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1M1N
Biol. Unit 1
Info
Asym.Unit (1.5 MB)
Biol.Unit 1 (749 KB)
Biol.Unit 2 (753 KB)
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(1)
Title
:
NITROGENASE MOFE PROTEIN FROM AZOTOBACTER VINELANDII
Authors
:
O. Einsle, F. A. Tezcan, S. L. A. Andrade, B. Schmid, M. Yoshida, J. B. Howard, D. C. Rees
Date
:
19 Jun 02 (Deposition) - 11 Sep 02 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.16
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Atomic Resolution, Femo Cofactor, Nitrogen Fixation, Central Nitrogen Ligand, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Einsle, F. A. Tezcan, S. L. Andrade, B. Schmid, M. Yoshida, J. B. Howard, D. C. Rees
Nitrogenase Mofe-Protein At 1. 16 A Resolution: A Central Ligand In The Femo-Cofactor.
Science V. 297 1696 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: FE(7)-MO-S(9)-N CLUSTER (CFNa)
2b: FE(7)-MO-S(9)-N CLUSTER (CFNb)
2c: FE(7)-MO-S(9)-N CLUSTER (CFNc)
2d: FE(7)-MO-S(9)-N CLUSTER (CFNd)
3a: FE(8)-S(7) CLUSTER (CLFa)
3b: FE(8)-S(7) CLUSTER (CLFb)
3c: FE(8)-S(7) CLUSTER (CLFc)
3d: FE(8)-S(7) CLUSTER (CLFd)
4a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
4b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
4c: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAc)
4d: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
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: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
7: AC9 (SOFTWARE)
8: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG B:108 , GLU B:109 , ASP D:353 , ASP D:357 , HOH D:7499 , HOH D:7568 , HOH D:8199
BINDING SITE FOR RESIDUE CA D 6492
2
AC2
SOFTWARE
ASP B:353 , ASP B:357 , HOH B:7493 , HOH B:7584 , HOH B:8212 , ARG D:108 , GLU D:109
BINDING SITE FOR RESIDUE CA B 7492
3
AC5
SOFTWARE
ALA A:65 , GLN A:191 , GLY A:424 , ILE A:425 , HIS A:442 , CFN A:6496 , HOH A:6501 , HOH A:6505 , HOH A:6512 , HOH A:6527 , HOH A:6551 , HOH A:6555 , HOH A:6640 , HOH A:6718 , HOH B:7500 , HOH B:7614
BINDING SITE FOR RESIDUE HCA A 6494
4
AC6
SOFTWARE
CYS A:62 , TYR A:64 , PRO A:85 , GLY A:87 , CYS A:88 , TYR A:91 , CYS A:154 , GLY A:185 , CYS B:70 , SER B:92 , CYS B:95 , TYR B:98 , CYS B:153 , SER B:188
BINDING SITE FOR RESIDUE CLF B 6498
5
AC7
SOFTWARE
VAL A:70 , ARG A:96 , HIS A:195 , TYR A:229 , CYS A:275 , GLY A:356 , GLY A:357 , LEU A:358 , ARG A:359 , PHE A:381 , HIS A:442 , HCA A:6494
BINDING SITE FOR RESIDUE CFN A 6496
6
AC8
SOFTWARE
ALA C:65 , GLN C:191 , GLY C:424 , ILE C:425 , HIS C:442 , CFN C:7496 , HOH C:7514 , HOH C:7516 , HOH C:7527 , HOH C:7538 , HOH C:7561 , HOH C:7581 , HOH C:7611 , HOH C:7728 , HOH D:7511 , HOH D:7547
BINDING SITE FOR RESIDUE HCA C 7494
7
AC9
SOFTWARE
CYS C:62 , TYR C:64 , PRO C:85 , GLY C:87 , CYS C:88 , TYR C:91 , CYS C:154 , GLY C:185 , CYS D:70 , SER D:92 , CYS D:95 , TYR D:98 , CYS D:153 , SER D:188
BINDING SITE FOR RESIDUE CLF D 7498
8
BC1
SOFTWARE
VAL 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:7494
BINDING SITE FOR RESIDUE CFN C 7496
[
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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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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: NITROGENASE_1_1 (B:88-95,D:88-95)
2: NITROGENASE_1_2 (B:151-165,D:151-165)
;
View:
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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.
