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Nickel in PDB 1q0d: Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State

Enzymatic activity of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State

All present enzymatic activity of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State, PDB code: 1q0d was solved by J.Wuerges, J.-W.Lee, Y.-I.Yim, H.-S.Yim, S.-O.Kang, K.Djinoviccarugo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.37 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 112.260, 113.749, 128.618, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 18

Nickel Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Nickel atom in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State (pdb code 1q0d). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State, PDB code: 1q0d:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 12 in 1q0d

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Nickel binding site 1 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni118

b:31.5
occ:1.00
 N A:CYS2 1.9 19.8 1.0
N A:HIS1 2.2 22.5 1.0
SG A:CYS2 2.2 19.7 1.0
SG A:CYS6 2.2 18.5 1.0
ND1 A:HIS1 2.7 30.3 1.0
C A:HIS1 2.8 22.8 1.0
CA A:CYS2 2.9 20.9 1.0
CA A:HIS1 3.0 24.0 1.0
CB A:CYS2 3.0 17.4 1.0
CB A:CYS6 3.4 18.7 1.0
O A:HOH9088 3.5 28.4 1.0
CG A:HIS1 3.6 27.6 1.0
CE1 A:HIS1 3.6 29.4 1.0
N A:ASP3 3.6 19.8 1.0
C A:CYS2 3.7 19.9 1.0
CB A:HIS1 3.8 25.8 1.0
N A:CYS6 3.9 20.3 1.0
O A:HIS1 4.0 23.8 1.0
O A:HOH9024 4.1 12.1 1.0
O A:VAL8 4.2 21.0 1.0
CA A:CYS6 4.3 20.2 1.0
OG C:SER20 4.5 24.0 1.0
O A:CYS2 4.8 21.5 1.0
NE2 A:HIS1 4.8 28.8 1.0
CD2 A:HIS1 4.8 28.8 1.0
N A:LEU4 4.9 18.9 1.0
N A:GLY7 4.9 21.7 1.0
C A:CYS6 4.9 21.6 1.0
CA A:ASP3 4.9 19.8 1.0
N A:VAL8 5.0 22.0 1.0

Nickel binding site 2 out of 12 in 1q0d

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Nickel binding site 2 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni118

b:28.9
occ:1.00
 N B:CYS2 1.8 22.5 1.0
N B:HIS1 2.2 25.7 1.0
SG B:CYS2 2.2 22.6 1.0
SG B:CYS6 2.3 21.8 1.0
C B:HIS1 2.7 23.8 1.0
ND1 B:HIS1 2.7 31.8 1.0
CA B:CYS2 2.8 22.1 1.0
CB B:CYS2 2.9 20.3 1.0
CA B:HIS1 2.9 25.2 1.0
CB B:CYS6 3.5 20.8 1.0
N B:ASP3 3.6 22.1 1.0
O B:HOH9028 3.6 32.1 1.0
CG B:HIS1 3.6 28.6 1.0
C B:CYS2 3.7 22.2 1.0
CE1 B:HIS1 3.7 31.5 1.0
CB B:HIS1 3.8 26.9 1.0
O B:HIS1 3.9 23.3 1.0
N B:CYS6 3.9 22.1 1.0
O B:HOH9005 4.1 21.2 1.0
O B:VAL8 4.3 23.3 1.0
CA B:CYS6 4.3 22.1 1.0
OG E:SER20 4.6 23.3 1.0
O B:CYS2 4.7 22.2 1.0
NE2 B:HIS1 4.8 31.0 1.0
CD2 B:HIS1 4.8 30.2 1.0
N B:LEU4 4.8 21.9 1.0
CA B:ASP3 4.9 22.6 1.0
N B:GLY7 4.9 21.8 1.0
C B:CYS6 5.0 22.2 1.0

