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1N2C
Asym. Unit
Info
Asym.Unit (454 KB)
Biol.Unit 1 (446 KB)
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(1)
Title
:
NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP-TETRAFLUOROALUMINATE
Authors
:
H. Schindelin, C. Kisker, D. C. Rees
Date
:
02 May 97 (Deposition) - 12 Nov 97 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Nitrogenase, Nitrogen Fixation, Signal Transduction, Electron Transfer, Atp Hydrolysis, Complex Of Nitrogenase Proteins
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Schindelin, C. Kisker, J. L. Schlessman, J. B. Howard, D. C. Rees
Structure Of Adp X Aif4(-)-Stabilized Nitrogenase Complex And Its Implications For Signal Transduction.
Nature V. 387 370 1997
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(8, 22)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: TETRAFLUOROALUMINATE ION (ALFa)
2b: TETRAFLUOROALUMINATE ION (ALFb)
2c: TETRAFLUOROALUMINATE ION (ALFc)
2d: TETRAFLUOROALUMINATE ION (ALFd)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
4a: FE-MO-S CLUSTER (CFMa)
4b: FE-MO-S CLUSTER (CFMb)
5a: FE(8)-S(7) CLUSTER (CLFa)
5b: FE(8)-S(7) CLUSTER (CLFb)
6a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
6b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
7c: MAGNESIUM ION (MGc)
7d: MAGNESIUM ION (MGd)
8a: IRON/SULFUR CLUSTER (SF4a)
8b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
ALF
4
Ligand/Ion
TETRAFLUOROALUMINATE ION
3
CA
2
Ligand/Ion
CALCIUM ION
4
CFM
2
Ligand/Ion
FE-MO-S CLUSTER
5
CLF
2
Ligand/Ion
FE(8)-S(7) CLUSTER
6
HCA
2
Ligand/Ion
3-HYDROXY-3-CARBOXY-ADIPIC ACID
7
MG
4
Ligand/Ion
MAGNESIUM ION
8
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:433 , ARG B:108 , GLU B:109 , ASP D:353 , ASP D:357
BINDING SITE FOR RESIDUE CA D 524
02
AC2
SOFTWARE
ASP B:353 , ASP B:357 , LYS C:433 , ARG D:108 , GLU D:109
BINDING SITE FOR RESIDUE CA B 524
03
AC3
SOFTWARE
SER E:16 , ASP E:39 , ADP E:291 , ALF E:293
BINDING SITE FOR RESIDUE MG E 292
04
AC4
SOFTWARE
GLY E:11 , GLY E:12 , LYS E:15 , SER E:16 , ASP E:39 , LYS E:41 , ASP E:43 , GLY E:128 , ADP E:291 , MG E:292 , LYS F:10
BINDING SITE FOR RESIDUE ALF E 293
05
AC5
SOFTWARE
SER F:16 , ASP F:39 , ASP F:43 , ADP F:291 , ALF F:293
BINDING SITE FOR RESIDUE MG F 292
06
AC6
SOFTWARE
LYS E:10 , GLY F:11 , GLY F:12 , LYS F:15 , SER F:16 , ASP F:39 , LYS F:41 , ASP F:43 , GLY F:128 , ADP F:291 , MG F:292
BINDING SITE FOR RESIDUE ALF F 293
07
AC7
SOFTWARE
SER G:16 , ASP G:39 , ADP G:291 , ALF G:293
BINDING SITE FOR RESIDUE MG G 292
08
AC8
