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4UQL
Asym. Unit
Info
Asym.Unit (594 KB)
Biol.Unit 1 (298 KB)
Biol.Unit 2 (293 KB)
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(1)
Title
:
HIGH-RESOLUTION STRUCTURE OF A NI-A NI-SOX MIXTURE OF THE D. FRUCTOSOVORANS NIFE-HYDROGENASE L122A MUTANT
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
:
1.22
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
)
[
close entry info
]
Hetero Components
(12, 33)
Info
All Hetero Components
01a: CHLORIDE ION (CLa)
02a: S-MERCAPTOCYSTEINE (CSSa)
02b: S-MERCAPTOCYSTEINE (CSSb)
03a: S-OXY CYSTEINE (CSXa)
03b: S-OXY CYSTEINE (CSXb)
04a: FE3-S4 CLUSTER (F3Sa)
04b: FE3-S4 CLUSTER (F3Sb)
05a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
05b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
06a: GLYCINE (GLYa)
06b: GLYCINE (GLYb)
06c: GLYCINE (GLYc)
07a: GLYCEROL (GOLa)
07b: GLYCEROL (GOLb)
07c: GLYCEROL (GOLc)
07d: GLYCEROL (GOLd)
07e: GLYCEROL (GOLe)
07f: GLYCEROL (GOLf)
07g: GLYCEROL (GOLg)
07h: GLYCEROL (GOLh)
07i: GLYCEROL (GOLi)
07j: GLYCEROL (GOLj)
07k: GLYCEROL (GOLk)
08a: HYDROSULFURIC ACID (H2Sa)
09a: MAGNESIUM ION (MGa)
09b: MAGNESIUM ION (MGb)
10a: NICKEL (II) ION (NIa)
10b: NICKEL (II) ION (NIb)
11a: IRON/SULFUR CLUSTER (SF4a)
11b: IRON/SULFUR CLUSTER (SF4b)
11c: IRON/SULFUR CLUSTER (SF4c)
11d: IRON/SULFUR CLUSTER (SF4d)
12a: MORPHOLINE-4-SULFONIC ACID (SOTa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
CSS
2
Mod. Amino Acid
S-MERCAPTOCYSTEINE
3
CSX
2
Mod. Amino Acid
S-OXY CYSTEINE
4
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
5
FCO
2
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
6
GLY
3
Mod. Amino Acid
GLYCINE
7
GOL
11
Ligand/Ion
GLYCEROL
8
H2S
1
Ligand/Ion
HYDROSULFURIC ACID
9
MG
2
Ligand/Ion
MAGNESIUM ION
10
NI
2
Ligand/Ion
NICKEL (II) ION
11
SF4
4
Ligand/Ion
IRON/SULFUR CLUSTER
12
SOT
1
Ligand/Ion
MORPHOLINE-4-SULFONIC ACID
[
close Hetero Component info
]
Sites
(29, 29)
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)
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 , LYS Q:225 , 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
BINDING SITE FOR RESIDUE SF4 A1267
04
AC4
SOFTWARE
ASP A:82 , GLN A:85 , HOH A:2060 , HOH A:2069 , HOH A:2078 , GLN B:129 , LYS B:131 , THR Q:360 , HOH Q:2094
BINDING SITE FOR RESIDUE GOL A1268
05
AC5
SOFTWARE
GLN A:62 , HOH A:2048 , HOH A:2053 , HOH A:2056 , HOH A:2141
BINDING SITE FOR RESIDUE GOL A1269
06
AC6
SOFTWARE
GLY B:107 , ILE B:108 , LYS B:140 , HOH B:2227 , HOH B:2296 , HOH B:2306
BINDING SITE FOR RESIDUE GLY B 301
07
AC7
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
08
AC8
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
09
AC9
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
10
BC1
SOFTWARE
TYR B:214 , PRO B:221
BINDING SITE FOR RESIDUE SOT B1268
11
BC2
SOFTWARE
