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2NYA
Biol. Unit 2
Info
Asym.Unit (283 KB)
Biol.Unit 1 (142 KB)
Biol.Unit 2 (140 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PERIPLASMIC NITRATE REDUCTASE (NAP) FROM ESCHERICHIA COLI
Authors
:
B. J. N. Jepson, D. J. Richardson, A. M. Hemmings
Date
:
20 Nov 06 (Deposition) - 05 Dec 06 (Release) - 24 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,F
Biol. Unit 1: A (1x)
Biol. Unit 2: F (1x)
Keywords
:
Molybdenum, Nitrate Reductase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. J. Jepson, S. Mohan, T. A. Clarke, A. J. Gates, J. A. Cole, C. S. Butler, J. N. Butt, A. M. Hemmings, D. J. Richardson
Spectropotentiometric And Structural Analysis Of The Periplasmic Nitrate Reductase From Escherichia Coli
J. Biol. Chem. V. 282 6425 2007
(for further references see the
PDB file header
)
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: MOLYBDENUM(VI) ION (6MOa)
1b: MOLYBDENUM(VI) ION (6MOb)
2a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
2b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
2c: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDc)
2d: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDd)
3a: IRON/SULFUR CLUSTER (SF4a)
3b: IRON/SULFUR CLUSTER (SF4b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
6MO
1
Ligand/Ion
MOLYBDENUM(VI) ION
2
MGD
2
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
3
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(4, 4)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
CYS F:10 , PHE F:12 , CYS F:13 , CYS F:17 , CYS F:45 , LYS F:47 , GLY F:48 , PRO F:185
BINDING SITE FOR RESIDUE SF4 F 5001
2
AC6
SOFTWARE
CYS F:143 , MGD F:6001 , MGD F:7001 , HOH F:7035
BINDING SITE FOR RESIDUE 6MO F 5002
3
AC7
SOFTWARE
ARG F:11 , GLN F:114 , ASN F:139 , CYS F:143 , GLN F:340 , GLN F:374 , CYS F:444 , THR F:445 , ASN F:446 , ALA F:450 , SER F:472 , ASP F:473 , PRO F:474 , THR F:477 , THR F:489 , ALA F:490 , MET F:491 , LYS F:495 , ASP F:522 , THR F:682 , GLY F:683 , ARG F:684 , TRP F:689 , HIS F:690 , THR F:691 , SER F:693 , PHE F:758 , ASN F:766 , PHE F:782 , LYS F:783 , 6MO F:5002 , MGD F:7001 , HOH F:7064 , HOH F:7242
BINDING SITE FOR RESIDUE MGD F 6001
4
AC8
SOFTWARE
CYS F:13 , LYS F:47 , CYS F:143 , TRP F:176 , GLY F:177 , ASN F:179 , GLU F:182 , MET F:183 , SER F:207 , THR F:208 , TYR F:209 , HIS F:211 , PHE F:223 , GLN F:226 , ASP F:228 , THR F:335 , MET F:336 , GLY F:337 , PHE F:338 , GLY F:373 , GLN F:374 , SER F:681 , GLY F:683 , ARG F:684 , VAL F:685 , LEU F:686 , HIS F:688 , TRP F:689 , HIS F:690 , TYR F:755 , LYS F:783 , LYS F:784 , 6MO F:5002 , MGD F:6001 , HOH F:7071 , HOH F:7171 , HOH F:7259
BINDING SITE FOR RESIDUE MGD F 7001
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_MOW_BIS_MGD (F:3-59)
2: MOLYBDOPTERIN_PROK_1 (F:8-25)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
NAPA_ECOLI
39-95
1
-
F:3-59
2
MOLYBDOPTERIN_PROK_1
PS00551
Prokaryotic molybdopterin oxidoreductases signature 1.
NAPA_ECOLI
44-61
1
-
F:8-25
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2nyaA03 (A:139-375,A:631-667)
1b: CATH_2nyaF03 (F:139-375,F:631-667)
2a: CATH_2nyaA02 (A:60-138,A:376-491,A:516-587)
2b: CATH_2nyaF02 (F:60-138,F:376-491,F:516-587)
3a: CATH_2nyaA04 (A:668-791)
3b: CATH_2nyaF04 (F:668-791)
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dimethylsulfoxide Reductase; domain 2
(37)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 2
(37)
Escherichia coli k12. Organism_taxid: 83333. Strain: k-12.
(1)
1a
2nyaA03
A:139-375,A:631-667
1b
2nyaF03
F:139-375,F:631-667
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.740, no name defined]
(37)
Escherichia coli k12. Organism_taxid: 83333. Strain: k-12.
(1)
2a
2nyaA02
A:60-138,A:376-491,A:516-587
2b
2nyaF02
F:60-138,F:376-491,F:516-587
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
Escherichia coli k12. Organism_taxid: 83333. Strain: k-12.
(1)
3a
2nyaA04
A:668-791
3b
2nyaF04
F:668-791
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Molydop_binding_2nyaF01 (F:678-786)
1b: PFAM_Molydop_binding_2nyaF02 (F:678-786)
2a: PFAM_Molybdop_Fe4S4_2nyaF03 (F:3-57)
2b: PFAM_Molybdop_Fe4S4_2nyaF04 (F:3-57)
3a: PFAM_Molybdopterin_2nyaF05 (F:60-532)
3b: PFAM_Molybdopterin_2nyaF06 (F:60-532)
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AcetylDC-like
(37)
Family
:
Molydop_binding
(24)
Escherichia coli (strain K12)
(9)
1a
Molydop_binding-2nyaF01
F:678-786
1b
Molydop_binding-2nyaF02
F:678-786
Clan
:
no clan defined [family: Molybdop_Fe4S4]
(17)
Family
:
Molybdop_Fe4S4
(17)
Escherichia coli (strain K12)
(3)
2a
Molybdop_Fe4S4-2nyaF03
F:3-57
2b
Molybdop_Fe4S4-2nyaF04
F:3-57
Clan
:
no clan defined [family: Molybdopterin]
(24)
Family
:
Molybdopterin
(24)
Escherichia coli (strain K12)
(9)
3a
Molybdopterin-2nyaF05
F:60-532
3b
Molybdopterin-2nyaF06
F:60-532
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Chain F
Asymmetric Unit 1
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Asym.Unit (283 KB)
Header - Asym.Unit
Biol.Unit 1 (142 KB)
Header - Biol.Unit 1
Biol.Unit 2 (140 KB)
Header - Biol.Unit 2
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