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4UQL
Biol. Unit 1
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
(9, 18)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: S-MERCAPTOCYSTEINE (CSSa)
2b: S-MERCAPTOCYSTEINE (CSSb)
3a: S-OXY CYSTEINE (CSXa)
3b: S-OXY CYSTEINE (CSXb)
4a: FE3-S4 CLUSTER (F3Sa)
4b: FE3-S4 CLUSTER (F3Sb)
5a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
5b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
6a: GLYCINE (GLYa)
6b: GLYCINE (GLYb)
6c: GLYCINE (GLYc)
7a: GLYCEROL (GOLa)
7b: GLYCEROL (GOLb)
7c: GLYCEROL (GOLc)
7d: GLYCEROL (GOLd)
7e: GLYCEROL (GOLe)
7f: GLYCEROL (GOLf)
7g: GLYCEROL (GOLg)
7h: GLYCEROL (GOLh)
7i: GLYCEROL (GOLi)
7j: GLYCEROL (GOLj)
7k: GLYCEROL (GOLk)
8a: HYDROSULFURIC ACID (H2Sa)
9a: MAGNESIUM ION (MGa)
9b: 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
1
Mod. Amino Acid
S-MERCAPTOCYSTEINE
3
CSX
1
Mod. Amino Acid
S-OXY CYSTEINE
4
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
5
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
6
GLY
2
Mod. Amino Acid
GLYCINE
7
GOL
8
Ligand/Ion
GLYCEROL
8
H2S
1
Ligand/Ion
HYDROSULFURIC ACID
9
MG
-1
Ligand/Ion
MAGNESIUM ION
10
NI
-1
Ligand/Ion
NICKEL (II) ION
11
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
12
SOT
1
Ligand/Ion
MORPHOLINE-4-SULFONIC ACID
[
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Sites
(19, 19)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: CC2 (SOFTWARE)
11: CC3 (SOFTWARE)
12: CC4 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC6 (SOFTWARE)
15: CC7 (SOFTWARE)
16: CC8 (SOFTWARE)
17: CC9 (SOFTWARE)
18: DC1 (SOFTWARE)
19: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
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
04
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
05
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
06
BC1
SOFTWARE
TYR B:214 , PRO B:221
BINDING SITE FOR RESIDUE SOT B1268
07
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
08
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
09
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
10
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
11
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
12
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
13
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
14
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
15
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
16
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
17
CC9
SOFTWARE
GOL B:1269 , ASN R:454 , HOH R:2066 , HOH R:2114 , HOH R:2247
BINDING SITE FOR RESIDUE GOL B1272
18
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
19
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 only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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Exons
(0, 0)
Info
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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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CATH Domains
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Info
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Pfam Domains
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Info
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (594 KB)
Header - Asym.Unit
Biol.Unit 1 (298 KB)
Header - Biol.Unit 1
Biol.Unit 2 (293 KB)
Header - Biol.Unit 2
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