SOFTWARE
GLY G:11 , GLY G:12 , LYS G:15 , SER G:16 , ASP G:39 , LYS G:41 , ASP G:43 , GLY G:128 , ADP G:291 , MG G:292 , LYS H:10
BINDING SITE FOR RESIDUE ALF G 293
09
AC9
SOFTWARE
SER H:16 , ASP H:39 , ADP H:291 , ALF H:293
BINDING SITE FOR RESIDUE MG H 292
10
BC1
SOFTWARE
LYS G:10 , GLY H:11 , GLY H:12 , LYS H:15 , SER H:16 , ASP H:39 , LYS H:41 , ASP H:43 , GLY H:128 , ADP H:291 , MG H:292
BINDING SITE FOR RESIDUE ALF H 293
11
BC2
SOFTWARE
GLN A:191 , GLY A:424 , ILE A:425 , HIS A:442 , CFM A:496
BINDING SITE FOR RESIDUE HCA A 494
12
BC3
SOFTWARE
VAL A:70 , ARG A:96 , HIS A:195 , TYR A:229 , ILE A:231 , CYS A:275 , SER A:278 , ILE A:355 , GLY A:356 , GLY A:357 , LEU A:358 , ARG A:359 , PHE A:381 , HIS A:442 , HCA A:494
BINDING SITE FOR RESIDUE CFM A 496
13
BC4
SOFTWARE
CYS A:62 , TYR A:64 , PRO A:85 , VAL A:86 , CYS A:88 , TYR A:91 , CYS A:154 , GLY A:185 , CYS B:70 , PRO B:72 , SER B:92 , GLY B:94 , CYS B:95 , TYR B:98 , CYS B:153 , SER B:188
BINDING SITE FOR RESIDUE CLF B 525
14
BC5
SOFTWARE
GLN C:191 , GLY C:424 , ILE C:425 , HIS C:442 , CFM C:496
BINDING SITE FOR RESIDUE HCA C 494
15
BC6
SOFTWARE
VAL C:70 , ARG C:96 , HIS C:195 , TYR C:229 , ILE C:231 , CYS C:275 , SER C:278 , ILE C:355 , GLY C:356 , GLY C:357 , LEU C:358 , ARG C:359 , PHE C:381 , HIS C:442 , HCA C:494
BINDING SITE FOR RESIDUE CFM C 496
16
BC7
SOFTWARE
CYS C:62 , TYR C:64 , PRO C:85 , VAL C:86 , CYS C:88 , TYR C:91 , CYS C:154 , GLY C:185 , CYS D:70 , PRO D:72 , SER D:92 , GLY D:94 , CYS D:95 , TYR D:98 , CYS D:153 , SER D:188
BINDING SITE FOR RESIDUE CLF D 525
17
BC8
SOFTWARE
LEU A:158 , VAL B:157 , CYS E:97 , ALA E:98 , GLY E:99 , VAL E:131 , CYS E:132 , CYS F:97 , ALA F:98 , GLY F:99 , VAL F:131 , CYS F:132
BINDING SITE FOR RESIDUE SF4 F 290
18
BC9
SOFTWARE
GLY E:12 , ILE E:13 , GLY E:14 , LYS E:15 , SER E:16 , THR E:17 , ASN E:185 , PRO E:212 , ARG E:213 , ASP E:214 , GLN E:218 , GLU E:221 , MG E:292 , ALF E:293 , LYS F:10 , GLU F:154 , MET F:156
BINDING SITE FOR RESIDUE ADP E 291
19
CC1
SOFTWARE
LYS E:10 , GLU E:154 , MET E:156 , GLY F:12 , ILE F:13 , GLY F:14 , LYS F:15 , SER F:16 , THR F:17 , ASN F:185 , PRO F:212 , ARG F:213 , ASP F:214 , GLN F:218 , GLU F:221 , MG F:292 , ALF F:293
BINDING SITE FOR RESIDUE ADP F 291
20
CC2
SOFTWARE
LEU C:158 , ILE C:159 , VAL D:157 , CYS G:97 , ALA G:98 , GLY G:99 , VAL G:131 , CYS G:132 , CYS H:97 , ALA H:98 , GLY H:99 , VAL H:131 , CYS H:132
BINDING SITE FOR RESIDUE SF4 G 290
21
CC3
SOFTWARE
GLY G:12 , ILE G:13 , GLY G:14 , LYS G:15 , SER G:16 , THR G:17 , ASN G:185 , PRO G:212 , ARG G:213 , ASP G:214 , GLN G:218 , GLU G:221 , MG G:292 , ALF G:293 , LYS H:10 , GLU H:154 , MET H:156
