Zinc in PDB 8zd5: Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp

Enzymatic activity of Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp

All present enzymatic activity of Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp, PDB code: 8zd5 was solved by Y.Shino, Y.Furukawa, N.Muraki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.15 / 2.89
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.915, 82.213, 187.612, 90, 108.46, 90
R / Rfree (%) 20.1 / 24.9

Other elements in 8zd5:

The structure of Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp (pdb code 8zd5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp, PDB code: 8zd5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8zd5

Go back to Zinc Binding Sites List in 8zd5
Zinc binding site 1 out of 4 in the Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:82.3
occ:1.00
 OD1 A:ASP83 2.0 96.2 1.0
OD2 A:ASP83 2.1 80.6 1.0
ND1 A:HIS71 2.1 97.2 1.0
ND1 A:HIS63 2.1 85.5 1.0
ND1 A:HIS80 2.2 85.4 1.0
CG A:ASP83 2.3 77.2 1.0
CE1 A:HIS71 3.0 104.9 1.0
CE1 A:HIS80 3.1 89.1 1.0
CE1 A:HIS63 3.1 95.9 1.0
CG A:HIS71 3.1 104.6 1.0
CG A:HIS63 3.1 88.8 1.0
CG A:HIS80 3.2 87.2 1.0
CB A:HIS63 3.4 79.3 1.0
CB A:HIS71 3.5 103.3 1.0
CB A:HIS80 3.6 90.1 1.0
O A:GLN136 3.8 132.1 1.0
CB A:ASP83 3.8 74.2 1.0
CA A:HIS71 3.9 94.8 1.0
NE2 A:HIS71 4.1 101.4 1.0
NE2 A:HIS80 4.2 96.5 1.0
CD2 A:HIS71 4.2 108.8 1.0
NE2 A:HIS63 4.2 94.3 1.0
CD2 A:HIS80 4.2 94.0 1.0
CD2 A:HIS63 4.2 94.8 1.0
CA A:ASP83 4.6 80.7 1.0
N A:GLY72 4.7 88.0 1.0
N A:HIS80 4.8 109.3 1.0
CA A:HIS80 4.8 97.2 1.0
C A:GLN136 4.9 121.7 1.0
C A:HIS71 4.9 90.7 1.0
N A:ASP83 4.9 81.5 1.0
N A:HIS71 4.9 98.0 1.0
CA A:HIS63 4.9 81.2 1.0

Zinc binding site 2 out of 4 in 8zd5

Go back to Zinc Binding Sites List in 8zd5
Zinc binding site 2 out of 4 in the Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:67.2
occ:1.00
 OD1 D:ASP83 2.0 65.8 1.0
ND1 D:HIS63 2.1 75.6 1.0
OD2 D:ASP83 2.1 70.6 1.0
ND1 D:HIS71 2.1 76.1 1.0
ND1 D:HIS80 2.1 52.0 1.0
CG D:ASP83 2.4 62.2 1.0
CE1 D:HIS80 3.0 57.9 1.0
CE1 D:HIS71 3.0 80.1 1.0
CE1 D:HIS63 3.1 89.0 1.0
CG D:HIS63 3.1 71.3 1.0
CG D:HIS71 3.2 69.2 1.0
CG D:HIS80 3.2 50.7 1.0
CB D:HIS63 3.4 66.4 1.0
CB D:HIS71 3.6 63.3 1.0
CB D:HIS80 3.6 54.5 1.0
O D:GLN136 3.8 86.1 1.0
CB D:ASP83 3.9 66.1 1.0
CA D:HIS71 4.0 63.7 1.0
NE2 D:HIS71 4.1 74.3 1.0
NE2 D:HIS80 4.2 62.3 1.0
NE2 D:HIS63 4.2 85.8 1.0
CD2 D:HIS63 4.2 90.1 1.0
CD2 D:HIS71 4.2 69.4 1.0
CD2 D:HIS80 4.2 58.9 1.0
CA D:ASP83 4.6 73.5 1.0
N D:GLY72 4.8 72.8 1.0
N D:HIS80 4.8 68.1 1.0
CA D:HIS80 4.8 60.5 1.0
C D:GLN136 4.9 79.3 1.0
CA D:HIS63 4.9 64.5 1.0
N D:ASP83 4.9 72.7 1.0
C D:HIS71 4.9 73.8 1.0
N D:HIS71 5.0 67.7 1.0

