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1Q0D
Biol. Unit 1
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 OXIDIZED STATE
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:
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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, 14)
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
6
Ligand/Ion
NICKEL (III) ION
2
SO4
8
Ligand/Ion
SULFATE ION
[
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Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: BC8 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:5 , GLY A:7 , TYR A:9 , ASP A:61 , LYS A:64 , HOH A:9100 , HOH A:9119 , HOH A:9125
BINDING SITE FOR RESIDUE SO4 A 9001
02
AC2
SOFTWARE
PRO B:5 , GLY B:7 , TYR B:9 , LYS B:64 , HOH B:9028 , HOH B:9085 , HOH B:9099
BINDING SITE FOR RESIDUE SO4 B 9002
03
AC3
SOFTWARE
PRO C:5 , GLY C:7 , TYR C:9 , LYS C:64 , HOH C:9041
BINDING SITE FOR RESIDUE SO4 C 9003
04
AC4
SOFTWARE
PRO D:5 , GLY D:7 , TYR D:9 , LYS D:64 , HOH D:9027 , 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
BINDING SITE FOR RESIDUE SO4 E 9005
06
AC6
SOFTWARE
PRO F:5 , GLY F:7 , TYR F:9 , LYS F:64 , HOH F:9092 , HOH F:9095 , HOH F:9113
BINDING SITE FOR RESIDUE SO4 F 9006
07
BC4
SOFTWARE
GLN A:46 , HOH A:9061 , HOH A:9072 , GLN B:46 , GLN D:46
BINDING SITE FOR RESIDUE SO4 A 9013
08
BC5
SOFTWARE
GLN C:46 , HOH C:9057 , HOH C:9059 , HOH C:9062 , GLN E:46 , GLN F:46
BINDING SITE FOR RESIDUE SO4 C 9014
09
BC8
SOFTWARE
HIS A:1 , CYS A:2 , ASP A:3 , CYS A:6
BINDING SITE FOR RESIDUE 3NI A 118
10
BC9
SOFTWARE
HIS B:1 , CYS B:2 , ASP B:3 , CYS B:6
BINDING SITE FOR RESIDUE 3NI B 118
11
CC1
SOFTWARE
HIS C:1 , CYS C:2 , ASP C:3 , CYS C:6
BINDING SITE FOR RESIDUE 3NI C 118
12
CC2
SOFTWARE
HIS D:1 , CYS D:2 , ASP D:3 , CYS D:6
BINDING SITE FOR RESIDUE 3NI D 118
13
CC3
SOFTWARE
HIS E:1 , CYS E:2 , ASP E:3 , CYS E:6
BINDING SITE FOR RESIDUE 3NI E 118
14
CC4
SOFTWARE
HIS F:1 , CYS F:2 , CYS F:6
BINDING SITE FOR RESIDUE 3NI F 118
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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
(, 0)
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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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1q0da_ (A:)
1b: SCOP_d1q0db_ (B:)
1c: SCOP_d1q0dc_ (C:)
1d: SCOP_d1q0dd_ (D:)
1e: SCOP_d1q0de_ (E:)
1f: SCOP_d1q0df_ (F:)
1g: SCOP_d1q0dg_ (G:)
1h: SCOP_d1q0dh_ (H:)
1i: SCOP_d1q0di_ (I:)
1j: SCOP_d1q0dj_ (J:)
1k: SCOP_d1q0dk_ (K:)
1l: SCOP_d1q0dl_ (L:)
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Protein Domains
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(
)
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
d1q0da_
A:
1b
d1q0db_
B:
1c
d1q0dc_
C:
1d
d1q0dd_
D:
1e
d1q0de_
E:
1f
d1q0df_
F:
1g
d1q0dg_
G:
1h
d1q0dh_
H:
1i
d1q0di_
I:
1j
d1q0dj_
J:
1k
d1q0dk_
K:
1l
d1q0dl_
L:
[
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CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1q0dA00 (A:1-117)
1b: CATH_1q0dB00 (B:1-117)
1c: CATH_1q0dC00 (C:1-117)
1d: CATH_1q0dD00 (D:1-117)
1e: CATH_1q0dE00 (E:1-117)
1f: CATH_1q0dF00 (F:1-117)
1g: CATH_1q0dG00 (G:1-117)
1h: CATH_1q0dH00 (H:1-117)
1i: CATH_1q0dI00 (I:1-117)
1j: CATH_1q0dJ00 (J:1-117)
1k: CATH_1q0dK00 (K:1-117)
1l: CATH_1q0dL00 (L:1-117)
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(
)
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
1q0dA00
A:1-117
1b
1q0dB00
B:1-117
1c
1q0dC00
C:1-117
1d
1q0dD00
D:1-117
1e
1q0dE00
E:1-117
1f
1q0dF00
F:1-117
1g
1q0dG00
G:1-117
1h
1q0dH00
H:1-117
1i
1q0dI00
I:1-117
1j
1q0dJ00
J:1-117
1k
1q0dK00
K:1-117
1l
1q0dL00
L:1-117
[
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Sod_Ni_1q0dL01 (L:1-115)
1b: PFAM_Sod_Ni_1q0dL02 (L:1-115)
1c: PFAM_Sod_Ni_1q0dL03 (L:1-115)
1d: PFAM_Sod_Ni_1q0dL04 (L:1-115)
1e: PFAM_Sod_Ni_1q0dL05 (L:1-115)
1f: PFAM_Sod_Ni_1q0dL06 (L:1-115)
1g: PFAM_Sod_Ni_1q0dL07 (L:1-115)
1h: PFAM_Sod_Ni_1q0dL08 (L:1-115)
1i: PFAM_Sod_Ni_1q0dL09 (L:1-115)
1j: PFAM_Sod_Ni_1q0dL10 (L:1-115)
1k: PFAM_Sod_Ni_1q0dL11 (L:1-115)
1l: PFAM_Sod_Ni_1q0dL12 (L:1-115)
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(
)
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(
)
(
)
Clan
:
no clan defined [family: Sod_Ni]
(8)
Family
:
Sod_Ni
(8)
Streptomyces seoulensis
(5)
1a
Sod_Ni-1q0dL01
L:1-115
1b
Sod_Ni-1q0dL02
L:1-115
1c
Sod_Ni-1q0dL03
L:1-115
1d
Sod_Ni-1q0dL04
L:1-115
1e
Sod_Ni-1q0dL05
L:1-115
1f
Sod_Ni-1q0dL06
L:1-115
1g
Sod_Ni-1q0dL07
L:1-115
1h
Sod_Ni-1q0dL08
L:1-115
1i
Sod_Ni-1q0dL09
L:1-115
1j
Sod_Ni-1q0dL10
L:1-115
1k
Sod_Ni-1q0dL11
L:1-115
1l
Sod_Ni-1q0dL12
L:1-115
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Asym.Unit (261 KB)
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