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4UPV
Biol. Unit 1
Info
Asym.Unit (596 KB)
Biol.Unit 1 (300 KB)
Biol.Unit 2 (294 KB)
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(1)
Title
:
LOW X-RAY DOSE 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
:
18 Jun 14 (Deposition) - 29 Oct 14 (Release) - 21 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.52
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, 20)
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)
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)
7l: GLYCEROL (GOLl)
7m: GLYCEROL (GOLm)
7n: GLYCEROL (GOLn)
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
10
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
[
close Hetero Component info
]
Sites
(21, 21)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC7 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (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)
20: DC3 (SOFTWARE)
21: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
ASP A:82 , GLN A:85 , HOH A:2469 , HOH A:2478 , GLN B:129 , LYS B:131 , THR Q:360 , HOH Q:2794
BINDING SITE FOR RESIDUE GOL A1268
02
AC7
SOFTWARE
GLY B:107 , ILE B:108 , LYS B:140 , HOH B:2625 , HOH B:2690 , HOH B:2697
BINDING SITE FOR RESIDUE GLY B 301
03
AC8
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
AC9
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
BC1
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 , HIS R:228
BINDING SITE FOR RESIDUE SF4 B1267
06
BC2
SOFTWARE
TYR B:214 , PRO B:221
BINDING SITE FOR RESIDUE SOT B1268
07
BC3
SOFTWARE
GLU B:205 , LYS B:209 , GOL B:1270 , GOL B:1273 , HOH B:2441 , HOH B:2651 , HOH B:2698 , ASN R:454
BINDING SITE FOR RESIDUE GOL B1269
08
BC4
SOFTWARE
LYS B:209 , GOL B:1269 , HOH B:2496
BINDING SITE FOR RESIDUE GOL B1270
09
BC5
SOFTWARE
H2S B:1272 , HOH B:2444 , HOH B:2473 , HOH B:2488 , HOH B:2541 , HOH B:2553 , HOH R:3257
BINDING SITE FOR RESIDUE GOL B1271
10
BC6
SOFTWARE
HIS B:5 , ASP B:68 , GOL B:1271 , HOH B:2480 , HOH B:2488 , HOH B:2541 , GLN R:175
BINDING SITE FOR RESIDUE H2S B1272
11
BC7
SOFTWARE
GOL B:1269 , ASN R:454 , HOH R:2766 , HOH R:2815 , HOH R:2947
BINDING SITE FOR RESIDUE GOL B1273
12
CC4
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:2794
BINDING SITE FOR RESIDUE GLY R 601
13
CC5
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 , CSS R:543 , CYS R:546 , NI R:1551 , HOH R:2701
BINDING SITE FOR RESIDUE FCO R1550
14
CC6
SOFTWARE
CYS R:72 , CSX R:75 , CSS R:543 , CYS R:546 , FCO R:1550 , HOH R:2701
BINDING SITE FOR RESIDUE NI R1551
15
CC7
SOFTWARE
GLU R:53 , LEU R:495 , HIS R:549 , HOH R:2702 , HOH R:2703 , HOH R:2704
BINDING SITE FOR RESIDUE MG R1552
16
CC8
SOFTWARE
ARG R:100 , ASN R:104 , PHE R:295 , ALA R:296 , THR R:297 , GLU R:445 , GOL R:1555 , HOH R:2783 , HOH R:2805
BINDING SITE FOR RESIDUE GOL R1553
17
CC9
SOFTWARE
SER R:313 , ASN R:326 , LYS R:395 , GOL R:1556 , HOH R:2823 , HOH R:2984 , HOH R:2994 , HOH R:3174
BINDING SITE FOR RESIDUE GOL R1554
18
DC1
SOFTWARE
GLN R:310 , TRP R:442 , GLU R:445 , GOL R:1553 , HOH R:2990 , HOH R:3042 , HOH R:3273
BINDING SITE FOR RESIDUE GOL R1555
19
DC2
SOFTWARE
LYS B:106 , HOH B:2621 , GLU R:303 , LEU R:306 , ASN R:326 , VAL R:327 , GOL R:1554 , HOH R:2776 , HOH R:3085 , HOH R:3230
BINDING SITE FOR RESIDUE GOL R1556
20
DC3
SOFTWARE
PRO R:15 , VAL R:17 , GLU R:33 , TRP R:43 , LYS R:365 , HOH R:3007 , HOH R:3248 , HOH R:3303
BINDING SITE FOR RESIDUE GOL R1557
21
DC4
SOFTWARE
VAL B:161 , LEU B:162 , GLY B:165 , GLU R:303 , LYS R:304 , HOH R:2880 , HOH R:2999
BINDING SITE FOR RESIDUE GOL R1558
[
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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
All PROSITE Patterns/Profiles
;
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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
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CATH Domains
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Pfam Domains
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Asymmetric Unit 1
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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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Asym.Unit (596 KB)
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