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2XX1
Asym. Unit
Info
Asym.Unit (326 KB)
Biol.Unit 1 (163 KB)
Biol.Unit 2 (161 KB)
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(1)
Title
:
STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS COMPLEXED WITH NITRITE
Authors
:
S. V. Antonyuk, N. G. H. Leferink, C. Han, D. J. Heyes, S. E. J. Rigby, M. A. R. R. Eady, N. S. Scrutton, S. S. Hasnain
Date
:
07 Nov 10 (Deposition) - 18 May 11 (Release) - 18 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,D,E (1x)
Biol. Unit 2: B,C,F (1x)
Keywords
:
Oxidoreductase, Proton Channel, Denitrification
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. G. H. Leferink, C. Han, S. V. Antonyuk, D. J. Heyes, S. E. J. Rigby, M. A. Hough, R. R. Eady, N. S. Scrutton, S. S. Hasnain
Proton-Coupled Electron Transfer In The Catalytic Cycle Of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase.
Biochemistry V. 50 4121 2011
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Hetero Components
(3, 39)
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)
1g: COPPER (II) ION (CUg)
1h: COPPER (II) ION (CUh)
1i: COPPER (II) ION (CUi)
1j: COPPER (II) ION (CUj)
1k: COPPER (II) ION (CUk)
1l: COPPER (II) ION (CUl)
2a: NITRITE ION (NO2a)
2b: NITRITE ION (NO2b)
2c: NITRITE ION (NO2c)
2d: NITRITE ION (NO2d)
2e: NITRITE ION (NO2e)
2f: NITRITE ION (NO2f)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
12
Ligand/Ion
COPPER (II) ION
2
NO2
6
Ligand/Ion
NITRITE ION
3
SO4
21
Ligand/Ion
SULFATE ION
[
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Sites
(39, 39)
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)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:89 , CYS A:130 , HIS A:139 , MET A:144
BINDING SITE FOR RESIDUE CU A1337
02
AC2
SOFTWARE
ASP A:92 , HIS A:94 , HIS A:129 , HIS E:300 , NO2 E:1337
BINDING SITE FOR RESIDUE CU A1338
03
AC3
SOFTWARE
HIS A:249 , ILE A:251 , HIS A:300 , ASP D:92 , HIS D:94 , HIS D:129 , CU D:1338
BINDING SITE FOR RESIDUE NO2 A1339
04
AC4
SOFTWARE
VAL A:14 , ALA A:15
BINDING SITE FOR RESIDUE SO4 A1340
05
AC5
SOFTWARE
ASN A:243 , ARG A:244 , ASP A:245 , ARG E:247 , ASN E:301 , GLU E:304
BINDING SITE FOR RESIDUE SO4 A1341
06
AC6
SOFTWARE
HIS A:22 , GLU A:23 , GLN A:24 , HIS A:165
BINDING SITE FOR RESIDUE SO4 A1342
07
AC7
SOFTWARE
ARG A:270
BINDING SITE FOR RESIDUE SO4 A1343
08
AC8
SOFTWARE
HIS B:89 , CYS B:130 , HIS B:139 , MET B:144
BINDING SITE FOR RESIDUE CU B1337
09
AC9
SOFTWARE
HIS B:94 , HIS B:129 , HIS F:300 , NO2 F:1337
BINDING SITE FOR RESIDUE CU B1338
10
BC1
SOFTWARE
HIS B:249 , ILE B:251 , HIS B:300 , ASP C:92 , HIS C:94 , HIS C:129 , CU C:1337
BINDING SITE FOR RESIDUE NO2 B1339
11
BC2
SOFTWARE
HIS B:22 , GLU B:23 , GLN B:24 , HIS B:165
BINDING SITE FOR RESIDUE SO4 B1340
12
BC3
SOFTWARE
