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1Q0F
Asym. Unit
Info
Asym.Unit (261 KB)
Biol.Unit 1 (129 KB)
Biol.Unit 2 (130 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NI-CONTAINING SUPEROXIDE DISMUTASE WITH NI-LIGATION CORRESPONDING TO THE STATE AFTER PARTIAL X-RAY-INDUCED REDUCTION
Authors
:
J. Wuerges, J. -W. Lee, Y. -I. Yim, H. -S. Yim, S. -O. Kang, K. Djinovic Carugo
Date
:
16 Jul 03 (Deposition) - 18 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Homohexamer Of Four-Helix Bundles, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Wuerges, J. -W. Lee, Y. -I. Yim, H. -S. Yim, S. -O. Kang, K. Djinovic Carugo
Crystal Structure Of Nickel-Containing Superoxide Dismutase Reveals Another Type Of Active Site
Proc. Natl. Acad. Sci. Usa V. 101 8569 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 28)
Info
All Hetero Components
1a: NICKEL (III) ION (3NIa)
1b: NICKEL (III) ION (3NIb)
1c: NICKEL (III) ION (3NIc)
1d: NICKEL (III) ION (3NId)
1e: NICKEL (III) ION (3NIe)
1f: NICKEL (III) ION (3NIf)
1g: NICKEL (III) ION (3NIg)
1h: NICKEL (III) ION (3NIh)
1i: NICKEL (III) ION (3NIi)
1j: NICKEL (III) ION (3NIj)
1k: NICKEL (III) ION (3NIk)
1l: NICKEL (III) ION (3NIl)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3NI
12
Ligand/Ion
NICKEL (III) ION
2
SO4
16
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:5 , GLY A:7 , TYR A:9 , LYS A:64 , HOH A:9086 , HOH A:9112
BINDING SITE FOR RESIDUE SO4 A 9001
02
AC2
SOFTWARE
PRO B:5 , GLY B:7 , TYR B:9 , LYS B:64 , HOH B:9037 , HOH B:9098 , HOH B:9112
BINDING SITE FOR RESIDUE SO4 B 9002
03
AC3
SOFTWARE
PRO C:5 , GLY C:7 , TYR C:9 , ASP C:61 , LYS C:64 , HOH C:9043
BINDING SITE FOR RESIDUE SO4 C 9003
04
AC4
SOFTWARE
PRO D:5 , GLY D:7 , TYR D:9 , LYS D:64 , HOH D:9103 , HOH D:9130
BINDING SITE FOR RESIDUE SO4 D 9004
05
AC5
SOFTWARE
PRO E:5 , GLY E:7 , TYR E:9 , LYS E:64 , HOH E:9040 , HOH E:9122
BINDING SITE FOR RESIDUE SO4 E 9005
06
AC6
SOFTWARE
PRO F:5 , GLY F:7 , TYR F:9 , LYS F:64 , HOH F:9093 , HOH F:9096 , HOH F:9113
BINDING SITE FOR RESIDUE SO4 F 9006
07
AC7
SOFTWARE
PRO G:5 , GLY G:7 , TYR G:9
BINDING SITE FOR RESIDUE SO4 G 9007
08
AC8
SOFTWARE
PRO H:5 , GLY H:7 , TYR H:9 , ASP H:61 , LYS H:64 , HOH H:9143
BINDING SITE FOR RESIDUE SO4 H 9008
09
AC9
SOFTWARE
PRO I:5 , GLY I:7 , TYR I:9 , ASP I:61 , LYS I:64 , HOH I:9088
BINDING SITE FOR RESIDUE SO4 I 9009
10
BC1
SOFTWARE
PRO J:5 , GLY J:7 , TYR J:9 , LYS J:64 , HOH J:9084 , HOH J:9142
BINDING SITE FOR RESIDUE SO4 J 9010
11
BC2
SOFTWARE
PRO K:5 , GLY K:7 , TYR K:9 , ASP K:61 , LYS K:64
BINDING SITE FOR RESIDUE SO4 K 9011
12
BC3
SOFTWARE
PRO L:5 , GLY L:7 , TYR L:9 , LYS L:64 , HOH L:9059 , HOH L:9069
BINDING SITE FOR RESIDUE SO4 L 9012
13
BC4
SOFTWARE
GLN A:46 , GLN B:46 , HOH B:9046 , HOH B:9054 , GLN D:46
BINDING SITE FOR RESIDUE SO4 B 9013
14
BC5
SOFTWARE
GLN C:46 , HOH C:9062 , HOH C:9065 , GLN E:46 , GLN F:46
BINDING SITE FOR RESIDUE SO4 C 9014
15
BC6
SOFTWARE
GLN G:46 , GLN H:46 , HOH H:9062 , HOH H:9067 , GLN J:46
BINDING SITE FOR RESIDUE SO4 H 9015
16
BC7
SOFTWARE
GLN I:46 , GLN K:46 , GLN L:46 , HOH L:9078 , HOH L:9082
BINDING SITE FOR RESIDUE SO4 L 9016
17
BC8
SOFTWARE
HIS A:1 , CYS A:2 , ASP A:3 , CYS A:6
BINDING SITE FOR RESIDUE 3NI A 118
18
BC9
SOFTWARE
HIS B:1 , CYS B:2 , ASP B:3 , CYS B:6
BINDING SITE FOR RESIDUE 3NI B 118
19
CC1
SOFTWARE
HIS C:1 , CYS C:2 , ASP C:3 , CYS C:6
