. FRUCTOSOVORANS NIFE-HYDROGENASE
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
:
16 Jun 14 (Deposition) - 29 Oct 14 (Release) - 21 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,Q,R,S
Biol. Unit 1: A,Q (1x)
Biol. Unit 2: B,R (1x)
Biol. Unit 3: C,S (1x)
Keywords
:
Oxidoreductase, Nife-Site, Ni-A State, Sulfenate
(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
)
[
close entry info
]
Hetero Components
(9, 30)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: S-OXY CYSTEINE (CSXa)
2b: S-OXY CYSTEINE (CSXb)
2c: S-OXY CYSTEINE (CSXc)
3a: FE3-S4 CLUSTER (F3Sa)
3b: FE3-S4 CLUSTER (F3Sb)
3c: FE3-S4 CLUSTER (F3Sc)
4a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
4b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
4c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
5e: GLYCEROL (GOLe)
6a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
7a: NICKEL (II) ION (NIa)
7b: NICKEL (II) ION (NIb)
7c: NICKEL (II) ION (NIc)
8a: PHOSPHATE ION (PO4a)
8b: PHOSPHATE ION (PO4b)
9a: IRON/SULFUR CLUSTER (SF4a)
9b: IRON/SULFUR CLUSTER (SF4b)
9c: IRON/SULFUR CLUSTER (SF4c)
9d: IRON/SULFUR CLUSTER (SF4d)
9e: IRON/SULFUR CLUSTER (SF4e)
9f: IRON/SULFUR CLUSTER (SF4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
CSX
3
Mod. Amino Acid
S-OXY CYSTEINE
3
F3S
3
Ligand/Ion
FE3-S4 CLUSTER
4
FCO
3
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
5
GOL
5
Ligand/Ion
GLYCEROL
6
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
7
NI
3
Ligand/Ion
NICKEL (II) ION
8
PO4
2
Ligand/Ion
PHOSPHATE ION
9
SF4
6
Ligand/Ion
IRON/SULFUR CLUSTER
[
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]
Sites
(27, 27)
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)
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
THR A:223 , ASN A:225 , CYS A:227 , PHE A:232 , TRP A:237 , CYS A:245 , LEU A:246 , CYS A:248 , GLN Q:230
BINDING SITE FOR RESIDUE F3S A1266
03
AC3
SOFTWARE
CYS A:17 , CYS A:20 , THR A:113 , CYS A:114 , GLY A:146 , CYS A:147 , PRO A:148 , ARG Q:70
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 , TRP B:237 , CYS B:245 , LEU B:246 , CYS B:248 , LYS R:225 , GLN R:230
BINDING SITE FOR RESIDUE F3S B1266
06
AC6
SOFTWARE
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 , TRP C:237 , CYS C:245 , LEU C:246 , CYS C:248 , LYS S:225 , GLN S:230
BINDING SITE FOR RESIDUE F3S C1266
09
AC9
SOFTWARE
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
CSX 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 , CYS Q:499 , CYS Q:546 , NI Q:1551 , HOH Q:2001
BINDING SITE FOR RESIDUE FCO Q1550
11
BC2
SOFTWARE
CYS Q:72 , CSX Q:75 , CYS Q:543 , CYS Q:546 , FCO Q:1550 , HOH Q:2001
BINDING SITE FOR RESIDUE NI Q1551
12
BC3
SOFTWARE
GLU Q:53 , LEU Q:495 , HIS Q:549 , HOH Q:2002 , HOH Q:2003 , HOH Q:2004
BINDING SITE FOR RESIDUE CA Q1552
13
BC4
SOFTWARE
ARG Q:100 , ASN Q:104 , PHE Q:295 , ALA Q:296 , GLU Q:445 , HOH Q:2050 , HOH Q:2091 , HOH Q:2157
BINDING SITE FOR RESIDUE GOL Q1561
14
BC5
SOFTWARE
ALA A:55 , PHE C:198 , HOH C:2155 , ASN Q:181 , ALA Q:182 , TYR Q:183 , LEU Q:185 , ARG Q:529 , HOH Q:2391
BINDING SITE FOR RESIDUE GOL Q1562
15
BC6
SOFTWARE
GLU Q:465 , SER Q:466 , LYS Q:467 , ARG Q:484 , HOH Q:2427
BINDING SITE FOR RESIDUE PO4 Q1564
16
BC7
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 , CYS R:499 , CYS R:546 , NI R:1551 , HOH R:2001
BINDING SITE FOR RESIDUE FCO R1550
17
BC8
SOFTWARE
CYS R:72 , CSX R:75 , CYS R:543 , CYS R:546 , FCO R:1550 , HOH R:2001
BINDING SITE FOR RESIDUE NI R1551
18
BC9
SOFTWARE
GLU R:53 , LEU R:495 , HIS R:549 , HOH R:2002 , HOH R:2003 , HOH R:2004
BINDING SITE FOR RESIDUE CA R1552
19
CC1
SOFTWARE
ARG R:100 , ASN R:104 , PHE R:295 , ALA R:296 , THR R:297 , GLU R:445 , HOH R:2054 , HOH R:2094 , HOH R:2161
BINDING SITE FOR RESIDUE GOL R1561
20
CC2
SOFTWARE
ALA B:55 , ASN R:181 , ALA R:182 , TYR R:183 , LEU R:185 , ARG R:529 , HOH R:2343
BINDING SITE FOR RESIDUE GOL R1562
21
CC3
SOFTWARE
ALA C:103 , LYS C:104 , SER R:466 , LYS R:467 , ARG R:484 , HOH R:2367
BINDING SITE FOR RESIDUE PO4 R1563
22
CC4
SOFTWARE
ASN R:181 , HOH R:2113 , HOH R:2212 , HOH R:2343
BINDING SITE FOR RESIDUE CA R1564
23
CC5
SOFTWARE
CSX 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 , CYS S:499 , CYS S:546 , NI S:1551 , HOH S:2001
BINDING SITE FOR RESIDUE FCO S1550
24
CC6
SOFTWARE
CYS S:72 , CSX S:75 , CYS S:543 , CYS S:546 , FCO S:1550 , HOH S:2001
BINDING SITE FOR RESIDUE NI S1551
25
CC7
SOFTWARE
GLU S:53 , LEU S:495 , HIS S:549 , HOH S:2002 , HOH S:2003 , HOH S:2004
BINDING SITE FOR RESIDUE CA S1552
26
CC8
SOFTWARE
ARG S:100 , ASN S:104 , PHE S:295 , ALA S:296 , THR S:297 , GLU S:445 , HOH S:2050 , HOH S:2087 , HOH S:2154
BINDING SITE FOR RESIDUE GOL S1561
27
CC9
SOFTWARE
SER R:156 , GLY S:450 , ALA S:451 , LYS S:452 , ASP S:453 , ASN S:454 , HOH S:2335 , HOH S:2376 , HOH S:2389
BINDING SITE FOR RESIDUE MES S1562
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
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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
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Sorry, no Info available
[
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CATH Domains
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all CATH domains
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Sorry, no Info available
[
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Pfam Domains
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all PFAM domains
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Sorry, no Info available
[
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Asym.Unit (841 KB)
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