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3K1A
Asym. Unit
Info
Asym.Unit (342 KB)
Biol.Unit 1 (335 KB)
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(1)
Title
:
INSIGHTS INTO SUBSTRATE BINDING AT FEMO-COFACTOR IN NITROGENASE FROM THE STRUCTURE OF AN ALPHA-70ILE MOFE PROTEIN VARIANT
Authors
:
J. W. Peters, R. Sarma, B. M. Barney, S. Keable, L. C. Seefeldt, D. R. Dean
Date
:
26 Sep 09 (Deposition) - 16 Feb 10 (Release) - 02 Mar 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.23
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Nitrogen Fixation, Mofe Protein, Nitrogenase, Isoleucine, Proton Reduction, Nitrogen, Acetylene, Hydride Reduction, Atp-Binding, Iron, Iron-Sulfur, Metal-Binding, Nucleotide- Binding, Oxidoreductase, Molybdenum
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Reference
:
R. Sarma, B. M. Barney, S. Keable, D. R. Dean, L. C. Seefeldt, J. W. Peters
Insights Into Substrate Binding At Femo-Cofactor In Nitrogenase From The Structure Of An Alpha-70(Ile) Mofe Protein Variant
J. Inorg. Biochem. V. 104 385 2010
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: FE(7)-MO-S(9)-N CLUSTER (CFNa)
2b: FE(7)-MO-S(9)-N CLUSTER (CFNb)
3a: FE(8)-S(7) CLUSTER (CLFa)
3b: FE(8)-S(7) CLUSTER (CLFb)
4a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
4b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CFN
2
Ligand/Ion
FE(7)-MO-S(9)-N CLUSTER
3
CLF
2
Ligand/Ion
FE(8)-S(7) 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
ALA A:65 , ARG A:96 , GLN A:191 , GLY A:424 , ILE A:425 , HIS A:442 , HOH A:497 , HOH A:498 , HOH A:505 , HOH A:516 , HOH A:530 , HOH A:590 , CFN A:6496
BINDING SITE FOR RESIDUE HCA A 494
2
AC2
SOFTWARE
ILE A:70 , ARG A:96 , HIS A:195 , TYR A:229 , CYS A:275 , GLY A:356 , GLY A:357 , ARG A:359 , PHE A:381 , HIS A:442 , HCA A:494
BINDING SITE FOR RESIDUE CFN A 6496
3
AC3
SOFTWARE
CYS A:62 , GLY A:87 , CYS A:88 , CYS A:154 , CYS B:70 , SER B:92 , CYS B:95 , TYR B:98 , THR B:152 , CYS B:153 , SER B:188
BINDING SITE FOR RESIDUE CLF B 6498
4
AC4
SOFTWARE
ASP B:353 , ASP B:357 , HOH B:835 , ARG D:108 , GLU D:109
BINDING SITE FOR RESIDUE CA B 524
5
AC5
SOFTWARE
ILE C:70 , ARG C:96 , HIS C:195 , TYR C:229 , CYS C:275 , GLY C:356 , GLY C:357 , ARG C:359 , PHE C:381 , HIS C:442 , HCA C:494
BINDING SITE FOR RESIDUE CFN C 7496
6
AC6
SOFTWARE
ALA C:65 , ARG C:96 , GLN C:191 , GLY C:424 , ILE C:425 , HIS C:442 , HOH C:500 , HOH C:502 , HOH C:530 , HOH C:534 , HOH C:560 , HOH C:607 , HOH C:685 , HOH C:781 , CFN C:7496
BINDING SITE FOR RESIDUE HCA C 494
7
AC7
SOFTWARE
ARG B:108 , GLU B:109 , ASP D:353 , ASP D:357 , HOH D:599
BINDING SITE FOR RESIDUE CA D 524
8
AC8
SOFTWARE
CYS C:62 , GLY C:87 , CYS C:88 , CYS C:154 , CYS D:70 , SER D:92 , CYS D:95 , TYR D:98 , THR D:152 , CYS D:153 , SER D:188 , HOH D:619
BINDING SITE FOR RESIDUE CLF D 7498
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: NITROGENASE_1_1 (A:81-88,C:81-88,B:88-95,D:88-95)
2: NITROGENASE_1_2 (B:151-165,D:151-165,A:152-166,C:15...)
