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4UEQ
Asym. Unit
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
(10, 69)
Info
All Hetero Components
01a: CALCIUM ION (CAa)
01b: CALCIUM ION (CAb)
01c: CALCIUM ION (CAc)
01d: CALCIUM ION (CAd)
01e: CALCIUM ION (CAe)
01f: CALCIUM ION (CAf)
02a: CARBONATE ION (CO3a)
03a: S-MERCAPTOCYSTEINE (CSSa)
03b: S-MERCAPTOCYSTEINE (CSSb)
03c: S-MERCAPTOCYSTEINE (CSSc)
03d: S-MERCAPTOCYSTEINE (CSSd)
03e: S-MERCAPTOCYSTEINE (CSSe)
03f: S-MERCAPTOCYSTEINE (CSSf)
04a: FE3-S4 CLUSTER (F3Sa)
04b: FE3-S4 CLUSTER (F3Sb)
04c: FE3-S4 CLUSTER (F3Sc)
04d: FE3-S4 CLUSTER (F3Sd)
04e: FE3-S4 CLUSTER (F3Se)
04f: FE3-S4 CLUSTER (F3Sf)
05a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
05b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
05c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
05d: CARBONMONOXIDE-(DICYANO) IRON (FCOd)
05e: CARBONMONOXIDE-(DICYANO) IRON (FCOe)
05f: CARBONMONOXIDE-(DICYANO) IRON (FCOf)
06a: GLYCEROL (GOLa)
06b: GLYCEROL (GOLb)
06c: GLYCEROL (GOLc)
06d: GLYCEROL (GOLd)
06e: GLYCEROL (GOLe)
06f: GLYCEROL (GOLf)
06g: GLYCEROL (GOLg)
06h: GLYCEROL (GOLh)
06i: GLYCEROL (GOLi)
06j: GLYCEROL (GOLj)
07a: HYDROSULFURIC ACID (H2Sa)
07b: HYDROSULFURIC ACID (H2Sb)
07c: HYDROSULFURIC ACID (H2Sc)
07d: HYDROSULFURIC ACID (H2Sd)
07e: HYDROSULFURIC ACID (H2Se)
07f: HYDROSULFURIC ACID (H2Sf)
08a: MAGNESIUM ION (MGa)
08b: MAGNESIUM ION (MGb)
08c: MAGNESIUM ION (MGc)
08d: MAGNESIUM ION (MGd)
08e: MAGNESIUM ION (MGe)
08f: MAGNESIUM ION (MGf)
08g: MAGNESIUM ION (MGg)
08h: MAGNESIUM ION (MGh)
08i: MAGNESIUM ION (MGi)
08j: MAGNESIUM ION (MGj)
09a: NICKEL (II) ION (NIa)
09b: NICKEL (II) ION (NIb)
09c: NICKEL (II) ION (NIc)
09d: NICKEL (II) ION (NId)
09e: NICKEL (II) ION (NIe)
09f: 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
6
Ligand/Ion
CALCIUM ION
2
CO3
1
Ligand/Ion
CARBONATE ION
3
CSS
6
Mod. Amino Acid
S-MERCAPTOCYSTEINE
4
F3S
6
Ligand/Ion
FE3-S4 CLUSTER
5
FCO
6
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
6
GOL
10
Ligand/Ion
GLYCEROL
7
H2S
6
Ligand/Ion
HYDROSULFURIC ACID
8
MG
10
Ligand/Ion
MAGNESIUM ION
9
NI
6
Ligand/Ion
NICKEL (II) ION
10
SF4
12
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(51, 51)
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)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (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
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 , HIS Q:228
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
BINDING SITE FOR RESIDUE SF4 B1265
05
AC5
SOFTWARE
ASN B:225 , CYS B:227 , PHE B:232 , CYS B:245 , LEU B:246 , CYS B:248 , LYS R:225 , GLN R:230
BINDING SITE FOR RESIDUE F3S B1266
06
AC6
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
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