VAL B:14 , ALA B:15
BINDING SITE FOR RESIDUE SO4 B1341
13
BC4
SOFTWARE
ILE B:328 , LYS B:329 , ALA B:330
BINDING SITE FOR RESIDUE SO4 B1342
14
BC5
SOFTWARE
ARG B:270
BINDING SITE FOR RESIDUE SO4 B1343
15
BC6
SOFTWARE
HIS C:89 , CYS C:130 , HIS C:139 , MET C:144
BINDING SITE FOR RESIDUE CU C1336
16
BC7
SOFTWARE
HIS B:300 , NO2 B:1339 , HIS C:94 , HIS C:129
BINDING SITE FOR RESIDUE CU C1337
17
BC8
SOFTWARE
ARG B:247 , ASN B:301 , GLU B:304 , ARG C:244 , ASP C:245
BINDING SITE FOR RESIDUE SO4 C1338
18
BC9
SOFTWARE
VAL C:14 , ALA C:15
BINDING SITE FOR RESIDUE SO4 C1339
19
CC1
SOFTWARE
HIS C:22 , GLU C:23 , GLN C:24 , HIS C:165
BINDING SITE FOR RESIDUE SO4 C1340
20
CC2
SOFTWARE
ARG C:270 , HOH C:2029
BINDING SITE FOR RESIDUE SO4 C1341
21
CC3
SOFTWARE
HIS D:89 , CYS D:130 , HIS D:139 , MET D:144
BINDING SITE FOR RESIDUE CU D1337
22
CC4
SOFTWARE
HIS A:300 , NO2 A:1339 , ASP D:92 , HIS D:94 , HIS D:129
BINDING SITE FOR RESIDUE CU D1338
23
CC5
SOFTWARE
ILE D:328 , LYS D:329 , ALA D:330
BINDING SITE FOR RESIDUE SO4 D1339
24
CC6
SOFTWARE
VAL D:14 , ALA D:15
BINDING SITE FOR RESIDUE SO4 D1340
25
CC7
SOFTWARE
ASP A:92 , HIS A:94 , HIS A:129 , CU A:1338 , HIS E:249 , ILE E:251 , HIS E:300
BINDING SITE FOR RESIDUE NO2 E1337
26
CC8
SOFTWARE
HIS E:89 , CYS E:130 , HIS E:139 , MET E:144
BINDING SITE FOR RESIDUE CU E1338
27
CC9
SOFTWARE
HIS D:300 , ASP E:92 , HIS E:94 , HIS E:129 , NO2 E:1340
BINDING SITE FOR RESIDUE CU E1339
28
DC1
SOFTWARE
HIS D:249 , ILE D:251 , HIS D:300 , ASP E:92 , HIS E:94 , HIS E:129 , CU E:1339
BINDING SITE FOR RESIDUE NO2 E1340
29
DC2
SOFTWARE
VAL E:14 , ALA E:15
BINDING SITE FOR RESIDUE SO4 E1341
30
DC3
SOFTWARE
HIS E:22 , GLU E:23 , GLN E:24 , HIS E:165
BINDING SITE FOR RESIDUE SO4 E1342
31
DC4
SOFTWARE
GLU D:307 , VAL E:201 , GLN E:202 , ARG E:205 , HOH E:2031
BINDING SITE FOR RESIDUE SO4 E1343
32
DC5
SOFTWARE
ARG E:270
BINDING SITE FOR RESIDUE SO4 E1344
33
DC6
SOFTWARE
ASN E:225
BINDING SITE FOR RESIDUE SO4 E1345
34
DC7
SOFTWARE
ASP B:92 , HIS B:94 , HIS B:129 , CU B:1338 , HIS F:249 , ILE F:251 , HIS F:300
BINDING SITE FOR RESIDUE NO2 F1337
35
DC8
SOFTWARE
HIS F:89 , CYS F:130 , HIS F:139 , MET F:144
BINDING SITE FOR RESIDUE CU F1338
36
DC9
SOFTWARE
HIS C:300 , ASP F:92 , HIS F:94 , HIS F:129 , NO2 F:1340
BINDING SITE FOR RESIDUE CU F1339
37
EC1
SOFTWARE
HIS C:249 , ILE C:251 , HIS C:300 , ASP F:92 , HIS F:94 , HIS F:129 , CU F:1339
BINDING SITE FOR RESIDUE NO2 F1340
38
EC2
SOFTWARE
HIS F:22 , GLU F:23 , GLN F:24 , HIS F:165 , HOH F:2025
BINDING SITE FOR RESIDUE SO4 F1341
39
EC3
SOFTWARE
VAL F:14 , ALA F:15
BINDING SITE FOR RESIDUE SO4 F1342
[
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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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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Label:
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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d2xx1a1 (A:2-159)
1b: SCOP_d2xx1a2 (A:160-336)
1c: SCOP_d2xx1b1 (B:2-159)
1d: SCOP_d2xx1b2 (B:160-336)
1e: SCOP_d2xx1c1 (C:2-159)
1f: SCOP_d2xx1c2 (C:160-335)
1g: SCOP_d2xx1d1 (D:2-159)
1h: SCOP_d2xx1d2 (D:160-336)
1i: SCOP_d2xx1e1 (E:2-159)
1j: SCOP_d2xx1e2 (E:160-336)
1k: SCOP_d2xx1f1 (F:2-159)
1l: SCOP_d2xx1f2 (F:160-336)
View:
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Classes
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)
(
)
Folds
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Superfamilies
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)
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Families
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Multidomain cupredoxins
(146)
Protein domain
:
automated matches
(10)
Achromobacter xylosoxidans [TaxId: 85698]
(8)
1a
d2xx1a1
A:2-159
1b
d2xx1a2
A:160-336
1c
d2xx1b1
B:2-159
1d
d2xx1b2
B:160-336
1e
d2xx1c1
C:2-159
1f
d2xx1c2
C:160-335
1g
d2xx1d1
D:2-159
1h
d2xx1d2
D:160-336
1i
d2xx1e1
E:2-159
1j
d2xx1e2
E:160-336
1k
d2xx1f1
F:2-159
1l
d2xx1f2
F:160-336
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
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Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Cu_oxidase_2xx1F01 (F:168-320)
1b: PFAM_Cu_oxidase_2xx1F02 (F:168-320)
1c: PFAM_Cu_oxidase_2xx1F03 (F:168-320)
1d: PFAM_Cu_oxidase_2xx1F04 (F:168-320)
1e: PFAM_Cu_oxidase_2xx1F05 (F:168-320)
1f: PFAM_Cu_oxidase_2xx1F06 (F:168-320)
2a: PFAM_Cu_oxidase_3_2xx1F07 (F:38-155)
2b: PFAM_Cu_oxidase_3_2xx1F08 (F:38-155)
2c: PFAM_Cu_oxidase_3_2xx1F09 (F:38-155)
2d: PFAM_Cu_oxidase_3_2xx1F10 (F:38-155)
2e: PFAM_Cu_oxidase_3_2xx1F11 (F:38-155)
2f: PFAM_Cu_oxidase_3_2xx1F12 (F:38-155)
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Clans
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)
(
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(
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(
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Organisms
(
)
(
)
Clan
:
CU_oxidase
(192)
Family
:
Cu-oxidase
(74)
Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)
(20)
1a
Cu-oxidase-2xx1F01
F:168-320
1b
Cu-oxidase-2xx1F02
F:168-320
1c
Cu-oxidase-2xx1F03
F:168-320
1d
Cu-oxidase-2xx1F04
F:168-320
1e
Cu-oxidase-2xx1F05
F:168-320
1f
Cu-oxidase-2xx1F06
F:168-320
Family
:
Cu-oxidase_3
(79)
Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)
(20)
2a
Cu-oxidase_3-2xx1F07
F:38-155
2b
Cu-oxidase_3-2xx1F08
F:38-155
2c
Cu-oxidase_3-2xx1F09
F:38-155
2d
Cu-oxidase_3-2xx1F10
F:38-155
2e
Cu-oxidase_3-2xx1F11
F:38-155
2f
Cu-oxidase_3-2xx1F12
F:38-155
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