Nickel binding site 3 out of 12 in 1q0d

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Nickel binding site 3 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni118

b:28.9
occ:1.00
 N C:CYS2 2.0 21.7 1.0
N C:HIS1 2.0 21.2 1.0
SG C:CYS6 2.2 22.0 1.0
SG C:CYS2 2.3 22.9 1.0
ND1 C:HIS1 2.6 31.1 1.0
C C:HIS1 2.8 22.2 1.0
CA C:HIS1 2.9 23.1 1.0
CA C:CYS2 2.9 22.5 1.0
CB C:CYS2 3.0 22.6 1.0
CB C:CYS6 3.4 23.2 1.0
CE1 C:HIS1 3.5 29.8 1.0
O C:HOH9041 3.5 30.4 1.0
CG C:HIS1 3.6 28.2 1.0
N C:ASP3 3.7 23.2 1.0
C C:CYS2 3.8 22.7 1.0
CB C:HIS1 3.8 25.2 1.0
N C:CYS6 4.0 25.1 1.0
O C:HIS1 4.0 22.6 1.0
O C:HOH9035 4.1 20.1 1.0
O C:VAL8 4.2 22.7 1.0
CA C:CYS6 4.3 24.6 1.0
OG A:SER20 4.5 28.4 1.0
NE2 C:HIS1 4.6 29.0 1.0
CD2 C:HIS1 4.7 28.4 1.0
O C:CYS2 4.8 22.2 1.0
N C:LEU4 4.9 21.1 1.0
N C:GLY7 4.9 24.9 1.0
C C:CYS6 5.0 25.3 1.0
CA C:ASP3 5.0 22.3 1.0

Nickel binding site 4 out of 12 in 1q0d

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Nickel binding site 4 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni118

b:30.2
occ:1.00
 N D:CYS2 2.0 19.0 1.0
N D:HIS1 2.1 20.1 1.0
SG D:CYS2 2.2 14.4 1.0
SG D:CYS6 2.3 18.7 1.0
ND1 D:HIS1 2.6 32.5 1.0
C D:HIS1 2.8 21.1 1.0
CA D:CYS2 2.9 18.7 1.0
CB D:CYS2 2.9 15.3 1.0
CA D:HIS1 2.9 22.2 1.0
CB D:CYS6 3.5 20.9 1.0
CE1 D:HIS1 3.5 32.7 1.0
CG D:HIS1 3.5 29.7 1.0
O D:HOH9027 3.6 31.7 1.0
N D:ASP3 3.7 19.0 1.0
C D:CYS2 3.7 18.6 1.0
CB D:HIS1 3.8 25.4 1.0
N D:CYS6 4.0 20.8 1.0
O D:HIS1 4.0 21.4 1.0
O D:HOH9005 4.2 13.9 1.0
O D:VAL8 4.2 21.2 1.0
CA D:CYS6 4.3 20.8 1.0
OG F:SER20 4.5 21.8 1.0
NE2 D:HIS1 4.6 32.2 1.0
CD2 D:HIS1 4.7 31.7 1.0
O D:CYS2 4.8 18.3 1.0
N D:LEU4 4.9 19.7 1.0
CA D:ASP3 5.0 18.2 1.0
N D:GLY7 5.0 22.0 1.0
C D:CYS6 5.0 21.9 1.0

Nickel binding site 5 out of 12 in 1q0d

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Nickel binding site 5 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni118

b:30.5
occ:1.00
 N E:CYS2 1.9 20.0 1.0
N E:HIS1 2.0 19.9 1.0
SG E:CYS6 2.2 20.9 1.0
SG E:CYS2 2.3 21.3 1.0
ND1 E:HIS1 2.6 29.5 1.0
C E:HIS1 2.8 20.9 1.0
CA E:HIS1 2.9 22.4 1.0
CA E:CYS2 2.9 20.8 1.0
CB E:CYS2 2.9 20.1 1.0
CB E:CYS6 3.5 23.4 1.0
CE1 E:HIS1 3.6 29.6 1.0
CG E:HIS1 3.6 27.0 1.0
O E:HOH9040 3.6 33.2 1.0
N E:ASP3 3.7 21.4 1.0
C E:CYS2 3.7 21.1 1.0
CB E:HIS1 3.8 24.1 1.0
N E:CYS6 4.0 23.0 1.0
O E:HIS1 4.0 21.4 1.0
O E:HOH9015 4.1 19.1 1.0
O E:VAL8 4.2 22.2 1.0
CA E:CYS6 4.3 23.5 1.0
OG B:SER20 4.6 26.6 1.0
NE2 E:HIS1 4.7 28.7 1.0
CD2 E:HIS1 4.7 28.8 1.0
O E:CYS2 4.8 20.3 1.0
N E:LEU4 4.9 21.6 1.0
N E:GLY7 5.0 23.6 1.0
CA E:ASP3 5.0 22.1 1.0