THR C:223 , ASN C:225 , CYS C:227 , PHE C:232 , TRP C:237 , CYS C:245 , LEU C:246 , CYS C:248 , 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
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
11
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
12
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
13
BC4
SOFTWARE
HIS E:184 , CYS E:187 , ARG E:189 , LEU E:190 , CYS E:212 , LEU E:213 , CYS E:218
BINDING SITE FOR RESIDUE SF4 E1265
14
BC5
SOFTWARE
ASN E:225 , CYS E:227 , PHE E:232 , CYS E:245 , LEU E:246 , CYS E:248 , LYS U:225 , GLN U:230
BINDING SITE FOR RESIDUE F3S E1266
15
BC6
SOFTWARE
GLU E:16 , CYS E:17 , CYS E:20 , THR E:113 , CYS E:114 , GLY E:146 , CYS E:147 , PRO E:148 , ARG U:70 , HIS U:228
BINDING SITE FOR RESIDUE SF4 E1267
16
BC7
SOFTWARE
HIS F:184 , CYS F:187 , ARG F:189 , LEU F:190 , CYS F:212 , LEU F:213 , CYS F:218 , PRO F:221
BINDING SITE FOR RESIDUE SF4 F1265
17
BC8
SOFTWARE
THR F:223 , ASN F:225 , CYS F:227 , PHE F:232 , TRP F:237 , CYS F:245 , LEU F:246 , CYS F:248 , GLN V:230
BINDING SITE FOR RESIDUE F3S F1266
18
BC9
SOFTWARE
GLU F:16 , CYS F:17 , CYS F:20 , THR F:113 , CYS F:114 , GLY F:146 , CYS F:147 , PRO F:148 , ARG V:70
BINDING SITE FOR RESIDUE SF4 F1267
19
CC1
SOFTWARE
CYS 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:2068
BINDING SITE FOR RESIDUE FCO Q1550
20
CC2
SOFTWARE
CYS Q:72 , CYS Q:75 , CYS Q:543 , CYS Q:546 , FCO Q:1550 , HOH Q:2068
BINDING SITE FOR RESIDUE NI Q1551
21
CC3
SOFTWARE
GLU Q:53 , LEU Q:495 , HIS Q:549 , HOH Q:2046 , HOH Q:2047 , HOH Q:2278
BINDING SITE FOR RESIDUE MG Q1553
22
CC4
SOFTWARE
HOH C:2167 , HOH C:2170 , HOH C:2188 , ASN Q:181 , HOH Q:2159 , HOH Q:2160
BINDING SITE FOR RESIDUE MG Q1560
23
CC5
SOFTWARE
ARG Q:100 , ASN Q:104 , PHE Q:295 , ALA Q:296 , THR Q:297 , GLU Q:445 , HOH Q:2105 , HOH Q:2247 , HOH Q:2396
BINDING SITE FOR RESIDUE GOL Q1561
24
CC6
SOFTWARE
ALA A:55 , PHE C:198 , HOH C:2168 , HOH C:2188 , ASN Q:181 , ALA Q:182 , TYR Q:183 , LEU Q:185 , ARG Q:529
BINDING SITE FOR RESIDUE GOL Q1562
25
CC7
SOFTWARE
CYS 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:2062
BINDING SITE FOR RESIDUE FCO R1550
26
CC8
SOFTWARE
CYS R:72 , CYS R:75 , CYS R:543 , CYS R:546 , FCO R:1550 , HOH R:2062
BINDING SITE FOR RESIDUE NI R1551
27
CC9
SOFTWARE
GLU R:53 , LEU R:495 , HIS R:549 , HOH R:2040 , HOH R:2041 , HOH R:2249
BINDING SITE FOR RESIDUE MG R1553
28
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
29
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
30
DC3
SOFTWARE
ARG R:100 , ASN R:104 , PHE R:295 , ALA R:296 , THR R:297 , GLU R:445 , HOH R:2092 , HOH R:2222 , HOH R:2345
BINDING SITE FOR RESIDUE GOL R1563
31
DC4
SOFTWARE
CYS 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 , SER S:499 , CYS S:546 , NI S:1551 , HOH S:2042
BINDING SITE FOR RESIDUE FCO S1550
32
DC5
SOFTWARE