BINDING SITE FOR RESIDUE ADP G 291
22
CC4
SOFTWARE
LYS G:10 , GLU G:154 , MET G:156 , GLY H:12 , ILE H:13 , GLY H:14 , LYS H:15 , SER H:16 , THR H:17 , ASN H:185 , PRO H:212 , ARG H:213 , ASP H:214 , GLN H:218 , GLU H:221 , MG H:292 , ALF H:293
BINDING SITE FOR RESIDUE ADP H 291
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(5, 20)
Info
All PROSITE Patterns/Profiles
1: NIFH_FRXC_3 (E:2-274,F:2-274,G:2-274,H:2-274)
2: NITROGENASE_1_1 (A:81-88,C:81-88,B:88-95,D:88-95)
3: NIFH_FRXC_1 (E:87-99,F:87-99,G:87-99,H:87-99)
4: NIFH_FRXC_2 (E:125-138,F:125-138,G:125-138,H:12...)
5: NITROGENASE_1_2 (B:151-165,D:151-165,A:152-166,C:15...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NIFH_FRXC_3
PS51026
NIFH_FRXC family profile.
NIFH1_AZOVI
3-275
4
E:2-274
F:2-274
G:2-274
H:2-274
2
NITROGENASE_1_1
PS00699
Nitrogenases component 1 alpha and beta subunits signature 1.
NIFD_AZOVI
81-88
2
A:81-88
C:81-88
NIFK_AZOVI
88-95
2
B:88-95
D:88-95
3
NIFH_FRXC_1
PS00746
NifH/frxC family signature 1.
NIFH1_AZOVI
88-100
4
E:87-99
F:87-99
G:87-99
H:87-99
4
NIFH_FRXC_2
PS00692
NifH/frxC family signature 2.
NIFH1_AZOVI
126-139
4
E:125-138
F:125-138
G:125-138
H:125-138
5
NITROGENASE_1_2
PS00090
Nitrogenases component 1 alpha and beta subunits signature 2.
NIFK_AZOVI
151-165
2
B:151-165
D:151-165
NIFD_AZOVI
152-166
2
A:152-166
C:152-166
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 8)
Info
All SCOP Domains
1a: SCOP_d1n2ca_ (A:)
1b: SCOP_d1n2cc_ (C:)
2a: SCOP_d1n2cb_ (B:)
2b: SCOP_d1n2cd_ (D:)
3a: SCOP_d1n2ce_ (E:)
3b: SCOP_d1n2cf_ (F:)
3c: SCOP_d1n2cg_ (G:)
3d: SCOP_d1n2ch_ (H:)
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)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Chelatase-like
(149)
Superfamily
:
Helical backbone metal receptor
(102)
Family
:
Nitrogenase iron-molybdenum protein
(41)
Protein domain
:
Nitrogenase iron-molybdenum protein, alpha chain
(15)
Azotobacter vinelandii [TaxId: 354]
(10)
1a
d1n2ca_
A:
1b
d1n2cc_
C:
Protein domain
:
Nitrogenase iron-molybdenum protein, beta chain
(20)
Azotobacter vinelandii [TaxId: 354]
(15)
2a
d1n2cb_
B:
2b
d1n2cd_
D:
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Nitrogenase iron protein-like
(152)
Protein domain
:
Nitrogenase iron protein
(21)
Azotobacter vinelandii [TaxId: 354]
(20)
3a
d1n2ce_
E:
3b
d1n2cf_
F:
3c
d1n2cg_
G:
3d
d1n2ch_
H:
[
close SCOP info
]
CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_1n2cA02 (A:63-205)
1b: CATH_1n2cB02 (B:216-320)
1c: CATH_1n2cD02 (D:216-320)
