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2RDZ
Biol. Unit 2
Info
Asym.Unit (362 KB)
Biol.Unit 1 (178 KB)
Biol.Unit 2 (176 KB)
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(1)
Title
:
HIGH RESOLUTION CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI CYTOCHROME C NITRITE REDUCTASE.
Authors
:
T. A. Clarke, A. M. Hemmings, D. J. Richardson
Date
:
25 Sep 07 (Deposition) - 25 Mar 08 (Release) - 24 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.74
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Decaheme, Reductase, Electron Transport, Iron, Metal-Binding, Oxidoreductase, Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. A. Clarke, G. L. Kemp, J. H. Wonderen, R. M. Doyle, J. A. Cole, N. Tovell, M. R. Cheesman, J. N. Butt, D. J. Richardson, A. M. Hemmings
Role Of A Conserved Glutamine Residue In Tuning The Catalytic Activity Of Escherichia Coli Cytochrome C Nitrite Reductase.
Biochemistry V. 47 3789 2008
[
close entry info
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Hetero Components
(3, 26)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: HEME C (HECa)
3b: HEME C (HECb)
3c: HEME C (HECc)
3d: HEME C (HECd)
3e: HEME C (HECe)
3f: HEME C (HECf)
3g: HEME C (HECg)
3h: HEME C (HECh)
3i: HEME C (HECi)
3j: HEME C (HECj)
3k: HEME C (HECk)
3l: HEME C (HECl)
3m: HEME C (HECm)
3n: HEME C (HECn)
3o: HEME C (HECo)
3p: HEME C (HECp)
3q: HEME C (HECq)
3r: HEME C (HECr)
3s: HEME C (HECs)
3t: HEME C (HECt)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
EDO
14
Ligand/Ion
1,2-ETHANEDIOL
3
HEC
10
Ligand/Ion
HEME C
4
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(30, 30)
Info
All Sites
01: DC4 (SOFTWARE)
02: DC5 (SOFTWARE)
03: DC6 (SOFTWARE)
04: DC7 (SOFTWARE)
05: DC8 (SOFTWARE)
06: DC9 (SOFTWARE)
07: EC1 (SOFTWARE)
08: EC2 (SOFTWARE)
09: EC3 (SOFTWARE)
10: EC4 (SOFTWARE)
11: EC5 (SOFTWARE)
12: EC6 (SOFTWARE)
13: EC7 (SOFTWARE)
14: EC8 (SOFTWARE)
15: EC9 (SOFTWARE)
16: FC1 (SOFTWARE)
17: FC2 (SOFTWARE)
18: FC3 (SOFTWARE)
19: FC4 (SOFTWARE)
20: FC5 (SOFTWARE)
21: FC6 (SOFTWARE)
22: FC7 (SOFTWARE)
23: FC8 (SOFTWARE)
24: FC9 (SOFTWARE)
25: GC1 (SOFTWARE)
26: GC2 (SOFTWARE)
27: GC3 (SOFTWARE)
28: GC4 (SOFTWARE)
29: GC5 (SOFTWARE)
30: GC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
DC4
SOFTWARE
GLU C:215 , TYR C:216 , LYS C:261 , GLN C:263 , HOH C:495 , HOH C:514
BINDING SITE FOR RESIDUE CA C1501
02
DC5
SOFTWARE
HEC C:3 , HEC C:4 , PRO C:91 , HOH C:609 , HOH C:712 , HOH C:769
BINDING SITE FOR RESIDUE CA C1502
03
DC6
SOFTWARE
HEC C:3 , TYR C:88 , ASN C:89 , ASP C:100 , THR C:104 , ARG C:106 , LEU C:118 , CYS C:122 , CYS C:125 , LYS C:126 , CYS C:212 , HIS C:213 , TYR C:216 , PHE C:218 , VAL C:225 , HIS C:264 , HIS C:388 , HOH C:486 , HOH C:491 , HOH C:505 , HOH C:507 , HOH C:517 , HOH C:518 , HOH C:522 , HOH C:558
BINDING SITE FOR RESIDUE HEC C 1
04
DC7
SOFTWARE
HEC C:3 , HIS C:49 , GLN C:52 , TYR C:53 , TRP C:56 , GLY C:159 , CYS C:160 , CYS C:163 , HIS C:164 , PHE C:171 , GLY C:174 , PRO C:176 , ARG C:201 , GLN C:205 , ILE C:283 , LYS C:289 , TYR C:298 , THR C:299 , HIS C:301 , HOH C:542 , HOH C:630
BINDING SITE FOR RESIDUE HEC C 2
05
DC8
SOFTWARE
HEC C:1 , HEC C:2 , HEC C:4 , GLN C:62 , PRO C:91 , ARG C:92 , GLY C:93 , HIS C:94 , PHE C:96 , ALA C:97 , ASP C:100 , CYS C:125 , LEU C:158 , VAL C:208 , CYS C:209 , CYS C:212 , HIS C:213 , HIS C:286 , MET C:287 , ILE C:303 , HOH C:640 , HOH C:712 , CA C:1502
BINDING SITE FOR RESIDUE HEC C 3
06
DC9
SOFTWARE
HEC C:3 , HEC C:5 , HIS C:213 , GLU C:266 , TRP C:270 , HIS C:275 , VAL C:280 , THR C:281 , CYS C:282 , CYS C:285 , HIS C:286 , ASN C:305 , PRO C:306 , VAL C:329 , HIS C:388 , HIS C:391 , MET C:392 , HIS C:393 , HOH C:578 , HOH C:660 , HOH C:674 , HOH C:769 , HOH C:884 , HOH C:963 , CA C:1502
BINDING SITE FOR RESIDUE HEC C 4
07
EC1
SOFTWARE
HEC C:4 , EDO C:12 , ILE C:274 , HIS C:275 , VAL C:280 , ASP C:284 , PHE C:307 , THR C:313 , CYS C:314 , CYS C:317 , HIS C:318 , ARG C:332 , MET C:392 , HOH C:493 , HOH C:500 , HEC D:5 , HIS D:318 , GLN D:320
BINDING SITE FOR RESIDUE HEC C 5
08
EC2
SOFTWARE
PHE C:307 , ASP C:308 , ASN C:309 , PHE C:310 , ALA C:311 , LYS C:322
BINDING SITE FOR RESIDUE SO4 C2001
09
EC3
SOFTWARE
MET C:233 , LYS C:234 , VAL C:235 , GLU C:268 , GLU C:397 , HOH C:508
BINDING SITE FOR RESIDUE EDO C 481
10
EC4
SOFTWARE
HEC C:5 , ILE C:274 , ARG C:332 , HEC D:5 , ILE D:274 , ARG D:332
BINDING SITE FOR RESIDUE EDO C 12
11
EC5
SOFTWARE
ASP C:407 , LYS C:408 , ASP C:411 , HOH C:889
BINDING SITE FOR RESIDUE EDO C 21
12
EC6
SOFTWARE
ASP C:411 , LYS C:415 , ARG C:418 , HOH C:681 , ARG D:413 , HOH D:639
BINDING SITE FOR RESIDUE EDO C 22
13
EC7
SOFTWARE
CYS C:285 , HIS C:286 , LYS C:302 , GLY C:304 , ASN C:305 , PRO C:306 , ASN C:309 , HOH C:759
BINDING SITE FOR RESIDUE EDO C 23
14
EC8
SOFTWARE
ASP C:345 , ILE C:431 , ILE C:434 , HOH C:529 , HOH C:689 , HOH C:807
BINDING SITE FOR RESIDUE EDO C 25
15
EC9
SOFTWARE
GLU D:215 , TYR D:216 , LYS D:261 , GLN D:263 , HOH D:497 , HOH D:520
BINDING SITE FOR RESIDUE CA D1501
16
FC1
SOFTWARE
HEC D:3 , HEC D:4 , PRO D:91 , HOH D:707 , HOH D:758
BINDING SITE FOR RESIDUE CA D1502
17
FC2
SOFTWARE
HEC D:3 , TYR D:88 , ASN D:89 , PRO D:91 , ASP D:100 , THR D:104 , ARG D:106 , LEU D:118 , CYS D:122 , CYS D:125 , LYS D:126 , CYS D:212 , HIS D:213 , TYR D:216 , VAL D:225 , HIS D:264 , HIS D:388 , HOH D:487 , HOH D:489 , HOH D:490 , HOH D:492 , HOH D:511 , HOH D:523 , HOH D:529 , HOH D:542 , HOH D:555
BINDING SITE FOR RESIDUE HEC D 1
18
FC3
SOFTWARE
HEC D:3 , HIS D:49 , GLN D:52 , TYR D:53 , TRP D:56 , GLY D:159 , CYS D:160 , CYS D:163 , HIS D:164 , PHE D:171 , GLY D:174 , ARG D:201 , GLN D:205 , ILE D:283 , MET D:287 , LYS D:289 , TYR D:298 , THR D:299 , HIS D:301 , HOH D:585 , HOH D:612
BINDING SITE FOR RESIDUE HEC D 2
19
FC4
SOFTWARE
HEC D:1 , HEC D:2 , HEC D:4 , GLN D:62 , PRO D:91 , ARG D:92 , GLY D:93 , HIS D:94 , PHE D:96 , ALA D:97 , ASP D:100 , CYS D:125 , LYS D:126 , LEU D:158 , VAL D:208 , CYS D:209 , CYS D:212 , HIS D:213 , HIS D:286 , MET D:287 , ILE D:303 , HOH D:522 , HOH D:707 , HOH D:776 , CA D:1502
