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1GQ1
Asym. Unit
Info
Asym.Unit (215 KB)
Biol.Unit 1 (208 KB)
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(1)
Title
:
CYTOCHROME CD1 NITRITE REDUCTASE, Y25S MUTANT, OXIDISED FORM
Authors
:
T. Sjogren, E. H. J. Gordon, M. Lofqvist, C. D. Richter, J. Hajdu, S. J. Ferguson
Date
:
19 Nov 01 (Deposition) - 28 Nov 02 (Release) - 19 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Reductase, Enzyme, Nitrite Reductase, Oxidoreductase, Denitrification, Electron Transport, Periplasmic
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. H. J. Gordon, T. Sjogren, M. Lofqvist, C. D. Richter, J. Allen, C. Higham, J. Hajdu, V. Fulop, S. J. Ferguson
Structure And Kinetic Properties Of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase With The D1 Heme Active Site Ligand Tyrosine 25 Replaced By Serine
J. Biol. Chem. V. 278 11773 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 15)
Info
All Hetero Components
1a: HEME D (DHEa)
1b: HEME D (DHEb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: HEME C (HECa)
3b: HEME C (HECb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DHE
2
Ligand/Ion
HEME D
2
GOL
3
Ligand/Ion
GLYCEROL
3
HEC
2
Ligand/Ion
HEME C
4
SO4
8
Ligand/Ion
SULFATE ION
[
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]
Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:345 , HIS A:388 , DHE A:602 , HOH A:2421 , HOH A:2639
BINDING SITE FOR RESIDUE SO4 A 603
02
AC2
SOFTWARE
ASP A:290 , GLU A:291 , GLN A:292 , HOH A:2643 , MET B:139
BINDING SITE FOR RESIDUE SO4 A 621
03
AC3
SOFTWARE
GLN A:35 , LYS A:237 , SER A:240 , HOH A:2645 , HOH A:2646 , HOH A:2647 , HOH A:2648
BINDING SITE FOR RESIDUE SO4 A 622
04
AC4
SOFTWARE
HIS B:345 , HIS B:388 , DHE B:602 , HOH B:2470 , HOH B:2688
BINDING SITE FOR RESIDUE SO4 B 603
05
AC5
SOFTWARE
TYR B:308 , ARG B:354 , LYS B:372 , HOH B:2691 , HOH B:2692 , HOH B:2693 , HOH B:2694
BINDING SITE FOR RESIDUE SO4 B 621
06
AC6
SOFTWARE
ASN B:31 , GLN B:35 , LYS B:237 , SER B:240 , HOH B:2695 , HOH B:2696 , HOH B:2697 , HOH B:2698
BINDING SITE FOR RESIDUE SO4 B 622
07
AC7
SOFTWARE
PHE B:395 , VAL B:396 , PRO B:449 , HOH B:2510 , HOH B:2569 , HOH B:2699 , HOH B:2700 , HOH B:2701 , HOH B:2702 , HOH B:2703
BINDING SITE FOR RESIDUE SO4 B 623
08
AC8
SOFTWARE
GLY B:439 , GLY B:440 , ASN B:461 , ILE B:466 , HOH B:2562 , HOH B:2581 , HOH B:2704 , HOH B:2705 , HOH B:2706
BINDING SITE FOR RESIDUE SO4 B 624
09
AC9
SOFTWARE
ASP A:16 , HIS A:17 , ASN A:23 , ARG A:64 , CYS A:65 , CYS A:68 , HIS A:69 , GLY A:78 , LYS A:79 , LEU A:81 , LEU A:89 , TYR A:93 , LEU A:94 , PHE A:97 , SER A:102 , PRO A:103 , HOH A:2111 , HOH A:2114 , HOH A:2634
BINDING SITE FOR RESIDUE HEC A 601
10
BC1
SOFTWARE
SER A:25 , PRO A:27 , SER A:28 , MET A:106 , TRP A:109 , ARG A:174 , HIS A:200 , ILE A:201 , ARG A:203 , ARG A:216 , ARG A:243 , SER A:244 , TYR A:263 , ALA A:302 , ILE A:303 , HIS A:345 , ARG A:391 , PHE A:444 , GLN A:507 , TRP A:522 , THR A:554 , GLY A:555 , PHE A:557 , SO4 A:603 , HOH A:2018 , HOH A:2304 , HOH A:2309 , HOH A:2331 , HOH A:2635 , HOH A:2636 , HOH A:2637 , HOH A:2638
