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Nickel in PDB 1q0m: Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction

Enzymatic activity of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction

All present enzymatic activity of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction, PDB code: 1q0m 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) 34.40 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.532, 119.428, 121.176, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction (pdb code 1q0m). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction, PDB code: 1q0m:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 1q0m

Go back to Nickel Binding Sites List in 1q0m
Nickel binding site 1 out of 6 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction


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 State After Full X- Ray-Induced Reduction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni118

b:29.1
occ:1.00
 N A:CYS2 1.9 29.4 1.0
N A:HIS1 2.1 29.6 1.0
SG A:CYS6 2.2 30.7 1.0
SG A:CYS2 2.2 31.1 1.0
C A:HIS1 2.8 27.9 1.0
CA A:CYS2 2.9 29.0 1.0
CA A:HIS1 2.9 28.7 1.0
CB A:CYS2 3.0 29.9 1.0
CB A:CYS6 3.3 29.6 1.0
N A:ASP3 3.7 28.9 1.0
C A:CYS2 3.7 31.6 1.0
O A:HOH9143 3.8 50.1 1.0
N A:CYS6 3.8 31.6 1.0
CG A:HIS1 3.8 33.9 1.0
ND1 A:HIS1 3.9 36.0 1.0
CB A:HIS1 3.9 30.1 1.0
O A:HIS1 4.0 28.6 1.0
CA A:CYS6 4.1 30.7 1.0
O A:HOH9012 4.2 30.9 1.0
O A:VAL8 4.3 30.0 1.0
CD2 A:HIS1 4.4 35.8 1.0
CE1 A:HIS1 4.4 34.0 1.0
OG C:SER20 4.6 36.5 1.0
NE2 A:HIS1 4.7 35.3 1.0
N A:LEU4 4.8 29.6 1.0
O A:CYS2 4.8 31.1 1.0
N A:GLY7 4.8 32.1 1.0
C A:CYS6 4.9 31.4 1.0
C A:PRO5 4.9 33.6 1.0
CA A:ASP3 4.9 30.7 1.0
N A:VAL8 5.0 29.3 1.0

Nickel binding site 2 out of 6 in 1q0m

Go back to Nickel Binding Sites List in 1q0m
Nickel binding site 2 out of 6 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction


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 State After Full X- Ray-Induced Reduction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni118

b:28.1
occ:1.00
 N B:CYS2 1.9 28.2 1.0
N B:HIS1 2.1 26.9 1.0
SG B:CYS6 2.2 29.9 1.0
SG B:CYS2 2.2 28.0 1.0
C B:HIS1 2.8 28.8 1.0
CA B:CYS2 2.9 28.6 1.0
CB B:CYS2 2.9 30.1 1.0
CA B:HIS1 3.0 30.4 1.0
CB B:CYS6 3.3 30.2 1.0
O B:HOH9060 3.5 41.9 1.0
N B:ASP3 3.6 27.2 1.0
C B:CYS2 3.7 29.2 1.0
N B:CYS6 3.8 28.9 1.0
CG B:HIS1 3.9 31.9 1.0
CB B:HIS1 4.0 30.2 1.0
ND1 B:HIS1 4.0 34.9 1.0
O B:HIS1 4.0 27.2 1.0
O B:HOH9014 4.0 28.3 1.0
CA B:CYS6 4.2 30.7 1.0
O B:VAL8 4.3 28.3 1.0
CD2 B:HIS1 4.4 33.7 1.0
OG E:SER20 4.5 35.7 1.0
CE1 B:HIS1 4.5 35.9 1.0
NE2 B:HIS1 4.7 33.7 1.0
O B:CYS2 4.8 30.7 1.0
N B:LEU4 4.8 28.1 1.0
N B:GLY7 4.9 30.3 1.0
C B:CYS6 4.9 30.1 1.0
C B:PRO5 4.9 32.7 1.0
CA B:ASP3 4.9 29.4 1.0

Nickel binding site 3 out of 6 in 1q0m

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Nickel binding site 3 out of 6 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction


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 State After Full X- Ray-Induced Reduction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni118

b:27.3
occ:1.00
 N C:CYS2 1.9 26.9 1.0
N C:HIS1 2.1 27.4 1.0
SG C:CYS6 2.2 30.1 1.0
SG C:CYS2 2.3 29.6 1.0
C C:HIS1 2.8 27.5 1.0
CA C:CYS2 2.9 26.9 1.0
CA C:HIS1 2.9 27.6 1.0
CB C:CYS2 3.0 28.5 1.0
CB C:CYS6 3.3 30.4 1.0
O C:HOH9083 3.5 44.8 1.0
N C:ASP3 3.7 28.1 1.0
C C:CYS2 3.7 28.5 1.0
N C:CYS6 3.8 30.4 1.0
CG C:HIS1 3.9 29.8 1.0
CB C:HIS1 4.0 28.3 1.0
O C:HIS1 4.0 28.1 1.0
ND1 C:HIS1 4.0 34.1 1.0
CA C:CYS6 4.1 30.9 1.0
O C:HOH9063 4.1 30.4 1.0
O C:VAL8 4.2 29.6 1.0
CD2 C:HIS1 4.3 32.6 1.0
OG A:SER20 4.4 38.0 1.0
CE1 C:HIS1 4.6 33.6 1.0
NE2 C:HIS1 4.7 31.7 1.0
N C:GLY7 4.8 29.5 1.0
O C:CYS2 4.8 27.6 1.0
N C:LEU4 4.8 29.8 1.0
C C:CYS6 4.8 29.6 1.0
C C:PRO5 4.9 31.5 1.0
CA C:ASP3 4.9 29.4 1.0
N C:VAL8 4.9 29.0 1.0