Nickel binding site 6 out of 12 in 1q0d

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Nickel binding site 6 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni118

b:29.9
occ:1.00
 N F:CYS2 1.9 19.3 1.0
N F:HIS1 2.1 22.9 1.0
SG F:CYS6 2.2 23.0 1.0
SG F:CYS2 2.3 20.7 1.0
ND1 F:HIS1 2.5 29.1 1.0
C F:HIS1 2.8 21.3 1.0
CA F:HIS1 2.9 23.1 1.0
CA F:CYS2 2.9 19.4 1.0
CB F:CYS2 3.0 19.2 1.0
O F:HOH9057 3.4 29.8 1.0
CE1 F:HIS1 3.4 28.6 1.0
CG F:HIS1 3.4 27.4 1.0
CB F:CYS6 3.5 22.9 1.0
CB F:HIS1 3.7 25.2 1.0
N F:ASP3 3.7 17.2 1.0
C F:CYS2 3.8 17.6 1.0
N F:CYS6 3.9 20.5 1.0
O F:HIS1 3.9 20.4 1.0
O F:HOH9011 4.0 18.9 1.0
O F:VAL8 4.1 17.6 1.0
CA F:CYS6 4.3 21.7 1.0
OG D:SER20 4.5 29.9 1.0
NE2 F:HIS1 4.6 27.2 1.0
CD2 F:HIS1 4.6 28.0 1.0
O F:CYS2 4.8 15.9 1.0
N F:LEU4 4.9 18.3 1.0
N F:GLY7 5.0 22.3 1.0
C F:PRO5 5.0 22.2 1.0
CA F:ASP3 5.0 17.1 1.0
N F:VAL8 5.0 20.5 1.0

Nickel binding site 7 out of 12 in 1q0d

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Nickel binding site 7 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni118

b:29.8
occ:1.00
 N G:CYS2 1.9 24.9 1.0
N G:HIS1 2.2 24.4 1.0
SG G:CYS6 2.2 26.4 1.0
SG G:CYS2 2.3 25.9 1.0
ND1 G:HIS1 2.6 32.9 1.0
C G:HIS1 2.8 25.5 1.0
CA G:CYS2 2.9 24.0 1.0
CA G:HIS1 2.9 26.3 1.0
CB G:CYS2 2.9 22.6 1.0
CB G:CYS6 3.4 25.3 1.0
CE1 G:HIS1 3.5 34.0 1.0
CG G:HIS1 3.5 31.5 1.0
N G:ASP3 3.7 23.5 1.0
O G:HOH9100 3.7 39.0 1.0
C G:CYS2 3.7 24.6 1.0
CB G:HIS1 3.8 29.4 1.0
N G:CYS6 3.8 25.7 1.0
O G:HIS1 4.0 24.9 1.0
O G:HOH9034 4.1 18.8 1.0
O G:VAL8 4.2 26.9 1.0
CA G:CYS6 4.2 25.9 1.0
NE2 G:HIS1 4.6 33.5 1.0
OG I:SER20 4.6 25.9 1.0
CD2 G:HIS1 4.7 33.0 1.0
O G:CYS2 4.8 23.9 1.0
N G:LEU4 4.8 21.9 1.0
C G:PRO5 4.9 26.4 1.0
N G:GLY7 4.9 26.4 1.0
C G:CYS6 5.0 26.5 1.0
CA G:ASP3 5.0 22.5 1.0

Nickel binding site 8 out of 12 in 1q0d

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Nickel binding site 8 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni118

