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3N3B
Asym. Unit
Info
Asym.Unit (281 KB)
Biol.Unit 1 (274 KB)
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(1)
Title
:
RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI IN COMPLEX WITH REDUCED NRDI WITH A TRAPPED PEROXIDE
Authors
:
A. K. Boal, J. A. Cotruvo Jr. , J. Stubbe, A. C. Rosenzweig
Date
:
19 May 10 (Deposition) - 18 Aug 10 (Release) - 24 Nov 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.36
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Ribonucleotide Reductase, Four-Helix Bundle, Dimanganese Cluster, Flavoprotein, Peroxide, Oxidoreductase
(Keyword Search:
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Reference
:
A. K. Boal, J. A. Cotruvo, J. Stubbe, A. C. Rosenzweig
Structural Basis For Activation Of Class Ib Ribonucleotide Reductase.
Science V. 329 1526 2010
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: FLAVIN MONONUCLEOTIDE (FMNa)
1b: FLAVIN MONONUCLEOTIDE (FMNb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
3a: HYDROGEN PEROXIDE (PEOa)
3b: HYDROGEN PEROXIDE (PEOb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
FMN
2
Ligand/Ion
FLAVIN MONONUCLEOTIDE
2
MN
4
Ligand/Ion
MANGANESE (II) ION
3
PEO
2
Ligand/Ion
HYDROGEN PEROXIDE
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:67 , GLU B:98 , HIS B:101 , GLU B:158 , GLU B:192 , MN B:321 , HOH B:375
BINDING SITE FOR RESIDUE MN B 320
2
AC2
SOFTWARE
GLU B:98 , GLU B:158 , GLU B:192 , HIS B:195 , MN B:320 , HOH B:381
BINDING SITE FOR RESIDUE MN B 321
3
AC3
SOFTWARE
SER B:159 , LYS B:260 , HOH B:329 , ASN C:83 , ASN C:85
BINDING SITE FOR RESIDUE PEO B 322
4
AC4
SOFTWARE
ARG B:25 , TYR B:197 , SER C:8 , SER C:9 , SER C:11 , GLU C:12 , ASN C:13 , THR C:14 , PRO C:47 , SER C:48 , TYR C:49 , GLY C:50 , GLY C:51 , GLY C:82 , ASN C:83 , PHE C:86 , ALA C:89 , TYR C:90 , GLY C:91 , LEU C:111 , HOH C:138 , HOH C:143
BINDING SITE FOR RESIDUE FMN C 134
5
AC5
SOFTWARE
ASP A:67 , GLU A:98 , HIS A:101 , GLU A:158 , GLU A:192 , HOH A:361
BINDING SITE FOR RESIDUE MN A 320
6
AC6
SOFTWARE
GLU A:98 , GLU A:158 , GLU A:192 , HIS A:195 , HOH A:334
BINDING SITE FOR RESIDUE MN A 321
7
AC7
SOFTWARE
SER A:159 , LYS A:260 , ASN A:264 , HOH A:359 , ASN D:83 , ASN D:85
BINDING SITE FOR RESIDUE PEO A 322
8
AC8
SOFTWARE
ARG A:25 , TYR A:197 , SER D:8 , SER D:9 , SER D:11 , GLU D:12 , ASN D:13 , THR D:14 , PRO D:47 , SER D:48 , TYR D:49 , GLY D:50 , SER D:81 , GLY D:82 , ASN D:83 , PHE D:86 , ALA D:89 , TYR D:90 , GLY D:91 , LEU D:111 , HOH D:136
BINDING SITE FOR RESIDUE FMN D 134
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RIBORED_SMALL (A:97-113,B:97-113)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBORED_SMALL
PS00368
Ribonucleotide reductase small subunit signature.
RIR4_ECOLI
97-113
2
A:97-113
B:97-113
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Exons
(0, 0)
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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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3n3ba_ (A:)
1b: SCOP_d3n3bb_ (B:)
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Protein Domains
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Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ribonucleotide reductase-like
(185)
Protein domain
:
automated matches
(42)
Escherichia coli K-12 [TaxId: 83333]
(6)
1a
d3n3ba_
A:
1b
d3n3bb_
B:
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CATH Domains
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all CATH domains
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Ribonuc_red_sm_3n3bB01 (B:5-281)
1b: PFAM_Ribonuc_red_sm_3n3bB02 (B:5-281)
2a: PFAM_Flavodoxin_NdrI_3n3bD01 (D:5-123)
2b: PFAM_Flavodoxin_NdrI_3n3bD02 (D:5-123)
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Clan
:
Ferritin
(185)
Family
:
Ribonuc_red_sm
(41)
Escherichia coli (strain K12)
(22)
1a
Ribonuc_red_sm-3n3bB01
B:5-281
1b
Ribonuc_red_sm-3n3bB02
B:5-281
Clan
:
Flavoprotein
(71)
Family
:
Flavodoxin_NdrI
(8)
Escherichia coli (strain K12)
(3)
2a
Flavodoxin_NdrI-3n3bD01
D:5-123
2b
Flavodoxin_NdrI-3n3bD02
D:5-123
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Asymmetric Unit 1
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Asym.Unit (281 KB)
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