BINDING SITE FOR RESIDUE 3NI C 118
20
CC2
SOFTWARE
HIS D:1 , CYS D:2 , ASP D:3 , CYS D:6
BINDING SITE FOR RESIDUE 3NI D 118
21
CC3
SOFTWARE
HIS E:1 , CYS E:2 , ASP E:3 , CYS E:6
BINDING SITE FOR RESIDUE 3NI E 118
22
CC4
SOFTWARE
HIS F:1 , CYS F:2 , ASP F:3 , CYS F:6
BINDING SITE FOR RESIDUE 3NI F 118
23
CC5
SOFTWARE
HIS G:1 , CYS G:2 , ASP G:3 , CYS G:6
BINDING SITE FOR RESIDUE 3NI G 118
24
CC6
SOFTWARE
HIS H:1 , CYS H:2 , ASP H:3 , CYS H:6
BINDING SITE FOR RESIDUE 3NI H 118
25
CC7
SOFTWARE
HIS I:1 , CYS I:2 , ASP I:3 , CYS I:6
BINDING SITE FOR RESIDUE 3NI I 118
26
CC8
SOFTWARE
HIS J:1 , CYS J:2 , ASP J:3 , CYS J:6
BINDING SITE FOR RESIDUE 3NI J 118
27
CC9
SOFTWARE
HIS K:1 , CYS K:2 , ASP K:3 , CYS K:6
BINDING SITE FOR RESIDUE 3NI K 118
28
DC1
SOFTWARE
HIS L:1 , CYS L:2 , CYS L:6
BINDING SITE FOR RESIDUE 3NI L 118
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1q0fa_ (A:)
1b: SCOP_d1q0fb_ (B:)
1c: SCOP_d1q0fc_ (C:)
1d: SCOP_d1q0fd_ (D:)
1e: SCOP_d1q0fe_ (E:)
1f: SCOP_d1q0ff_ (F:)
1g: SCOP_d1q0fg_ (G:)
1h: SCOP_d1q0fh_ (H:)
1i: SCOP_d1q0fi_ (I:)
1j: SCOP_d1q0fj_ (J:)
1k: SCOP_d1q0fk_ (K:)
1l: SCOP_d1q0fl_ (L:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Nickel-containing superoxide dismutase, NiSOD
(11)
Family
:
Nickel-containing superoxide dismutase, NiSOD
(11)
Protein domain
:
Nickel-containing superoxide dismutase, NiSOD
(8)
Streptomyces seoulensis [TaxId: 73044]
(5)
1a
d1q0fa_
A:
1b
d1q0fb_
B:
1c
d1q0fc_
C:
1d
d1q0fd_
D:
1e
d1q0fe_
E:
1f
d1q0ff_
F:
1g
d1q0fg_
G:
1h
d1q0fh_
H:
1i
d1q0fi_
I:
1j
d1q0fj_
J:
1k
d1q0fk_
K:
1l
d1q0fl_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1q0fA00 (A:1-117)
1b: CATH_1q0fB00 (B:1-117)
1c: CATH_1q0fC00 (C:1-117)
1d: CATH_1q0fD00 (D:1-117)
1e: CATH_1q0fE00 (E:1-117)
1f: CATH_1q0fF00 (F:1-117)
1g: CATH_1q0fG00 (G:1-117)
1h: CATH_1q0fH00 (H:1-117)
1i: CATH_1q0fI00 (I:1-117)
1j: CATH_1q0fJ00 (J:1-117)
1k: CATH_1q0fK00 (K:1-117)
1l: CATH_1q0fL00 (L:1-117)
View:
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Classes
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)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
Nickel-containing superoxide dismutase, NiSOD
(11)
Streptomyces seoulensis. Organism_taxid: 73044
(5)
1a
1q0fA00
A:1-117
1b
1q0fB00
B:1-117
1c
1q0fC00
C:1-117
1d
1q0fD00
D:1-117
1e
1q0fE00
E:1-117
1f
1q0fF00
F:1-117
1g
1q0fG00
G:1-117
1h
1q0fH00
H:1-117
1i
1q0fI00
I:1-117
1j
1q0fJ00
J:1-117
1k
1q0fK00
K:1-117
1l
1q0fL00
L:1-117
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Sod_Ni_1q0fL01 (L:1-115)
1b: PFAM_Sod_Ni_1q0fL02 (L:1-115)
1c: PFAM_Sod_Ni_1q0fL03 (L:1-115)
1d: PFAM_Sod_Ni_1q0fL04 (L:1-115)
1e: PFAM_Sod_Ni_1q0fL05 (L:1-115)
1f: PFAM_Sod_Ni_1q0fL06 (L:1-115)
1g: PFAM_Sod_Ni_1q0fL07 (L:1-115)
1h: PFAM_Sod_Ni_1q0fL08 (L:1-115)
1i: PFAM_Sod_Ni_1q0fL09 (L:1-115)
1j: PFAM_Sod_Ni_1q0fL10 (L:1-115)
1k: PFAM_Sod_Ni_1q0fL11 (L:1-115)
1l: PFAM_Sod_Ni_1q0fL12 (L:1-115)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Sod_Ni]
(8)
Family
:
Sod_Ni
(8)
Streptomyces seoulensis
(5)
1a
Sod_Ni-1q0fL01
L:1-115
1b
Sod_Ni-1q0fL02
L:1-115
1c
Sod_Ni-1q0fL03
L:1-115
1d
Sod_Ni-1q0fL04
L:1-115
1e
Sod_Ni-1q0fL05
L:1-115
1f
Sod_Ni-1q0fL06
L:1-115
1g
Sod_Ni-1q0fL07
L:1-115
1h
Sod_Ni-1q0fL08
L:1-115
1i
Sod_Ni-1q0fL09
L:1-115
1j
Sod_Ni-1q0fL10
L:1-115
1k
Sod_Ni-1q0fL11
L:1-115
1l
Sod_Ni-1q0fL12
L:1-115
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