GLU B:205 , LYS B:209 , GOL B:1272 , HOH B:2043 , HOH B:2163 , HOH B:2255 , HOH B:2305 , ASN R:454
BINDING SITE FOR RESIDUE GOL B1269
12
BC3
SOFTWARE
H2S B:1271 , HOH B:2046 , HOH B:2075 , HOH B:2090 , HOH B:2143 , HOH B:2155 , HOH B:2290
BINDING SITE FOR RESIDUE GOL B1270
13
BC4
SOFTWARE
HIS B:5 , ASP B:68 , GOL B:1270 , HOH B:2082 , HOH B:2090 , HOH B:2143 , GLN R:175
BINDING SITE FOR RESIDUE H2S B1271
14
BC5
SOFTWARE
ILE Q:24 , GLU Q:25 , HIS Q:118 , ASP Q:541 , HOH Q:2005 , HOH Q:2006 , HOH Q:2071 , HOH Q:2078
BINDING SITE FOR RESIDUE GLY Q 601
15
BC6
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 , SER Q:499 , CYS Q:546 , NI Q:1551 , HOH Q:2001
BINDING SITE FOR RESIDUE FCO Q1550
16
BC7
SOFTWARE
CYS Q:72 , CSX Q:75 , CSS Q:543 , CYS Q:546 , FCO Q:1550 , HOH Q:2001
BINDING SITE FOR RESIDUE NI Q1551
17
BC8
SOFTWARE
GLU Q:53 , LEU Q:495 , HIS Q:549 , HOH Q:2002 , HOH Q:2003 , HOH Q:2004
BINDING SITE FOR RESIDUE MG Q1552
18
BC9
SOFTWARE
ARG Q:100 , ASN Q:104 , PHE Q:295 , ALA Q:296 , THR Q:297 , GLU Q:445 , HOH Q:2007 , HOH Q:2095 , HOH Q:2120
BINDING SITE FOR RESIDUE GOL Q1553
19
CC1
SOFTWARE
LYS Q:189 , ARG Q:529
BINDING SITE FOR RESIDUE CL Q1554
20
CC2
SOFTWARE
ILE R:24 , GLU R:25 , HIS R:118 , ARG R:476 , ASP R:541 , HOH R:2005 , HOH R:2006 , HOH R:2007 , HOH R:2008 , HOH R:2093
BINDING SITE FOR RESIDUE GLY R 601
21
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:1551 , HOH R:2001
BINDING SITE FOR RESIDUE FCO R1550
22
CC4
SOFTWARE
CYS R:72 , CSX R:75 , CSS R:543 , CYS R:546 , FCO R:1550 , HOH R:2001
BINDING SITE FOR RESIDUE NI R1551
23
CC5
SOFTWARE
GLU R:53 , LEU R:495 , HIS R:549 , HOH R:2002 , HOH R:2003 , HOH R:2004
BINDING SITE FOR RESIDUE MG R1552
24
CC6
SOFTWARE
ARG R:100 , ASN R:104 , PHE R:295 , ALA R:296 , THR R:297 , GLU R:445 , GOL R:1555 , HOH R:2083 , HOH R:2104
BINDING SITE FOR RESIDUE GOL R1553
25
CC7
SOFTWARE
SER R:313 , ASN R:326 , LYS R:395 , GOL R:1556 , HOH R:2122 , HOH R:2284 , HOH R:2294 , HOH R:2478
BINDING SITE FOR RESIDUE GOL R1554
26
CC8
SOFTWARE
GLN R:310 , TRP R:442 , GLU R:445 , GOL R:1553 , HOH R:2290 , HOH R:2342 , HOH R:2584
BINDING SITE FOR RESIDUE GOL R1555
27
CC9
SOFTWARE
GOL B:1269 , ASN R:454 , HOH R:2066 , HOH R:2114 , HOH R:2247
BINDING SITE FOR RESIDUE GOL B1272
28
DC1
SOFTWARE
LYS B:106 , HOH B:2224 , GLU R:303 , LEU R:306 , ASN R:326 , VAL R:327 , GOL R:1554 , HOH R:2076 , HOH R:2385 , HOH R:2537
BINDING SITE FOR RESIDUE GOL R1556
29
DC2
SOFTWARE
PRO R:15 , VAL R:17 , GLU R:33 , TRP R:43 , LYS R:365 , HOH R:2308 , HOH R:2555
BINDING SITE FOR RESIDUE GOL R1557
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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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
(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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]
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