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3ERZ
Biol. Unit 1
Info
Asym.Unit (351 KB)
Biol.Unit 1 (683 KB)
Biol.Unit 2 (683 KB)
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(1)
Title
:
DIRECTING NOBLE METAL ION CHEMISTRY WITHIN A DESIGNED FERRITIN PROTEIN. MERCURY IONS ON THE THREE-FOLD CHANNEL
Authors
:
L. Di Costanzo, D. W. Christianson
Date
:
03 Oct 08 (Deposition) - 21 Oct 08 (Release) - 08 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.06
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (4x)
Biol. Unit 2: G,H,I,J,K,L (4x)
Keywords
:
Ferritin Mutant, Nanoparticle, 3-Fold Channel, Mercury Ions, Iron, Iron Storage, Metal-Binding, Oxidoreductase, Phosphoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Butts, J. Swift, S. G. Kang, L. Di Costanzo, D. W. Christianson, J. G. Saven, I. J. Dmochowski
Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein.
Biochemistry V. 47 12729 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 24)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
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)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
3d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
3e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
3f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
3g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
3h: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDh)
3i: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDi)
3j: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDj)
3k: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDk)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
HG
-1
Ligand/Ion
MERCURY (II) ION
3
MPD
24
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
ZN
-1
Ligand/Ion
ZINC 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
LEU A:28 , SER A:31 , TYR A:32 , LEU F:28 , SER F:31 , TYR F:32
BINDING SITE FOR RESIDUE MPD A 533
02
AC2
SOFTWARE
ASP A:126 , PRO A:127 , CYS A:130 , HOH A:823
BINDING SITE FOR RESIDUE HG A 524
03
AC3
SOFTWARE
GLU A:134 , GLU C:134 , GLU E:134
BINDING SITE FOR RESIDUE CA A 812
04
AC4
SOFTWARE
HIS A:173 , HIS D:173
BINDING SITE FOR RESIDUE ZN A 706
05
AC5
SOFTWARE
HIS B:60 , ARG B:63 , CYS B:64
BINDING SITE FOR RESIDUE MPD B 540
06
AC6
SOFTWARE
LEU B:28 , SER B:31 , ARG B:63
BINDING SITE FOR RESIDUE MPD B 630
07
AC7
SOFTWARE
ALA B:121 , ASP B:126 , CYS B:130
BINDING SITE FOR RESIDUE HG B 526
08
AC8
SOFTWARE
HIS B:173 , HIS C:173 , HIS E:173 , HIS F:173
BINDING SITE FOR RESIDUE ZN B 708
09
AC9
SOFTWARE
SER C:31 , TYR C:32 , ARG C:63 , TYR D:32 , ARG D:63
BINDING SITE FOR RESIDUE MPD C 535
10
BC1
SOFTWARE
HOH A:832 , CYS C:130
BINDING SITE FOR RESIDUE HG C 525
11
BC2
SOFTWARE
THR D:122 , CYS D:130
BINDING SITE FOR RESIDUE HG D 527
12
BC3
SOFTWARE
LEU E:28 , SER E:31 , TYR E:32 , ARG E:63
BINDING SITE FOR RESIDUE MPD E 631
13
BC4
SOFTWARE
CYS E:130
BINDING SITE FOR RESIDUE HG E 523
14
BC5
SOFTWARE
GLU F:61 , CYS F:140 , CYS F:143 , HOH F:552
BINDING SITE FOR RESIDUE MPD F 543
15
BC6
SOFTWARE
THR F:122 , ASP F:126 , PRO F:127 , CYS F:130 , HOH F:565
BINDING SITE FOR RESIDUE HG F 528
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 72)
Info
All PROSITE Patterns/Profiles
1: FERRITIN_LIKE (A:10-159,B:10-159,C:10-159,D:10-15...)
2: FERRITIN_1 (A:61-79,B:61-79,C:61-79,D:61-79,E:...)
3: FERRITIN_2 (A:126-146,B:126-146,C:126-146,D:12...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FERRITIN_LIKE
PS50905
Ferritin-like diiron domain profile.
FRIH_HUMAN
11-160
24
A:10-159
B:10-159
C:10-159
D:10-159
E:10-159
F:10-159
-
-
-
-
-
-
2
FERRITIN_1
PS00540
Ferritin iron-binding regions signature 1.
FRIH_HUMAN
62-80
24
A:61-79
B:61-79
C:61-79
D:61-79
E:61-79
F:61-79
-
-
-
-
-
-
3
FERRITIN_2
PS00204
Ferritin iron-binding regions signature 2.
FRIH_HUMAN
127-147
24
A:126-146
B:126-146
C:126-146
D:126-146
E:126-146
F:126-146
-
-
-
-
-
-
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
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CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3erzA00 (A:5-176)
1b: CATH_3erzB00 (B:5-176)
1c: CATH_3erzC00 (C:5-176)
1d: CATH_3erzD00 (D:5-176)
1e: CATH_3erzE00 (E:5-176)
1f: CATH_3erzF00 (F:5-176)
1g: CATH_3erzG00 (G:5-176)
1h: CATH_3erzH00 (H:5-176)
1i: CATH_3erzI00 (I:5-176)
1j: CATH_3erzJ00 (J:5-176)
1k: CATH_3erzK00 (K:5-176)
1l: CATH_3erzL00 (L:5-176)
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Classes
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(
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(
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(
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(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Human (Homo sapiens)
(16)
1a
3erzA00
A:5-176
1b
3erzB00
B:5-176
1c
3erzC00
C:5-176
1d
3erzD00
D:5-176
1e
3erzE00
E:5-176
1f
3erzF00
F:5-176
1g
3erzG00
G:5-176
1h
3erzH00
H:5-176
1i
3erzI00
I:5-176
1j
3erzJ00
J:5-176
1k
3erzK00
K:5-176
1l
3erzL00
L:5-176
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Pfam Domains
(0, 0)
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all PFAM domains
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Asym.Unit (351 KB)
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