b:31.8
occ:1.00
 N H:CYS2 1.9 17.6 1.0
N H:HIS1 2.0 19.5 1.0
SG H:CYS2 2.2 18.2 1.0
SG H:CYS6 2.3 20.3 1.0
ND1 H:HIS1 2.7 31.1 1.0
C H:HIS1 2.8 20.0 1.0
CA H:CYS2 2.9 18.8 1.0
CA H:HIS1 2.9 21.7 1.0
CB H:CYS2 2.9 18.5 1.0
O H:HOH9123 3.3 33.1 1.0
CB H:CYS6 3.5 23.5 1.0
CE1 H:HIS1 3.6 31.6 1.0
CG H:HIS1 3.6 28.1 1.0
N H:ASP3 3.6 19.1 1.0
C H:CYS2 3.7 18.6 1.0
CB H:HIS1 3.8 23.9 1.0
N H:CYS6 4.0 24.5 1.0
O H:HIS1 4.0 18.4 1.0
O H:HOH9041 4.1 16.8 1.0
O H:VAL8 4.3 16.9 1.0
CA H:CYS6 4.3 23.2 1.0
OG K:SER20 4.5 25.6 1.0
O H:CYS2 4.7 18.2 1.0
NE2 H:HIS1 4.7 30.8 1.0
CD2 H:HIS1 4.8 30.0 1.0
N H:LEU4 4.8 20.8 1.0
CA H:ASP3 4.9 20.4 1.0
N H:GLY7 5.0 21.9 1.0
C H:CYS6 5.0 22.4 1.0

Nickel binding site 9 out of 12 in 1q0d

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Nickel binding site 9 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ni118

b:27.8
occ:1.00
 N I:CYS2 1.9 21.5 1.0
N I:HIS1 2.2 23.2 1.0
SG I:CYS6 2.2 21.2 1.0
SG I:CYS2 2.3 20.4 1.0
ND1 I:HIS1 2.7 30.5 1.0
C I:HIS1 2.8 22.5 1.0
CA I:CYS2 2.9 20.8 1.0
CA I:HIS1 2.9 23.3 1.0
CB I:CYS2 3.0 18.5 1.0
O I:HOH9132 3.3 37.9 1.0
CB I:CYS6 3.5 20.2 1.0
CG I:HIS1 3.6 28.6 1.0
CE1 I:HIS1 3.7 31.1 1.0
N I:ASP3 3.7 20.6 1.0
C I:CYS2 3.7 20.9 1.0
CB I:HIS1 3.8 25.4 1.0
N I:CYS6 3.9 21.6 1.0
O I:HIS1 4.0 22.2 1.0
O I:HOH9044 4.1 15.9 1.0
O I:VAL8 4.2 23.7 1.0
CA I:CYS6 4.3 21.8 1.0
OG G:SER20 4.8 29.3 1.0
NE2 I:HIS1 4.8 29.6 1.0
CD2 I:HIS1 4.8 29.4 1.0
O I:CYS2 4.8 21.4 1.0
N I:LEU4 4.8 20.8 1.0
N I:GLY7 4.9 22.5 1.0
C I:CYS6 5.0 21.8 1.0
CA I:ASP3 5.0 21.4 1.0

Nickel binding site 10 out of 12 in 1q0d

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Nickel binding site 10 out of 12 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ni118

b:27.3
occ:1.00
 N J:CYS2 1.8 19.7 1.0
N J:HIS1 2.2 23.6 1.0
SG J:CYS2 2.2 20.8 1.0
SG J:CYS6 2.3 22.3 1.0
ND1 J:HIS1 2.7 31.5 1.0
C J:HIS1 2.7 20.9 1.0
CA J:CYS2 2.8 19.6 1.0
CA J:HIS1 2.9 23.9 1.0
CB J:CYS2 2.9 18.8 1.0
O J:HOH9144 3.4 42.6 1.0
CB J:CYS6 3.5 21.5 1.0
N J:ASP3 3.6 19.5 1.0
CE1 J:HIS1 3.6 32.0 1.0
CG J:HIS1 3.6 30.0 1.0
C J:CYS2 3.7 18.7 1.0
CB J:HIS1 3.8 26.9 1.0
O J:HIS1 3.9 20.2 1.0
N J:CYS6 3.9 21.8 1.0
O J:HOH9013 4.0 19.9 1.0
O J:VAL8 4.2 20.1 1.0
CA J:CYS6 4.3 21.7 1.0
OG L:SER20 4.7 27.9 1.0
O J:CYS2 4.7 18.2 1.0
NE2 J:HIS1 4.8 31.2 1.0
CD2 J:HIS1 4.8 31.0 1.0
N J:LEU4 4.8 21.3 1.0
CA J:ASP3 4.9 20.5 1.0

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.
ISSN: ISSN 0027-8424
PubMed: 15173586
DOI: 10.1073/PNAS.0308514101
Page generated: Wed Oct 9 16:17:24 2024

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