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1YFD
Asym. Unit
Info
Asym.Unit (128 KB)
Biol.Unit 1 (122 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE Y122H MUTANT OF RIBONUCLEOTIDE REDUCTASE R2 PROTEIN FROM E. COLI
Authors
:
M. Kolberg, D. T. Logan, G. Bleifuss, S. Poetsch, B. M. Sjoeberg, A. Graeslund, W. Lubitz, G. Lassmann, F. Lendzian
Date
:
31 Dec 04 (Deposition) - 15 Feb 05 (Release) - 01 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Di-Iron Center, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kolberg, D. T. Logan, G. Bleifuss, S. Poetsch, B. M. Sjoeberg, A. Graeslund, W. Lubitz, G. Lassmann, F. Lendzian
A New Tyrosyl Radical On Phe208 As Ligand To The Diiron Center In Escherichia Coli Ribonucleotide Reductase, Mutant R2-Y122H. Combined X-Ray Diffraction And Epr/Endor Studies
J. Biol. Chem. V. 280 11233 2005
(for further references see the
PDB file header
)
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Hetero Components
(2, 15)
Info
All Hetero Components
1a: MU-OXO-DIIRON (FEOa)
1b: MU-OXO-DIIRON (FEOb)
2a: MERCURY (II) ION (HGa)
2b: MERCURY (II) ION (HGb)
2c: MERCURY (II) ION (HGc)
2d: MERCURY (II) ION (HGd)
2e: MERCURY (II) ION (HGe)
2f: MERCURY (II) ION (HGf)
2g: MERCURY (II) ION (HGg)
2h: MERCURY (II) ION (HGh)
2i: MERCURY (II) ION (HGi)
2j: MERCURY (II) ION (HGj)
2k: MERCURY (II) ION (HGk)
2l: MERCURY (II) ION (HGl)
2m: MERCURY (II) ION (HGm)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FEO
2
Ligand/Ion
MU-OXO-DIIRON
2
HG
13
Ligand/Ion
MERCURY (II) 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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:157 , CYS A:196 , VAL A:200 , HOH A:623
BINDING SITE FOR RESIDUE HG A 601
02
AC2
SOFTWARE
TYR B:157 , CYS B:196 , VAL B:200 , HG B:604
BINDING SITE FOR RESIDUE HG B 602
03
AC3
SOFTWARE
TYR B:194 , ALA B:265 , CYS B:268 , LYS B:269 , HG B:613 , HOH B:752
BINDING SITE FOR RESIDUE HG B 603
04
AC4
SOFTWARE
TYR B:156 , TYR B:157 , CYS B:196 , VAL B:200 , HG B:602 , HOH B:637
BINDING SITE FOR RESIDUE HG B 604
05
AC5
SOFTWARE
TYR A:194 , ALA A:265 , CYS A:272 , HOH A:766
BINDING SITE FOR RESIDUE HG A 605
06
AC6
SOFTWARE
VAL A:210 , CYS A:214
BINDING SITE FOR RESIDUE HG A 606
07
AC7
SOFTWARE
ASN B:76 , CYS B:214 , LEU B:290 , LEU B:304
BINDING SITE FOR RESIDUE HG B 607
08
AC8
SOFTWARE
MET B:198 , CYS B:272 , LEU B:275 , PHE B:276
BINDING SITE FOR RESIDUE HG B 608
09
AC9
SOFTWARE
CYS A:305 , GLU A:309
BINDING SITE FOR RESIDUE HG A 609
10
BC1
SOFTWARE
CYS B:305 , GLN B:306 , GLU B:309 , HG B:611 , HOH B:794
BINDING SITE FOR RESIDUE HG B 610
11
BC2
SOFTWARE
LYS B:284 , CYS B:305 , GLU B:309 , HG B:610
BINDING SITE FOR RESIDUE HG B 611
12
BC3
SOFTWARE
LYS B:191 , ILE B:264 , GLU B:267 , CYS B:268
BINDING SITE FOR RESIDUE HG B 612
13
BC4
SOFTWARE
TYR B:194 , ALA B:265 , HG B:603
BINDING SITE FOR RESIDUE HG B 613
14
BC5
SOFTWARE
ASP A:84 , GLU A:115 , HIS A:118 , GLU A:204 , GLU A:238 , HIS A:241 , HOH A:610 , HOH A:611 , HOH A:612
BINDING SITE FOR RESIDUE FEO A 501
15
BC6
SOFTWARE
ASP B:84 , GLU B:115 , HIS B:118 , GLU B:204 , GLU B:238 , HIS B:241 , HOH B:614 , HOH B:615 , HOH B:616
BINDING SITE FOR RESIDUE FEO B 502
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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: RIBORED_SMALL (A:114-130,B:114-130)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBORED_SMALL
PS00368
Ribonucleotide reductase small subunit signature.
RIR2_ECOLI
115-131
2
A:114-130
B:114-130
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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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_d1yfda1 (A:1-340)
1b: SCOP_d1yfdb_ (B:)
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Classes
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)
(
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Folds
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Superfamilies
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ribonucleotide reductase-like
(185)
Protein domain
:
Ribonucleotide reductase R2
(45)
Escherichia coli [TaxId: 562]
(24)
1a
d1yfda1
A:1-340
1b
d1yfdb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1yfdB00 (B:1-341)
1b: CATH_1yfdA00 (A:1-340)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Ribonucleotide Reductase, subunit A
(86)
Homologous Superfamily
:
Ribonucleotide Reductase, subunit A
(86)
Escherichia coli. Organism_taxid: 562.
(10)
1a
1yfdB00
B:1-341
1b
1yfdA00
A:1-340
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Ribonuc_red_sm_1yfdB01 (B:181-335)
1b: PFAM_Ribonuc_red_sm_1yfdB02 (B:181-335)
1c: PFAM_Ribonuc_red_sm_1yfdB03 (B:181-335)
1d: PFAM_Ribonuc_red_sm_1yfdB04 (B:181-335)
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Clans
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)
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)
Clan
:
Ferritin
(185)
Family
:
Ribonuc_red_sm
(41)
Escherichia coli (strain K12)
(22)
1a
Ribonuc_red_sm-1yfdB01
B:181-335
1b
Ribonuc_red_sm-1yfdB02
B:181-335
1c
Ribonuc_red_sm-1yfdB03
B:181-335
1d
Ribonuc_red_sm-1yfdB04
B:181-335
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Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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