CYS S:72 , CYS S:75 , CYS S:543 , CYS S:546 , FCO S:1550 , HOH S:2042
BINDING SITE FOR RESIDUE NI S1551
33
DC6
SOFTWARE
GLU S:53 , LEU S:495 , HIS S:549 , HOH S:2024 , HOH S:2025 , HOH S:2182
BINDING SITE FOR RESIDUE MG S1553
34
DC7
SOFTWARE
ARG S:100 , ASN S:104 , PHE S:295 , ALA S:296 , GLN S:310 , GLU S:445 , HOH S:2068 , HOH S:2164 , HOH S:2247
BINDING SITE FOR RESIDUE GOL S1561
35
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
36
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
37
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
38
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
39
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
40
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
41
EC5
SOFTWARE
CYS U:75 , VAL U:78 , HIS U:79 , ALA U:474 , PRO U:475 , ARG U:476 , LEU U:479 , VAL U:497 , PRO U:498 , SER U:499 , CYS U:546 , NI U:1551 , HOH U:2073
BINDING SITE FOR RESIDUE FCO U1550
42
EC6
SOFTWARE
CYS U:72 , CYS U:75 , CYS U:543 , CYS U:546 , FCO U:1550 , HOH U:2073
BINDING SITE FOR RESIDUE NI U1551
43
EC7
SOFTWARE
GLU U:53 , LEU U:495 , HIS U:549 , HOH U:2048 , HOH U:2049 , HOH U:2255
BINDING SITE FOR RESIDUE MG U1553
44
EC8
SOFTWARE
HOH A:2228 , HOH A:2231 , HOH A:2251 , ASN U:181 , HOH U:2152 , HOH U:2153
BINDING SITE FOR RESIDUE MG U1560
45
EC9
SOFTWARE
PHE A:198 , HOH A:2229 , HOH A:2251 , ALA E:55 , ASN U:181 , ALA U:182 , TYR U:183 , LEU U:185 , ARG U:529
BINDING SITE FOR RESIDUE GOL U1561
46
FC1
SOFTWARE
ARG U:100 , ASN U:104 , PHE U:295 , ALA U:296 , THR U:297 , GLN U:310 , TRP U:442 , GLU U:445 , HOH U:2102 , HOH U:2224 , HOH U:2348
BINDING SITE FOR RESIDUE GOL U1563
47
FC2
SOFTWARE
CYS V:75 , VAL V:78 , HIS V:79 , ALA V:474 , PRO V:475 , ARG V:476 , LEU V:479 , VAL V:497 , PRO V:498 , SER V:499 , CYS V:546 , NI V:1551 , HOH V:2042
BINDING SITE FOR RESIDUE FCO V1550
48
FC3
SOFTWARE
CYS V:72 , CYS V:75 , CYS V:543 , CYS V:546 , FCO V:1550 , HOH V:2042
BINDING SITE FOR RESIDUE NI V1551
49
FC4
SOFTWARE
GLU V:53 , LEU V:495 , HIS V:549 , HOH V:2024 , HOH V:2025 , HOH V:2181
BINDING SITE FOR RESIDUE MG V1553
50
FC5
SOFTWARE
ARG V:100 , ASN V:104 , PHE V:295 , ALA V:296 , THR V:297 , GLN V:310 , GLU V:445 , HOH V:2073 , HOH V:2167 , HOH V:2241
BINDING SITE FOR RESIDUE GOL V1561
51
FC6
SOFTWARE
LYS F:122 , ASP F:252
BINDING SITE FOR RESIDUE CO3 V1562
[
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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select residue range 5 to 10 in chain 'A'
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show SS bonds with a radius of 100 units (=0.4Å)
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show bonds with a radius of 100 units (=0.4Å)
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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)
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