BINDING SITE FOR RESIDUE DHE A 602
11
BC2
SOFTWARE
ASP B:16 , HIS B:17 , ASN B:23 , ARG B:64 , CYS B:65 , CYS B:68 , HIS B:69 , GLY B:78 , LYS B:79 , LEU B:81 , LEU B:89 , TYR B:93 , LEU B:94 , PHE B:97 , SER B:102 , PRO B:103 , MET B:123 , HOH B:2145 , HOH B:2682 , HOH B:2683
BINDING SITE FOR RESIDUE HEC B 601
12
BC3
SOFTWARE
SER B:25 , PRO B:27 , SER B:28 , MET B:106 , TRP B:109 , ARG B:174 , HIS B:200 , ILE B:201 , ARG B:203 , ARG B:216 , ARG B:243 , SER B:244 , TYR B:263 , ALA B:302 , ILE B:303 , HIS B:345 , ARG B:391 , PHE B:444 , GLN B:507 , THR B:554 , GLY B:555 , PHE B:557 , SO4 B:603 , HOH B:2029 , HOH B:2345 , HOH B:2347 , HOH B:2380 , HOH B:2684 , HOH B:2685 , HOH B:2686 , HOH B:2687
BINDING SITE FOR RESIDUE DHE B 602
13
BC4
SOFTWARE
ASN A:23 , ARG A:24 , SER A:25 , GLU A:26 , PRO A:27 , GLU A:63 , ARG A:64 , THR A:111 , HOH A:2640 , HOH A:2641
BINDING SITE FOR RESIDUE GOL A 611
14
BC5
SOFTWARE
PHE A:395 , VAL A:396 , PRO A:449 , SER A:451 , ILE A:475 , HOH A:2509 , HOH A:2642
BINDING SITE FOR RESIDUE GOL A 612
15
BC6
SOFTWARE
ASN B:23 , ARG B:24 , SER B:25 , GLU B:26 , PRO B:27 , GLU B:63 , ARG B:64 , ALA B:104 , THR B:111 , HOH B:2689 , HOH B:2690
BINDING SITE FOR RESIDUE GOL B 611
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: CYTC (A:52-131,B:52-131)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
NIRS_PARPN
81-160
2
A:52-131
B:52-131
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1gq1a1 (A:9-133)
1b: SCOP_d1gq1b1 (B:9-133)
2a: SCOP_d1gq1a2 (A:134-567)
2b: SCOP_d1gq1b2 (B:134-567)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
(22)
Protein domain
:
N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
(22)
Paracoccus pantotrophus [TaxId: 82367]
(11)
1a
d1gq1a1
A:9-133
1b
d1gq1b1
B:9-133
Class
:
All beta proteins
(24004)
Fold
:
8-bladed beta-propeller
(135)
Superfamily
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Family
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Protein domain
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Paracoccus pantotrophus [TaxId: 82367]
(11)
2a
d1gq1a2
A:134-567
2b
d1gq1b2
B:134-567
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1gq1A01 (A:36-135)
1b: CATH_1gq1B01 (B:36-135)
2a: CATH_1gq1A02 (A:136-567)
2b: CATH_1gq1B02 (B:136-567)
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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)
Paracoccus pantotrophus. Organism_taxid: 82367.
(2)
1a
1gq1A01
A:36-135
1b
1gq1B01
B:36-135
Class
:
Mainly Beta
(13760)
Architecture
:
8 Propellor
(110)
Topology
:
Methanol Dehydrogenase; Chain A
(110)
Homologous Superfamily
:
[code=2.140.10.20, no name defined]
(22)
Paracoccus pantotrophus. Organism_taxid: 82367.
(1)
2a
1gq1A02
A:136-567
2b
1gq1B02
B:136-567
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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