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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy