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2RF7
Asym. Unit
Info
Asym.Unit (350 KB)
Biol.Unit 1 (173 KB)
Biol.Unit 2 (172 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI NRFA MUTANT Q263E
Authors
:
T. A. Clarke, D. J. Richardson, A. M. Hemmings
Date
:
28 Sep 07 (Deposition) - 25 Mar 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.04
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Oxidoreductase, Calcium Ligand, Electron Transport, Heme, Iron, Metal-Binding, Periplasm, 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
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 43)
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)
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)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
3
HEC
20
Ligand/Ion
HEME C
[
close Hetero Component info
]
Sites
(43, 43)
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)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:215 , TYR A:216 , LYS A:261 , GLU A:263 , HOH A:516 , HOH A:535
BINDING SITE FOR RESIDUE CA A 1501
02
AC2
SOFTWARE
HEC A:3 , HEC A:4 , PRO A:91
BINDING SITE FOR RESIDUE CA A 1502
03
AC3
SOFTWARE
GLU B:215 , TYR B:216 , LYS B:261 , GLU B:263 , HOH B:494 , HOH B:583
BINDING SITE FOR RESIDUE CA B 1501
04
AC4
SOFTWARE
HEC B:3 , HEC B:4 , PRO B:91
BINDING SITE FOR RESIDUE CA B 1502
05
AC5
SOFTWARE
GLU C:215 , TYR C:216 , LYS C:261 , GLU C:263 , HOH C:886 , HOH C:913
BINDING SITE FOR RESIDUE CA C 1501
06
AC6
SOFTWARE
HEC C:3 , HEC C:4 , PRO C:91
BINDING SITE FOR RESIDUE CA C 1502
07
AC7
SOFTWARE
GLU D:215 , TYR D:216 , LYS D:261 , GLU D:263 , HOH D:507 , HOH D:666
BINDING SITE FOR RESIDUE CA D 1501
08
AC8
SOFTWARE
HEC D:3 , HEC D:4 , PRO D:91
BINDING SITE FOR RESIDUE CA D 1502
09
AC9
SOFTWARE
HEC A:3 , TYR A:88 , ASN A:89 , ASP A:100 , THR A:104 , ARG A:106 , LEU A:118 , CYS A:122 , CYS A:125 , LYS A:126 , CYS A:212 , HIS A:213 , TYR A:216 , VAL A:225 , HIS A:264 , HIS A:388 , HOH A:490 , HOH A:493 , HOH A:506 , HOH A:515 , HOH A:521 , HOH A:542 , HOH A:575 , HOH A:879 , HOH A:880
BINDING SITE FOR RESIDUE HEC A 1
10
BC1
SOFTWARE
HEC A:3 , HIS A:49 , GLN A:52 , TRP A:56 , GLY A:159 , CYS A:160 , CYS A:163 , HIS A:164 , PHE A:171 , GLY A:174 , ARG A:201 , GLN A:205 , ILE A:283 , LYS A:289 , TYR A:298 , THR A:299 , HIS A:301 , HOH A:705 , HOH A:727 , HOH A:844
BINDING SITE FOR RESIDUE HEC A 2
11
BC2
SOFTWARE
HEC A:1 , HEC A:2 , GLN A:62 , PRO A:91 , ARG A:92 , GLY A:93 , HIS A:94 , PHE A:96 , ALA A:97 , ASP A:100 , CYS A:125 , LEU A:158 , VAL A:208 , CYS A:209 , CYS A:212 , HIS A:213 , HIS A:286 , MET A:287 , ILE A:303 , HOH A:518 , HOH A:821 , CA A:1502
BINDING SITE FOR RESIDUE HEC A 3
12
BC3
SOFTWARE
HEC A:5 , HIS A:213 , GLU A:266 , TRP A:270 , HIS A:275 , VAL A:280 , THR A:281 , CYS A:282 , CYS A:285 , HIS A:286 , ASN A:305 , PRO A:306 , PHE A:307 , VAL A:329 , HIS A:391 , MET A:392 , HIS A:393 , HOH A:553 , HOH A:688 , HOH A:710 , HOH A:753 , HOH A:799 , HOH A:800 , CA A:1502
BINDING SITE FOR RESIDUE HEC A 4
13
BC4
SOFTWARE
HEC A:4 , ILE A:274 , HIS A:275 , VAL A:280 , PHE A:307 , THR A:313 , CYS A:314 , CYS A:317 , HIS A:318 , ARG A:332 , MET A:392 , HOH A:618 , HOH A:641 , HOH A:810 , HEC B:5 , HIS B:318 , GLN B:320 , HOH B:721
BINDING SITE FOR RESIDUE HEC A 5
14
BC5
SOFTWARE
PHE A:307 , ASP A:308 , ASN A:309 , PHE A:310 , ALA A:311 , LYS A:322 , HOH A:915
