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1Q0G
Biol. Unit 1
Info
Asym.Unit (264 KB)
Biol.Unit 1 (131 KB)
Biol.Unit 2 (132 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NI-CONTAINING SUPEROXIDE DISMUTASE WITH NI-LIGATION CORRESPONDING TO THE STATE AFTER FULL 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
:
1.60
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)
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)
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
(1, 8)
Info
All Hetero Components
1a: NICKEL (II) ION (NIa)
1b: NICKEL (II) ION (NIb)
1c: NICKEL (II) ION (NIc)
1d: NICKEL (II) ION (NId)
1e: NICKEL (II) ION (NIe)
1f: NICKEL (II) ION (NIf)
1g: NICKEL (II) ION (NIg)
1h: NICKEL (II) ION (NIh)
1i: NICKEL (II) ION (NIi)
1j: NICKEL (II) ION (NIj)
1k: NICKEL (II) ION (NIk)
1l: NICKEL (II) ION (NIl)
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
NI
-1
Ligand/Ion
NICKEL (II) 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: BC6 (SOFTWARE)
10: BC7 (SOFTWARE)
11: BC8 (SOFTWARE)
12: BC9 (SOFTWARE)
13: CC7 (SOFTWARE)
14: CC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:1 , CYS A:2 , ASP A:3 , CYS A:6
BINDING SITE FOR RESIDUE NI A 118
02
AC2
SOFTWARE
HIS B:1 , CYS B:2 , ASP B:3 , CYS B:6
BINDING SITE FOR RESIDUE NI B 118
03
AC3
SOFTWARE
HIS C:1 , CYS C:2 , ASP C:3 , CYS C:6
BINDING SITE FOR RESIDUE NI C 118
04
AC4
SOFTWARE
HIS D:1 , CYS D:2 , ASP D:3 , CYS D:6
BINDING SITE FOR RESIDUE NI D 118
05
AC5
SOFTWARE
HIS E:1 , CYS E:2 , CYS E:6
BINDING SITE FOR RESIDUE NI E 118
06
AC6
SOFTWARE
HIS F:1 , CYS F:2 , ASP F:3 , CYS F:6
BINDING SITE FOR RESIDUE NI F 118
07
BC4
SOFTWARE
PRO A:5 , GLY A:7 , TYR A:9 , ASP A:61 , LYS A:64 , HOH A:9088 , HOH A:9100 , HOH A:9118 , HOH A:9149
BINDING SITE FOR RESIDUE SO4 A 9001
08
BC5
SOFTWARE
PRO B:5 , GLY B:7 , TYR B:9 , LYS B:64 , HOH B:9028 , HOH B:9094
BINDING SITE FOR RESIDUE SO4 B 9002
09
BC6
SOFTWARE
PRO C:5 , GLY C:7 , TYR C:9 , LYS C:64 , HOH C:9041 , HOH C:9109
BINDING SITE FOR RESIDUE SO4 C 9003
10
BC7
SOFTWARE
PRO D:5 , GLY D:7 , TYR D:9 , LYS D:64 , HOH D:9027 , HOH D:9115 , HOH D:9119
BINDING SITE FOR RESIDUE SO4 D 9004
11
BC8
SOFTWARE
PRO E:5 , GLY E:7 , TYR E:9 , LYS E:64 , HOH E:9138
BINDING SITE FOR RESIDUE SO4 E 9005
12
BC9
SOFTWARE
PRO F:5 , GLY F:7 , TYR F:9 , LYS F:64 , HOH F:9093 , HOH F:9096 , HOH F:9113 , HOH F:9152
BINDING SITE FOR RESIDUE SO4 F 9006
13
CC7
SOFTWARE
GLN A:46 , HOH A:9061 , GLN B:46 , GLN D:46
BINDING SITE FOR RESIDUE SO4 A 9013
14
CC8
SOFTWARE
GLN C:46 , HOH C:9057 , HOH C:9059 , GLN E:46 , GLN F:46
BINDING SITE FOR RESIDUE SO4 C 9014