Nickel binding site 4 out of 6 in 1q0m

Go back to Nickel Binding Sites List in 1q0m
Nickel binding site 4 out of 6 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction


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 State After Full X- Ray-Induced Reduction within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni118

b:27.7
occ:1.00
 N D:CYS2 2.0 26.4 1.0
N D:HIS1 2.1 27.2 1.0
SG D:CYS6 2.2 29.0 1.0
SG D:CYS2 2.2 30.4 1.0
C D:HIS1 2.8 26.5 1.0
CA D:CYS2 2.9 27.8 1.0
CA D:HIS1 2.9 27.7 1.0
CB D:CYS2 3.0 27.1 1.0
CB D:CYS6 3.3 29.9 1.0
O D:HOH9063 3.4 45.4 1.0
N D:ASP3 3.6 26.7 1.0
C D:CYS2 3.7 26.6 1.0
CG D:HIS1 3.8 32.7 1.0
N D:CYS6 3.8 30.2 1.0
CB D:HIS1 3.9 28.1 1.0
ND1 D:HIS1 4.0 35.5 1.0
O D:HIS1 4.0 27.2 1.0
O D:HOH9012 4.1 32.1 1.0
CA D:CYS6 4.2 32.0 1.0
O D:VAL8 4.3 29.1 1.0
OG F:SER20 4.3 35.8 1.0
CD2 D:HIS1 4.3 35.2 1.0
CE1 D:HIS1 4.5 35.7 1.0
NE2 D:HIS1 4.7 35.5 1.0
N D:LEU4 4.8 29.9 1.0
O D:CYS2 4.8 29.2 1.0
N D:GLY7 4.8 31.0 1.0
C D:CYS6 4.9 32.1 1.0
C D:PRO5 4.9 32.7 1.0
CA D:ASP3 4.9 28.6 1.0
CB F:SER20 5.0 29.4 1.0
N D:VAL8 5.0 27.1 1.0

Nickel binding site 5 out of 6 in 1q0m

Go back to Nickel Binding Sites List in 1q0m
Nickel binding site 5 out of 6 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction


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 State After Full X- Ray-Induced Reduction within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni118

b:29.0
occ:1.00
 N E:CYS2 1.9 29.0 1.0
N E:HIS1 2.1 31.0 1.0
SG E:CYS6 2.2 30.1 1.0
SG E:CYS2 2.3 31.8 1.0
C E:HIS1 2.8 30.5 1.0
CA E:CYS2 2.9 29.3 1.0
CB E:CYS2 2.9 30.0 1.0
CA E:HIS1 3.0 31.4 1.0
CB E:CYS6 3.4 32.1 1.0
O E:HOH9079 3.5 44.2 1.0
N E:ASP3 3.7 28.7 1.0
C E:CYS2 3.7 29.6 1.0
N E:CYS6 3.8 31.1 1.0
CG E:HIS1 3.9 34.7 1.0
ND1 E:HIS1 3.9 33.6 1.0
CB E:HIS1 4.0 30.3 1.0
O E:HIS1 4.0 32.1 1.0
O E:HOH9017 4.1 33.6 1.0
CA E:CYS6 4.2 31.1 1.0
O E:VAL8 4.3 28.7 1.0
CD2 E:HIS1 4.4 34.9 1.0
OG B:SER20 4.5 38.4 1.0
CE1 E:HIS1 4.5 33.2 1.0
NE2 E:HIS1 4.8 35.9 1.0
O E:CYS2 4.8 30.1 1.0
N E:GLY7 4.8 32.3 1.0
N E:LEU4 4.8 29.8 1.0
C E:CYS6 4.8 32.5 1.0
C E:PRO5 4.9 33.3 1.0
N E:VAL8 4.9 30.7 1.0
CA E:ASP3 4.9 30.1 1.0

Nickel binding site 6 out of 6 in 1q0m

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Nickel binding site 6 out of 6 in the Crystal Structure of Ni-Containing Superoxide Dismutase with Ni-Ligation Corresponding to the State After Full X- Ray-Induced Reduction


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 State After Full X- Ray-Induced Reduction within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni118

b:28.9
occ:1.00
 N F:CYS2 1.9 30.9 1.0
N F:HIS1 2.0 30.1 1.0
SG F:CYS6 2.2 30.4 1.0
SG F:CYS2 2.2 30.8 1.0
C F:HIS1 2.8 30.6 1.0
CA F:CYS2 2.9 31.1 1.0
CB F:CYS2 2.9 31.4 1.0
CA F:HIS1 3.0 30.2 1.0
CB F:CYS6 3.3 31.4 1.0
O F:HOH9076 3.5 48.0 1.0
N F:ASP3 3.7 30.2 1.0
C F:CYS2 3.7 31.5 1.0
N F:CYS6 3.8 29.1 1.0
CG F:HIS1 3.9 33.5 1.0
CB F:HIS1 4.0 31.3 1.0
ND1 F:HIS1 4.0 36.2 1.0
O F:HIS1 4.0 29.6 1.0
O F:HOH9010 4.1 32.5 1.0
CA F:CYS6 4.1 33.8 1.0
O F:VAL8 4.2 30.7 1.0
OG D:SER20 4.4 37.6 1.0
CD2 F:HIS1 4.4 33.7 1.0
CE1 F:HIS1 4.5 34.3 1.0
NE2 F:HIS1 4.8 33.9 1.0
O F:CYS2 4.8 29.8 1.0
N F:LEU4 4.8 30.8 1.0
C F:CYS6 4.9 33.4 1.0
N F:GLY7 4.9 32.9 1.0
C F:PRO5 4.9 34.2 1.0
CA F:ASP3 4.9 31.3 1.0
N F:VAL8 5.0 30.7 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 16:18:29 2024

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