BINDING SITE FOR RESIDUE EDO A 480
15
BC6
SOFTWARE
MET A:233 , LYS A:234 , VAL A:235 , GLU A:268 , GLU A:397 , MET A:401 , HOH A:525
BINDING SITE FOR RESIDUE EDO A 7
16
BC7
SOFTWARE
ASP A:411 , THR A:414 , LYS A:415 , ARG A:418 , HOH A:751 , HOH A:850 , ARG B:413
BINDING SITE FOR RESIDUE EDO A 10
17
BC8
SOFTWARE
HEC B:3 , TYR B:88 , ASN B:89 , ASP B:100 , THR B:104 , ARG B:106 , CYS B:122 , CYS B:125 , LYS B:126 , CYS B:212 , HIS B:213 , TYR B:216 , HIS B:264 , HIS B:388 , HOH B:482 , HOH B:486 , HOH B:487 , HOH B:490 , HOH B:491 , HOH B:493 , HOH B:546 , HOH B:924 , HOH B:925
BINDING SITE FOR RESIDUE HEC B 1
18
BC9
SOFTWARE
HEC B:3 , HIS B:49 , GLN B:52 , TRP B:56 , GLY B:159 , CYS B:160 , CYS B:163 , HIS B:164 , PHE B:171 , GLY B:174 , ARG B:201 , GLN B:205 , ILE B:283 , LYS B:289 , TYR B:298 , THR B:299 , HIS B:301 , HOH B:552 , HOH B:578
BINDING SITE FOR RESIDUE HEC B 2
19
CC1
SOFTWARE
HEC B:1 , HEC B:2 , HEC B:4 , GLN B:62 , PRO B:91 , ARG B:92 , GLY B:93 , HIS B:94 , PHE B:96 , ALA B:97 , ASP B:100 , CYS B:125 , LEU B:158 , VAL B:208 , CYS B:209 , CYS B:212 , HIS B:213 , HIS B:286 , MET B:287 , ILE B:303 , HOH B:500 , HOH B:665 , CA B:1502
BINDING SITE FOR RESIDUE HEC B 3
20
CC2
SOFTWARE
HEC B:3 , HEC B:5 , CYS B:209 , HIS B:213 , GLU B:266 , TRP B:270 , HIS B:275 , VAL B:280 , THR B:281 , CYS B:282 , CYS B:285 , HIS B:286 , ASN B:305 , PRO B:306 , PHE B:307 , VAL B:329 , HIS B:388 , HIS B:391 , MET B:392 , HIS B:393 , HOH B:527 , HOH B:615 , HOH B:641 , HOH B:695 , HOH B:748 , HOH B:809 , CA B:1502
BINDING SITE FOR RESIDUE HEC B 4
21
CC3
SOFTWARE
HEC A:5 , ILE A:274 , HIS A:318 , GLN A:320 , HEC B:4 , EDO B:15 , ILE B:274 , HIS B:275 , VAL B:280 , ASP B:284 , PHE B:307 , THR B:313 , CYS B:314 , CYS B:317 , HIS B:318 , ARG B:332 , MET B:392 , HOH B:659 , HOH B:685
BINDING SITE FOR RESIDUE HEC B 5
22
CC4
SOFTWARE
PHE B:307 , ASP B:308 , PHE B:310 , ALA B:311 , LYS B:322
BINDING SITE FOR RESIDUE EDO B 480
23
CC5
SOFTWARE
LYS A:198 , GLU B:197 , GLN B:204 , HOH B:662
BINDING SITE FOR RESIDUE EDO B 481
24
CC6
SOFTWARE
MET B:233 , LYS B:234 , VAL B:235 , GLU B:397 , MET B:401 , HOH B:598
BINDING SITE FOR RESIDUE EDO B 6
25
CC7
SOFTWARE
THR B:99 , ARG B:102 , ASN B:157 , GLU B:467 , HOH B:679 , HOH B:853
BINDING SITE FOR RESIDUE EDO B 8
26
CC8
SOFTWARE
ALA B:246 , SER B:248 , PRO B:258 , HOH B:645
BINDING SITE FOR RESIDUE EDO B 12
27
CC9
SOFTWARE
SER B:55 , TYR B:298 , ASP B:300 , HOH B:716 , HOH B:878 , HOH B:892
BINDING SITE FOR RESIDUE EDO B 14
28
DC1
SOFTWARE
HEC B:5 , ASP B:284 , ASN B:316 , HOH B:676 , HOH C:1087
BINDING SITE FOR RESIDUE EDO B 15
29
DC2
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 , HIS C:264 , HIS C:388 , HOH C:863 , HOH C:865 , HOH C:866 , HOH C:887 , HOH C:893 , HOH C:894 , HOH C:905 , HOH C:1329 , HOH C:1330
BINDING SITE FOR RESIDUE HEC C 1
30
DC3
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 , ARG C:201 , GLN C:205 , ILE C:283 , LYS C:289 , TYR C:298 , THR C:299 , HIS C:301 , HOH C:933 , HOH C:953
BINDING SITE FOR RESIDUE HEC C 2
31
DC4
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:875 , HOH C:916 , CA C:1502
BINDING SITE FOR RESIDUE HEC C 3
32
DC5
SOFTWARE
HEC C:3 , HEC C:5 , HIS C:213 , 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 , PHE C:307 , HIS C:388 , HIS C:391 , MET C:392 , HIS C:393 , HOH C:975 , HOH C:1060 , HOH C:1300 , HOH C:1309 , CA C:1502
