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1MIO
Asym. Unit
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Asym.Unit (312 KB)
Biol.Unit 1 (303 KB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF THE NITROGENASE MOLYBDENUM-IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM AT 3.0 ANGSTROMS RESOLUTION
Authors
:
J. Kim, D. Woo, D. C. Rees
Date
:
24 Mar 93 (Deposition) - 31 Oct 93 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Molybdenum-Iron Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Kim, D. Woo, D. C. Rees
X-Ray Crystal Structure Of The Nitrogenase Molybdenum-Iron Protein From Clostridium Pasteurianum At 3. 0-A Resolution.
Biochemistry V. 32 7104 1993
(for further references see the
PDB file header
)
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: FE-MO-S CLUSTER (CFMa)
2b: FE-MO-S CLUSTER (CFMb)
3a: FE-S CLUSTER (CLPa)
3b: FE-S CLUSTER (CLPb)
4a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
4b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CFM
2
Ligand/Ion
FE-MO-S CLUSTER
3
CLP
2
Ligand/Ion
FE-S CLUSTER
4
HCA
2
Ligand/Ion
3-HYDROXY-3-CARBOXY-ADIPIC ACID
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE B:60 , LYS B:61 , GLU B:62 , TYR B:420 , ASP D:301 , ASP D:305
BINDING SITE FOR RESIDUE CA B 492
2
AC2
SOFTWARE
ASP B:301 , ASP B:305 , LYS D:61 , GLU D:62
BINDING SITE FOR RESIDUE CA D 492
3
AC3
SOFTWARE
ALA A:56 , ARG A:87 , GLN A:182 , GLY A:464 , ILE A:465 , GLN A:480 , HIS A:482 , CFM B:496
BINDING SITE FOR RESIDUE HCA B 494
4
AC4
SOFTWARE
VAL A:61 , ARG A:87 , HIS A:186 , TYR A:216 , ILE A:218 , CYS A:262 , SER A:265 , VAL A:343 , GLY A:344 , GLY A:345 , ARG A:347 , PHE A:369 , HIS A:482 , HCA B:494
BINDING SITE FOR RESIDUE CFM B 496
5
AC5
SOFTWARE
CYS A:53 , TYR A:55 , PRO A:76 , GLY A:78 , CYS A:79 , CYS A:145 , GLY A:176 , CYS B:23 , PRO B:25 , SER B:45 , GLY B:47 , CYS B:48 , HIS B:52 , THR B:105 , CYS B:106 , SER B:141
BINDING SITE FOR RESIDUE CLP B 498
6
AC6
SOFTWARE
GLN C:182 , GLY C:464 , ILE C:465 , LYS C:466 , HIS C:482 , CFM D:496
BINDING SITE FOR RESIDUE HCA D 494
7
AC7
SOFTWARE
VAL C:61 , ARG C:87 , GLN C:182 , HIS C:186 , TYR C:216 , CYS C:262 , SER C:265 , VAL C:343 , GLY C:344 , GLY C:345 , ARG C:347 , PHE C:369 , HIS C:482 , HCA D:494
BINDING SITE FOR RESIDUE CFM D 496
8
AC8
SOFTWARE
CYS C:53 , TYR C:55 , PRO C:76 , GLY C:78 , CYS C:79 , CYS C:145 , GLY C:176 , CYS D:23 , PRO D:25 , SER D:45 , GLY D:47 , CYS D:48 , TYR D:51 , CYS D:106 , SER D:141
BINDING SITE FOR RESIDUE CLP D 498
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: NITROGENASE_1_1 (B:41-48,D:41-48,A:72-79,C:72-79)
2: NITROGENASE_1_2 (B:104-118,D:104-118,A:143-157,C:14...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NITROGENASE_1_1
PS00699
Nitrogenases component 1 alpha and beta subunits signature 1.
NIFK_CLOPA
41-48
2
B:41-48
D:41-48
NIFD_CLOPA
72-79
2
A:72-79
C:72-79
2
NITROGENASE_1_2
PS00090
Nitrogenases component 1 alpha and beta subunits signature 2.
NIFK_CLOPA
104-118
2
B:104-118
D:104-118
NIFD_CLOPA
143-157
2
A:143-157
C:143-157
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Exons
(0, 0)
Info
All Exons
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1mioa_ (A:)
1b: SCOP_d1mioc_ (C:)
2a: SCOP_d1miob_ (B:)
2b: SCOP_d1miod_ (D:)
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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)
Clostridium pasteurianum [TaxId: 1501]
(1)
1a
d1mioa_
A:
1b
d1mioc_
C:
Protein domain
:
Nitrogenase iron-molybdenum protein, beta chain
(20)
Clostridium pasteurianum [TaxId: 1501]
(1)
2a
d1miob_
B:
2b
d1miod_
D:
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CATH Domains
(2, 14)
Info
all CATH domains
1a: CATH_1mioA02 (A:54-196)
1b: CATH_1mioC02 (C:54-196)
1c: CATH_1mioA01 (A:2-53,A:333-519)
1d: CATH_1mioC01 (C:2-53,C:333-519)
1e: CATH_1mioB01 (B:22-162)
1f: CATH_1mioD01 (D:22-162)
1g: CATH_1mioA03 (A:197-308)
1h: CATH_1mioC03 (C:197-308)
1i: CATH_1mioB02 (B:163-266)
1j: CATH_1mioD02 (D:163-266)
1k: CATH_1mioB04 (B:313-410)
1l: CATH_1mioD04 (D:313-410)
2a: CATH_1mioB03 (B:267-312,B:426-458)
2b: CATH_1mioD03 (D:267-312,D:426-458)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Nitrogenase molybdenum iron protein domain
(45)
Clostridium pasteurianum. Organism_taxid: 1501.
(1)
1a
1mioA02
A:54-196
1b
1mioC02
C:54-196
1c
1mioA01
A:2-53,A:333-519
1d
1mioC01
C:2-53,C:333-519
1e
1mioB01
B:22-162
1f
1mioD01
D:22-162
1g
1mioA03
A:197-308
1h
1mioC03
C:197-308
1i
1mioB02
B:163-266
1j
1mioD02
D:163-266
1k
1mioB04
B:313-410
1l
1mioD04
D:313-410
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)
Clostridium pasteurianum. Organism_taxid: 1501.
(1)
2a
1mioB03
B:267-312,B:426-458
2b
1mioD03
D:267-312,D:426-458
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain D
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