1d: CATH_1n2cA01 (A:4-62,A:345-479)
1e: CATH_1n2cC01 (C:4-62,C:345-479)
1f: CATH_1n2cC02 (C:63-205)
1g: CATH_1n2cB01 (B:70-215)
1h: CATH_1n2cD01 (D:70-215)
1i: CATH_1n2cA03 (A:206-320)
1j: CATH_1n2cC03 (C:206-320)
1k: CATH_1n2cB03 (B:365-470)
1l: CATH_1n2cD03 (D:365-470)
2a: CATH_1n2cE00 (E:1-274)
2b: CATH_1n2cF00 (F:1-274)
2c: CATH_1n2cG00 (G:1-274)
2d: CATH_1n2cH00 (H:1-274)
3a: CATH_1n2cB04 (B:321-364,B:485-523)
3b: CATH_1n2cD04 (D:321-364,D:485-523)
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Topologies
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)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Nitrogenase molybdenum iron protein domain
(45)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
1a
1n2cA02
A:63-205
1b
1n2cB02
B:216-320
1c
1n2cD02
D:216-320
1d
1n2cA01
A:4-62,A:345-479
1e
1n2cC01
C:4-62,C:345-479
1f
1n2cC02
C:63-205
1g
1n2cB01
B:70-215
1h
1n2cD01
D:70-215
1i
1n2cA03
A:206-320
1j
1n2cC03
C:206-320
1k
1n2cB03
B:365-470
1l
1n2cD03
D:365-470
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
2a
1n2cE00
E:1-274
2b
1n2cF00
F:1-274
2c
1n2cG00
G:1-274
2d
1n2cH00
H:1-274
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Nitrogenase Molybdenum-iron Protein, subunit B; domain 4
(19)
Homologous Superfamily
:
Nitrogenase Molybdenum-iron Protein, subunit B, domain 4
(19)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
3a
1n2cB04
B:321-364,B:485-523
3b
1n2cD04
D:321-364,D:485-523
[
close CATH info
]
Pfam Domains
(3, 10)
Info
all PFAM domains
1a: PFAM_Fer4_NifH_1n2cH01 (H:3-274)
1b: PFAM_Fer4_NifH_1n2cH02 (H:3-274)
1c: PFAM_Fer4_NifH_1n2cH03 (H:3-274)
1d: PFAM_Fer4_NifH_1n2cH04 (H:3-274)
2a: PFAM_DUF3364_1n2cD01 (D:2-56)
2b: PFAM_DUF3364_1n2cD02 (D:2-56)
3a: PFAM_Oxidored_nitro_1n2cC01 (C:62-468)
3b: PFAM_Oxidored_nitro_1n2cC02 (C:62-468)
3c: PFAM_Oxidored_nitro_1n2cD03 (D:70-502)
3d: PFAM_Oxidored_nitro_1n2cD04 (D:70-502)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Fer4_NifH
(10)
Azotobacter vinelandii
(10)
1a
Fer4_NifH-1n2cH01
H:3-274
1b
Fer4_NifH-1n2cH02
H:3-274
1c
Fer4_NifH-1n2cH03
H:3-274
1d
Fer4_NifH-1n2cH04
H:3-274
Clan
:
no clan defined [family: DUF3364]
(10)
Family
:
DUF3364
(10)
Azotobacter vinelandii
(8)
2a
DUF3364-1n2cD01
D:2-56
2b
DUF3364-1n2cD02
D:2-56
Clan
:
no clan defined [family: Oxidored_nitro]
(12)
Family
:
Oxidored_nitro
(12)
Azotobacter vinelandii
(8)
3a
Oxidored_nitro-1n2cC01
C:62-468
3b
Oxidored_nitro-1n2cC02
C:62-468
3c
Oxidored_nitro-1n2cD03
D:70-502
3d
Oxidored_nitro-1n2cD04
D:70-502
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