Zinc binding site 3 out of 4 in 8zd5

Go back to Zinc Binding Sites List in 8zd5
Zinc binding site 3 out of 4 in the Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:118.9
occ:1.00
 OD2 G:ASP83 2.0 118.6 1.0
OD1 G:ASP83 2.0 115.6 1.0
ND1 G:HIS80 2.1 126.1 1.0
ND1 G:HIS71 2.1 132.7 1.0
ND1 G:HIS63 2.3 127.0 1.0
CG G:ASP83 2.3 111.0 1.0
CE1 G:HIS80 3.0 121.3 1.0
CE1 G:HIS71 3.1 122.4 1.0
CG G:HIS80 3.1 132.4 1.0
CG G:HIS71 3.1 135.4 1.0
CG G:HIS63 3.2 109.9 1.0
CE1 G:HIS63 3.3 131.1 1.0
CB G:HIS80 3.5 131.7 1.0
CB G:HIS63 3.5 96.5 1.0
CB G:HIS71 3.5 132.2 1.0
CB G:ASP83 3.8 106.6 1.0
CA G:HIS71 3.8 126.5 1.0
O G:GLN136 3.9 158.1 1.0
NE2 G:HIS80 4.1 129.2 1.0
CD2 G:HIS80 4.1 132.1 1.0
NE2 G:HIS71 4.2 117.7 1.0
CD2 G:HIS71 4.2 131.2 1.0
NE2 G:HIS63 4.4 118.0 1.0
CD2 G:HIS63 4.4 117.7 1.0
N G:HIS80 4.6 153.6 1.0
CA G:ASP83 4.6 107.4 1.0
N G:GLY72 4.6 110.8 1.0
CA G:HIS80 4.6 138.7 1.0
C G:HIS71 4.8 118.0 1.0
N G:HIS71 4.9 124.9 1.0
N G:ASP83 4.9 114.1 1.0
C G:GLN136 4.9 147.7 1.0
CA G:HIS63 5.0 98.9 1.0
O G:GLY72 5.0 119.2 1.0

Zinc binding site 4 out of 4 in 8zd5

Go back to Zinc Binding Sites List in 8zd5
Zinc binding site 4 out of 4 in the Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of E40K Variant of Cu/Zn-Superoxide Dismutase From Dog (Canis Familiaris) in the Holo Form Complexed with 22E1 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:102.0
occ:1.00
 OD1 J:ASP83 2.0 66.7 1.0
OD2 J:ASP83 2.1 84.3 1.0
ND1 J:HIS71 2.1 117.0 1.0
ND1 J:HIS80 2.1 105.6 1.0
ND1 J:HIS63 2.2 105.8 1.0
CG J:ASP83 2.3 73.5 1.0
CE1 J:HIS71 3.0 132.5 1.0
CE1 J:HIS80 3.0 107.3 1.0
CG J:HIS71 3.1 124.0 1.0
CG J:HIS80 3.1 95.5 1.0
CE1 J:HIS63 3.1 118.2 1.0
CG J:HIS63 3.2 100.0 1.0
CB J:HIS63 3.4 105.4 1.0
CB J:HIS80 3.5 94.2 1.0
CB J:HIS71 3.5 125.2 1.0
O J:GLN136 3.8 106.5 1.0
CB J:ASP83 3.8 86.8 1.0
CA J:HIS71 3.9 109.8 1.0
NE2 J:HIS80 4.1 93.5 1.0
NE2 J:HIS71 4.1 142.2 1.0
CD2 J:HIS80 4.2 94.2 1.0
CD2 J:HIS71 4.2 134.0 1.0
NE2 J:HIS63 4.3 109.4 1.0
CD2 J:HIS63 4.3 104.1 1.0
CA J:ASP83 4.6 95.2 1.0
N J:HIS80 4.7 111.5 1.0
N J:GLY72 4.7 101.4 1.0
CA J:HIS80 4.7 102.2 1.0
C J:GLN136 4.9 126.1 1.0
C J:HIS71 4.9 106.2 1.0
N J:HIS71 4.9 104.7 1.0
N J:ASP83 4.9 110.4 1.0
CA J:HIS63 5.0 97.9 1.0

Reference:

Y.Shino, N.Muraki, Y.Furukawa. Disulfide-Mediated Oligomerization of Mutant Cu/Zn-Superoxide Dismutase Associated with Canine Degenerative Myelopathy To Be Published.
Page generated: Tue Dec 10 21:55:47 2024

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