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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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1m1na_ (A:)
1b: SCOP_d1m1nc_ (C:)
1c: SCOP_d1m1ne_ (E:)
1d: SCOP_d1m1ng_ (G:)
2a: SCOP_d1m1nb_ (B:)
2b: SCOP_d1m1nd_ (D:)
2c: SCOP_d1m1nf_ (F:)
2d: SCOP_d1m1nh_ (H:)
View:
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Classes
(
)
(
)
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(
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(
)
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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
d1m1na_
A:
1b
d1m1nc_
C:
1c
d1m1ne_
E:
1d
d1m1ng_
G:
Protein domain
:
Nitrogenase iron-molybdenum protein, beta chain
(20)
Azotobacter vinelandii [TaxId: 354]
(15)
2a
d1m1nb_
B:
2b
d1m1nd_
D:
2c
d1m1nf_
F:
2d
d1m1nh_
H:
[
close SCOP info
]
CATH Domains
(2, 28)
Info
all CATH domains
1a: CATH_1m1nA02 (A:63-205)
1b: CATH_1m1nC02 (C:63-205)
1c: CATH_1m1nH01 (H:70-215)
1d: CATH_1m1nA03 (A:206-320)
1e: CATH_1m1nC03 (C:206-320)
1f: CATH_1m1nE03 (E:206-320)
1g: CATH_1m1nG03 (G:206-320)
1h: CATH_1m1nE02 (E:63-205)
1i: CATH_1m1nB03 (B:365-470)
1j: CATH_1m1nD03 (D:365-470)
1k: CATH_1m1nF03 (F:365-470)
1l: CATH_1m1nH03 (H:365-470)
1m: CATH_1m1nB02 (B:216-320)
1n: CATH_1m1nD02 (D:216-320)
1o: CATH_1m1nG02 (G:63-205)
1p: CATH_1m1nF02 (F:216-320)
1q: CATH_1m1nH02 (H:216-320)
1r: CATH_1m1nA01 (A:4-62,A:345-479)
1s: CATH_1m1nC01 (C:4-62,C:345-479)
1t: CATH_1m1nE01 (E:4-62,E:345-479)
1u: CATH_1m1nG01 (G:4-62,G:345-479)
1v: CATH_1m1nB01 (B:70-215)
1w: CATH_1m1nD01 (D:70-215)
1x: CATH_1m1nF01 (F:70-215)
2a: CATH_1m1nB04 (B:321-364,B:485-523)
2b: CATH_1m1nD04 (D:321-364,D:485-523)
2c: CATH_1m1nF04 (F:321-364,F:485-523)
2d: CATH_1m1nH04 (H:321-364,H:485-523)
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)
Topologies
(
)
(
)
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.
(3)
1a
1m1nA02
A:63-205
1b
1m1nC02
C:63-205
1c
1m1nH01
H:70-215
1d
1m1nA03
A:206-320
1e
1m1nC03
C:206-320
1f
1m1nE03
E:206-320
1g
1m1nG03
G:206-320
1h
1m1nE02
E:63-205
1i
1m1nB03
B:365-470
1j
1m1nD03
D:365-470
1k
1m1nF03
F:365-470
1l
1m1nH03
H:365-470
1m
1m1nB02
B:216-320
1n
1m1nD02
D:216-320
1o
1m1nG02
G:63-205
1p
1m1nF02
F:216-320
1q
1m1nH02
H:216-320
1r
1m1nA01
A:4-62,A:345-479
1s
1m1nC01
C:4-62,C:345-479
1t
1m1nE01
E:4-62,E:345-479
1u
1m1nG01
G:4-62,G:345-479
1v
1m1nB01
B:70-215
1w
1m1nD01
D:70-215
1x
1m1nF01
F:70-215
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.
(3)
2a
1m1nB04
B:321-364,B:485-523
2b
1m1nD04
D:321-364,D:485-523
2c
1m1nF04
F:321-364,F:485-523
2d
1m1nH04
H:321-364,H:485-523
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_DUF3364_1m1nH01 (H:2-56)
1b: PFAM_DUF3364_1m1nH02 (H:2-56)
1c: PFAM_DUF3364_1m1nH03 (H:2-56)
1d: PFAM_DUF3364_1m1nH04 (H:2-56)
2a: PFAM_Oxidored_nitro_1m1nG01 (G:62-468)
2b: PFAM_Oxidored_nitro_1m1nG02 (G:62-468)
2c: PFAM_Oxidored_nitro_1m1nG03 (G:62-468)
2d: PFAM_Oxidored_nitro_1m1nG04 (G:62-468)
2e: PFAM_Oxidored_nitro_1m1nH05 (H:70-502)
2f: PFAM_Oxidored_nitro_1m1nH06 (H:70-502)
2g: PFAM_Oxidored_nitro_1m1nH07 (H:70-502)
2h: PFAM_Oxidored_nitro_1m1nH08 (H:70-502)
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(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DUF3364]
(10)
Family
:
DUF3364
(10)
Azotobacter vinelandii
(8)
1a
DUF3364-1m1nH01
H:2-56
1b
DUF3364-1m1nH02
H:2-56
1c
DUF3364-1m1nH03
H:2-56
1d
DUF3364-1m1nH04
H:2-56
Clan
:
no clan defined [family: Oxidored_nitro]
(12)
Family
:
Oxidored_nitro
(12)
Azotobacter vinelandii
(8)
2a
Oxidored_nitro-1m1nG01
G:62-468
2b
Oxidored_nitro-1m1nG02
G:62-468
2c
Oxidored_nitro-1m1nG03
G:62-468
2d
Oxidored_nitro-1m1nG04
G:62-468
2e
Oxidored_nitro-1m1nH05
H:70-502
2f
Oxidored_nitro-1m1nH06
H:70-502
2g
Oxidored_nitro-1m1nH07
H:70-502
2h
Oxidored_nitro-1m1nH08
H:70-502
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