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2ZON
Asym. Unit
Info
Asym.Unit (192 KB)
Biol.Unit 1 (186 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ELECTRON TRANSFER COMPLEX OF NITRITE REDUCTASE WITH CYTOCHROME C
Authors
:
M. Nojiri, H. Koteishi, K. Yamaguchi, S. Suzuki
Date
:
27 May 08 (Deposition) - 09 Jun 09 (Release) - 18 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,G
Biol. Unit 1: A,B,C,G (1x)
Keywords
:
Nitrite, Electron Transfer, Denitrification, Oxidoreductase-Electron Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Nojiri, H. Koteishi, T. Nakagami, K. Kobayashi, T. Inoue, K. Yamaguchi, S. Suzuki
Structural Basis Of Inter-Protein Electron Transfer For Nitrite Reduction In Denitrification
Nature V. 462 117 2009
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
1e: COPPER (II) ION (CUe)
1f: COPPER (II) ION (CUf)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
6
Ligand/Ion
COPPER (II) ION
2
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:89 , CYS A:130 , HIS A:139 , MET A:144
BINDING SITE FOR RESIDUE CU A 400
2
AC2
SOFTWARE
HIS A:94 , HIS A:129 , HIS B:300
BINDING SITE FOR RESIDUE CU A 401
3
AC3
SOFTWARE
HIS B:89 , CYS B:130 , HIS B:139 , MET B:144
BINDING SITE FOR RESIDUE CU B 400
4
AC4
SOFTWARE
HIS B:94 , HIS B:129 , HIS C:300
BINDING SITE FOR RESIDUE CU B 401
5
AC5
SOFTWARE
HIS C:89 , CYS C:130 , HIS C:139 , MET C:144
BINDING SITE FOR RESIDUE CU C 400
6
AC6
SOFTWARE
HIS A:300 , HIS C:94 , HIS C:129
BINDING SITE FOR RESIDUE CU C 401
7
AC7
SOFTWARE
MET A:87 , CYS G:20 , CYS G:23 , HIS G:24 , ALA G:29 , ALA G:31 , PHE G:43 , THR G:54 , LYS G:59 , ALA G:61 , MET G:62 , PRO G:63 , ARG G:65 , GLY G:66 , LEU G:75 , MET G:82
BINDING SITE FOR RESIDUE HEM G 200
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
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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, 7)
Info
All SCOP Domains
1a: SCOP_d2zong_ (G:)
2a: SCOP_d2zona1 (A:2-159)
2b: SCOP_d2zona2 (A:160-335)
2c: SCOP_d2zonb1 (B:2-159)
2d: SCOP_d2zonb2 (B:160-335)
2e: SCOP_d2zonc1 (C:2-159)
2f: SCOP_d2zonc2 (C:160-335)
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Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
automated matches
(31)
Protein domain
:
automated matches
(31)
Achromobacter xylosoxidans [TaxId: 85698]
(1)
1a
d2zong_
G:
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Multidomain cupredoxins
(146)
Protein domain
:
Nitrite reductase, NIR
(79)
Alcaligenes xylosoxidans [TaxId: 85698]
(23)
2a
d2zona1
A:2-159
2b
d2zona2
A:160-335
2c
d2zonb1
B:2-159
2d
d2zonb2
B:160-335
2e
d2zonc1
C:2-159
2f
d2zonc2
C:160-335
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CATH Domains
(2, 7)
Info
all CATH domains
1a: CATH_2zonG00 (G:7-87)
2a: CATH_2zonA01 (A:2-152)
2b: CATH_2zonB01 (B:2-152)
2c: CATH_2zonC01 (C:2-152)
2d: CATH_2zonA02 (A:153-319)
2e: CATH_2zonB02 (B:153-319)
2f: CATH_2zonC02 (C:153-319)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Alcaligenes xylosoxidans (Achromobacter xylosoxidans)
(1)
1a
2zonG00
G:7-87
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Alcaligenes xylosoxidans (Achromobacter xylosoxidans)
(1)
2a
2zonA01
A:2-152
2b
2zonB01
B:2-152
2c
2zonC01
C:2-152
2d
2zonA02
A:153-319
2e
2zonB02
B:153-319
2f
2zonC02
C:153-319
[
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Pfam Domains
(3, 7)
Info
all PFAM domains
1a: PFAM_Cu_oxidase_2zonC01 (C:168-320)
1b: PFAM_Cu_oxidase_2zonC02 (C:168-320)
1c: PFAM_Cu_oxidase_2zonC03 (C:168-320)
2a: PFAM_Cu_oxidase_3_2zonC04 (C:38-155)
2b: PFAM_Cu_oxidase_3_2zonC05 (C:38-155)
2c: PFAM_Cu_oxidase_3_2zonC06 (C:38-155)
3a: PFAM_Cytochrome_CBB3_2zonG01 (G:7-82)
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Clans
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Organisms
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)
(
)
Clan
:
CU_oxidase
(192)
Family
:
Cu-oxidase
(74)
Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)
(20)
1a
Cu-oxidase-2zonC01
C:168-320
1b
Cu-oxidase-2zonC02
C:168-320
1c
Cu-oxidase-2zonC03
C:168-320
Family
:
Cu-oxidase_3
(79)
Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)
(20)
2a
Cu-oxidase_3-2zonC04
C:38-155
2b
Cu-oxidase_3-2zonC05
C:38-155
2c
Cu-oxidase_3-2zonC06
C:38-155
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrome_CBB3
(20)
Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)
(1)
3a
Cytochrome_CBB3-2zonG01
G:7-82
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