BINDING SITE FOR RESIDUE HEC C 4
33
DC6
SOFTWARE
HEC C:4 , ILE C:274 , HIS C:275 , ASN C:278 , VAL C:280 , THR C:313 , CYS C:314 , CYS C:317 , HIS C:318 , ARG C:332 , MET C:392 , HOH C:1118 , HEC D:5 , ILE D:274 , HIS D:318 , GLN D:320
BINDING SITE FOR RESIDUE HEC C 5
34
DC7
SOFTWARE
MET C:233 , LYS C:234 , VAL C:235 , GLU C:268 , GLU C:397 , MET C:401 , HOH C:944
BINDING SITE FOR RESIDUE EDO C 9
35
DC8
SOFTWARE
ASP C:411 , THR C:414 , LYS C:415 , ARG C:418 , HOH C:1014 , HOH C:1084 , ARG D:413
BINDING SITE FOR RESIDUE EDO C 11
36
DC9
SOFTWARE
ALA C:311 , ALA C:315
BINDING SITE FOR RESIDUE EDO C 13
37
EC1
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 , ALA D:121 , CYS D:122 , CYS D:125 , LYS D:126 , CYS D:212 , HIS D:213 , TYR D:216 , HIS D:264 , HIS D:388 , HOH D:485 , HOH D:489 , HOH D:490 , HOH D:498 , HOH D:499 , HOH D:526 , HOH D:543 , HOH D:760 , HOH D:761
BINDING SITE FOR RESIDUE HEC D 1
38
EC2
SOFTWARE
HIS D:49 , GLN D:52 , TRP D:56 , GLY D:159 , CYS D:160 , CYS D:163 , HIS D:164 , GLY D:174 , PRO D:176 , LEU D:178 , ARG D:201 , GLN D:205 , ILE D:283 , LYS D:289 , TYR D:298 , THR D:299 , HIS D:301 , ILE D:303
BINDING SITE FOR RESIDUE HEC D 2
39
EC3
SOFTWARE
HEC D:1 , 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 , CA D:1502
BINDING SITE FOR RESIDUE HEC D 3
40
EC4
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 , HIS D:388 , HIS D:391 , MET D:392 , HIS D:393 , HOH D:534 , HOH D:702 , CA D:1502
BINDING SITE FOR RESIDUE HEC D 4
41
EC5
SOFTWARE
HEC C:5 , ILE C:274 , HIS C:318 , GLN C:320 , HEC D:4 , HIS D:275 , PHE D:307 , THR D:313 , CYS D:314 , CYS D:317 , HIS D:318 , ARG D:332 , MET D:392 , HOH D:619 , HOH D:682 , HOH D:748
BINDING SITE FOR RESIDUE HEC D 5
42
EC6
SOFTWARE
PHE D:307 , ASP D:308 , ASN D:309 , PHE D:310 , ALA D:311 , LYS D:322 , HOH D:786
BINDING SITE FOR RESIDUE EDO D 480
43
EC7
SOFTWARE
ARG C:413 , HOH C:1034 , ASP D:411 , THR D:414 , LYS D:415 , ARG D:418 , HOH D:785
BINDING SITE FOR RESIDUE EDO D 481
[
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (A:155-323,B:155-323,C:155-323,D:15...)
;
View:
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
NRFA_ECOLI
155-323
4
A:155-323
B:155-323
C:155-323
D:155-323
[
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2rf7a_ (A:)
1b: SCOP_d2rf7b_ (B:)
1c: SCOP_d2rf7c_ (C:)
1d: SCOP_d2rf7d_ (D:)
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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
:
Cytochrome c nitrite reductase
(7)
Escherichia coli K-12 [TaxId: 83333]
(1)
1a
d2rf7a_
A:
1b
d2rf7b_
B:
1c
d2rf7c_
C:
1d
d2rf7d_
D:
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CATH Domains
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cytochrom_C552_2rf7D01 (D:41-474)
1b: PFAM_Cytochrom_C552_2rf7D02 (D:41-474)
1c: PFAM_Cytochrom_C552_2rf7D03 (D:41-474)
1d: PFAM_Cytochrom_C552_2rf7D04 (D:41-474)
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Clan
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Multiheme_cytos
(34)
Family
:
Cytochrom_C552
(6)
Escherichia coli (strain K12)
(3)
1a
Cytochrom_C552-2rf7D01
D:41-474
1b
Cytochrom_C552-2rf7D02
D:41-474
1c
Cytochrom_C552-2rf7D03
D:41-474
1d
Cytochrom_C552-2rf7D04
D:41-474
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select residue range 5 to 10 in chain 'A'
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