;
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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.
NIFD_AZOVI
81-88
2
A:81-88
C:81-88
NIFK_AZOVI
88-95
2
B:88-95
D:88-95
2
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
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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_d3k1aa_ (A:)
1b: SCOP_d3k1ac_ (C:)
2a: SCOP_d3k1ab_ (B:)
2b: SCOP_d3k1ad_ (D:)
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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
:
automated matches
(6)
Azotobacter vinelandii [TaxId: 354]
(6)
1a
d3k1aa_
A:
1b
d3k1ac_
C:
Protein domain
:
Nitrogenase iron-molybdenum protein, beta chain
(20)
Azotobacter vinelandii [TaxId: 354]
(15)
2a
d3k1ab_
B:
2b
d3k1ad_
D:
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CATH Domains
(2, 14)
Info
all CATH domains
1a: CATH_3k1aA02 (A:63-205)
1b: CATH_3k1aC02 (C:63-205)
1c: CATH_3k1aA01 (A:5-62,A:345-479)
1d: CATH_3k1aC01 (C:5-62,C:345-479)
1e: CATH_3k1aB01 (B:70-215)
1f: CATH_3k1aD01 (D:70-215)
1g: CATH_3k1aA03 (A:206-320)
1h: CATH_3k1aC03 (C:206-320)
1i: CATH_3k1aB04 (B:365-470)
1j: CATH_3k1aD04 (D:365-470)
1k: CATH_3k1aB02 (B:216-320)
1l: CATH_3k1aD02 (D:216-320)
2a: CATH_3k1aB03 (B:321-364,B:485-523)
2b: CATH_3k1aD03 (D:321-364,D:485-523)
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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)
Azotobacter vinelandii. Organism_taxid: 354.
(1)
1a
3k1aA02
A:63-205
1b
3k1aC02
C:63-205
1c
3k1aA01
A:5-62,A:345-479
1d
3k1aC01
C:5-62,C:345-479
1e
3k1aB01
B:70-215
1f
3k1aD01
D:70-215
1g
3k1aA03
A:206-320
1h
3k1aC03
C:206-320
1i
3k1aB04
B:365-470
1j
3k1aD04
D:365-470
1k
3k1aB02
B:216-320
1l
3k1aD02
D:216-320
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.
(1)
2a
3k1aB03
B:321-364,B:485-523
2b
3k1aD03
D:321-364,D:485-523
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_DUF3364_3k1aD01 (D:2-56)
1b: PFAM_DUF3364_3k1aD02 (D:2-56)
2a: PFAM_Oxidored_nitro_3k1aC01 (C:62-468)
2b: PFAM_Oxidored_nitro_3k1aC02 (C:62-468)
2c: PFAM_Oxidored_nitro_3k1aD03 (D:70-502)
2d: PFAM_Oxidored_nitro_3k1aD04 (D:70-502)
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Clans
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(
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Organisms
(
)
(
)
Clan
:
no clan defined [family: DUF3364]
(10)
Family
:
DUF3364
(10)
Azotobacter vinelandii
(8)
1a
DUF3364-3k1aD01
D:2-56
1b
DUF3364-3k1aD02
D:2-56
Clan
:
no clan defined [family: Oxidored_nitro]
(12)
Family
:
Oxidored_nitro
(12)
Azotobacter vinelandii
(8)
2a
Oxidored_nitro-3k1aC01
C:62-468
2b
Oxidored_nitro-3k1aC02
C:62-468
2c
Oxidored_nitro-3k1aD03
D:70-502
2d
Oxidored_nitro-3k1aD04
D:70-502
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