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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)
Info
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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_d1q0ga_ (A:)
1b: SCOP_d1q0gb_ (B:)
1c: SCOP_d1q0gk_ (K:)
1d: SCOP_d1q0gl_ (L:)
1e: SCOP_d1q0gc_ (C:)
1f: SCOP_d1q0gd_ (D:)
1g: SCOP_d1q0ge_ (E:)
1h: SCOP_d1q0gf_ (F:)
1i: SCOP_d1q0gg_ (G:)
1j: SCOP_d1q0gh_ (H:)
1k: SCOP_d1q0gi_ (I:)
1l: SCOP_d1q0gj_ (J:)
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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
d1q0ga_
A:
1b
d1q0gb_
B:
1c
d1q0gk_
K:
1d
d1q0gl_
L:
1e
d1q0gc_
C:
1f
d1q0gd_
D:
1g
d1q0ge_
E:
1h
d1q0gf_
F:
1i
d1q0gg_
G:
1j
d1q0gh_
H:
1k
d1q0gi_
I:
1l
d1q0gj_
J:
[
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CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1q0gA00 (A:1-117)
1b: CATH_1q0gB00 (B:1-117)
1c: CATH_1q0gK00 (K:1-117)
1d: CATH_1q0gL00 (L:1-117)
1e: CATH_1q0gC00 (C:1-117)
1f: CATH_1q0gD00 (D:1-117)
1g: CATH_1q0gE00 (E:1-117)
1h: CATH_1q0gF00 (F:1-117)
1i: CATH_1q0gG00 (G:1-117)
1j: CATH_1q0gH00 (H:1-117)
1k: CATH_1q0gI00 (I:1-117)
1l: CATH_1q0gJ00 (J: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
1q0gA00
A:1-117
1b
1q0gB00
B:1-117
1c
1q0gK00
K:1-117
1d
1q0gL00
L:1-117
1e
1q0gC00
C:1-117
1f
1q0gD00
D:1-117
1g
1q0gE00
E:1-117
1h
1q0gF00
F:1-117
1i
1q0gG00
G:1-117
1j
1q0gH00
H:1-117
1k
1q0gI00
I:1-117
1l
1q0gJ00
J:1-117
[
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Sod_Ni_1q0gL01 (L:1-115)
1b: PFAM_Sod_Ni_1q0gL02 (L:1-115)
1c: PFAM_Sod_Ni_1q0gL03 (L:1-115)
1d: PFAM_Sod_Ni_1q0gL04 (L:1-115)
1e: PFAM_Sod_Ni_1q0gL05 (L:1-115)
1f: PFAM_Sod_Ni_1q0gL06 (L:1-115)
1g: PFAM_Sod_Ni_1q0gL07 (L:1-115)
1h: PFAM_Sod_Ni_1q0gL08 (L:1-115)
1i: PFAM_Sod_Ni_1q0gL09 (L:1-115)
1j: PFAM_Sod_Ni_1q0gL10 (L:1-115)
1k: PFAM_Sod_Ni_1q0gL11 (L:1-115)
1l: PFAM_Sod_Ni_1q0gL12 (L:1-115)
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Clans
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)
(
)
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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-1q0gL01
L:1-115
1b
Sod_Ni-1q0gL02
L:1-115
1c
Sod_Ni-1q0gL03
L:1-115
1d
Sod_Ni-1q0gL04
L:1-115
1e
Sod_Ni-1q0gL05
L:1-115
1f
Sod_Ni-1q0gL06
L:1-115
1g
Sod_Ni-1q0gL07
L:1-115
1h
Sod_Ni-1q0gL08
L:1-115
1i
Sod_Ni-1q0gL09
L:1-115
1j
Sod_Ni-1q0gL10
L:1-115
1k
Sod_Ni-1q0gL11
L:1-115
1l
Sod_Ni-1q0gL12
L:1-115
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Asym.Unit (264 KB)
Header - Asym.Unit
Biol.Unit 1 (131 KB)
Header - Biol.Unit 1
Biol.Unit 2 (132 KB)
Header - Biol.Unit 2
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