BINDING SITE FOR RESIDUE HEC D 3
20
FC5
SOFTWARE
HEC D:3 , HEC D:5 , HIS D:213 , GLU D:266 , TRP D:270 , HIS D:275 , VAL D:280 , THR D:281 , CYS D:282 , CYS D:285 , HIS D:286 , ASN D:305 , PRO D:306 , VAL D:329 , HIS D:391 , MET D:392 , HIS D:393 , HOH D:604 , HOH D:659 , HOH D:681 , HOH D:700 , HOH D:709 , HOH D:738 , HOH D:779 , CA D:1502
BINDING SITE FOR RESIDUE HEC D 4
21
FC6
SOFTWARE
HEC C:5 , EDO C:12 , HIS C:318 , GLN C:320 , HEC D:4 , ILE D:274 , HIS D:275 , VAL D:280 , PRO D:306 , PHE D:307 , THR D:313 , CYS D:314 , CYS D:317 , HIS D:318 , ARG D:332 , MET D:392 , HOH D:525 , HOH D:550 , HOH D:567 , HOH D:667
BINDING SITE FOR RESIDUE HEC D 5
22
FC7
SOFTWARE
PHE D:307 , ASP D:308 , ASN D:309 , PHE D:310 , ALA D:311 , LYS D:322
BINDING SITE FOR RESIDUE SO4 D2001
23
FC8
SOFTWARE
ARG D:65 , ASN D:89 , ARG D:92 , ASP D:100 , HOH D:614 , HOH D:1029
BINDING SITE FOR RESIDUE EDO D 481
24
FC9
SOFTWARE
ARG C:413 , HOH C:554 , HOH C:622 , THR D:414 , LYS D:415 , ARG D:418
BINDING SITE FOR RESIDUE EDO D 482
25
GC1
SOFTWARE
MET D:233 , LYS D:234 , VAL D:235 , GLU D:268 , GLU D:397 , HOH D:623 , HOH D:1011
BINDING SITE FOR RESIDUE EDO D 6
26
GC2
SOFTWARE
SER D:55 , TYR D:298 , ASP D:300 , LYS D:302 , HOH D:689 , HOH D:928 , HOH D:995
BINDING SITE FOR RESIDUE EDO D 21
27
GC3
SOFTWARE
GLY D:81 , TYR D:82 , PRO D:83 , ARG D:86 , LEU D:446 , HOH D:528 , HOH D:642
BINDING SITE FOR RESIDUE EDO D 22
28
GC4
SOFTWARE
ASP D:345 , VAL D:348 , HIS D:349 , HOH D:730
BINDING SITE FOR RESIDUE EDO D 23
29
GC5
SOFTWARE
MET D:120 , ASP D:137 , GLY D:141 , TYR D:142 , HIS D:144 , ARG D:149 , HOH D:512
BINDING SITE FOR RESIDUE EDO D 24
30
GC6
SOFTWARE
THR A:436 , HOH A:753 , HOH C:646 , GLU D:236 , GLU D:239 , ARG D:380 , HOH D:510 , HOH D:649 , HOH D:1035
BINDING SITE FOR RESIDUE EDO D 25
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (C:155-323,D:155-323)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
NRFA_ECOLI
155-323
2
-
-
C:155-323
D:155-323
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2rdza_ (A:)
1b: SCOP_d2rdzb_ (B:)
1c: SCOP_d2rdzc_ (C:)
1d: SCOP_d2rdzd_ (D:)
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Organisms
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Class
:
All alpha proteins
(14657)
Fold
:
Multiheme cytochromes
(149)
Superfamily
:
Multiheme cytochromes
(149)
Family
:
Di-heme elbow motif
(53)
Protein domain
:
automated matches
(16)
Escherichia coli [TaxId: 562]
(2)
1a
d2rdza_
A:
1b
d2rdzb_
B:
1c
d2rdzc_
C:
1d
d2rdzd_
D:
[
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cytochrom_C552_2rdzD01 (D:41-474)
1b: PFAM_Cytochrom_C552_2rdzD02 (D:41-474)
1c: PFAM_Cytochrom_C552_2rdzD03 (D:41-474)
1d: PFAM_Cytochrom_C552_2rdzD04 (D:41-474)
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Clan
:
Multiheme_cytos
(34)
Family
:
Cytochrom_C552
(6)
Escherichia coli (strain K12)
(3)
1a
Cytochrom_C552-2rdzD01
D:41-474
1b
Cytochrom_C552-2rdzD02
D:41-474
1c
Cytochrom_C552-2rdzD03
D:41-474
1d
Cytochrom_C552-2rdzD04
D:41-474
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