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Copper 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:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 4 binding sites of Copper 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 Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 8zd5

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Copper 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 Copper with other atoms in the Cu 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:Cu202

b:89.3
occ:1.00
 NE2 A:HIS120 2.0 85.0 1.0
ND1 A:HIS46 2.0 75.1 1.0
NE2 A:HIS48 2.1 76.7 1.0
CD2 A:HIS120 2.9 77.5 1.0
CG A:HIS46 2.9 71.3 1.0
CE1 A:HIS48 3.0 75.5 1.0
CD2 A:HIS48 3.1 74.5 1.0
CE1 A:HIS120 3.1 82.0 1.0
CB A:HIS46 3.1 72.6 1.0
CE1 A:HIS46 3.1 82.5 1.0
NE2 A:HIS63 3.3 94.3 1.0
CD2 A:HIS63 3.8 94.8 1.0
CG A:HIS120 4.0 71.5 1.0
CE1 A:HIS63 4.1 95.9 1.0
CD2 A:HIS46 4.1 74.7 1.0
ND1 A:HIS120 4.1 80.1 1.0
ND1 A:HIS48 4.2 69.5 1.0
NE2 A:HIS46 4.2 73.3 1.0
CB A:VAL118 4.2 67.4 1.0
CG A:HIS48 4.2 72.0 1.0
CA A:HIS46 4.2 76.3 1.0
CG1 A:VAL118 4.2 71.2 1.0
N A:HIS46 4.3 80.1 1.0
O A:VAL118 4.4 67.8 1.0
O A:HIS46 4.5 70.2 1.0
CG A:HIS63 4.7 88.8 1.0
C A:HIS46 4.7 73.2 1.0
ND1 A:HIS63 4.8 85.5 1.0

Copper binding site 2 out of 4 in 8zd5

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Copper 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 Copper with other atoms in the Cu 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:Cu202

b:78.1
occ:1.00
 NE2 D:HIS48 2.0 64.0 1.0
NE2 D:HIS120 2.1 73.4 1.0
ND1 D:HIS46 2.1 77.8 1.0
CG D:HIS46 2.9 62.2 1.0
CD2 D:HIS120 2.9 62.3 1.0
CB D:HIS46 3.0 59.0 1.0
CD2 D:HIS48 3.0 57.5 1.0
CE1 D:HIS48 3.1 64.7 1.0
CE1 D:HIS120 3.1 74.7 1.0
CE1 D:HIS46 3.2 77.7 1.0
NE2 D:HIS63 3.3 85.8 1.0
CD2 D:HIS63 3.8 90.1 1.0
CG D:HIS120 4.0 65.4 1.0
CD2 D:HIS46 4.0 68.2 1.0
CE1 D:HIS63 4.1 89.0 1.0
CA D:HIS46 4.1 59.1 1.0
ND1 D:HIS120 4.1 63.2 1.0
CB D:VAL118 4.2 52.1 1.0
CG D:HIS48 4.2 58.2 1.0
ND1 D:HIS48 4.2 65.0 1.0
N D:HIS46 4.2 63.3 1.0
NE2 D:HIS46 4.2 69.1 1.0
CG1 D:VAL118 4.2 50.5 1.0
O D:HIS46 4.4 78.7 1.0
O D:VAL118 4.4 67.1 1.0
C D:HIS46 4.6 59.5 1.0
CG D:HIS63 4.7 71.3 1.0
ND1 D:HIS63 4.8 75.6 1.0
CG2 D:VAL118 5.0 59.0 1.0

Copper binding site 3 out of 4 in 8zd5

Go back to Copper Binding Sites List in 8zd5
Copper 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 Copper with other atoms in the Cu 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:Cu202

b:114.2
occ:1.00
 NE2 G:HIS120 2.0 115.0 1.0
NE2 G:HIS48 2.0 91.7 1.0
ND1 G:HIS46 2.1 122.8 1.0
CE1 G:HIS48 2.9 93.2 1.0
CD2 G:HIS120 2.9 107.3 1.0
CG G:HIS46 3.0 108.8 1.0
CE1 G:HIS120 3.0 108.0 1.0
CD2 G:HIS48 3.1 96.2 1.0
CE1 G:HIS46 3.1 125.8 1.0
NE2 G:HIS63 3.1 118.0 1.0
CB G:HIS46 3.2 111.3 1.0
CD2 G:HIS63 3.6 117.7 1.0
CE1 G:HIS63 3.9 131.1 1.0
CG G:HIS120 4.0 100.3 1.0
ND1 G:HIS48 4.1 93.8 1.0
ND1 G:HIS120 4.1 108.8 1.0
CD2 G:HIS46 4.1 114.1 1.0
CG G:HIS48 4.2 102.6 1.0
NE2 G:HIS46 4.2 120.0 1.0
CG1 G:VAL118 4.4 122.8 1.0
CB G:VAL118 4.4 116.0 1.0
CA G:HIS46 4.4 110.0 1.0
N G:HIS46 4.5 104.8 1.0
CG G:HIS63 4.5 109.9 1.0
O G:VAL118 4.6 104.2 1.0
ND1 G:HIS63 4.7 127.0 1.0
O G:HIS46 4.7 122.1 1.0
C G:HIS46 4.9 106.2 1.0

Copper binding site 4 out of 4 in 8zd5

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Copper 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 Copper with other atoms in the Cu 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:Cu202

b:104.8
occ:1.00
 NE2 J:HIS120 2.0 113.5 1.0
ND1 J:HIS46 2.1 96.6 1.0
NE2 J:HIS48 2.1 93.6 1.0
CD2 J:HIS120 2.9 113.6 1.0
CE1 J:HIS48 3.0 84.8 1.0
CG J:HIS46 3.0 86.0 1.0
CE1 J:HIS120 3.0 108.2 1.0
NE2 J:HIS63 3.1 109.4 1.0
CE1 J:HIS46 3.1 95.7 1.0
CD2 J:HIS48 3.2 77.8 1.0
CB J:HIS46 3.2 85.1 1.0
CD2 J:HIS63 3.5 104.1 1.0
CE1 J:HIS63 3.9 118.2 1.0
CG J:HIS120 4.0 111.7 1.0
ND1 J:HIS120 4.1 108.5 1.0
ND1 J:HIS48 4.1 89.5 1.0
CD2 J:HIS46 4.1 84.5 1.0
NE2 J:HIS46 4.2 94.2 1.0
CG J:HIS48 4.2 83.7 1.0
CA J:HIS46 4.4 84.9 1.0
CG1 J:VAL118 4.4 77.5 1.0
CB J:VAL118 4.4 77.9 1.0
CG J:HIS63 4.5 100.0 1.0
N J:HIS46 4.5 98.8 1.0
ND1 J:HIS63 4.6 105.8 1.0
O J:VAL118 4.7 93.6 1.0
O J:HIS46 4.7 99.1 1.0
C J:HIS46 4.9 93.7 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 19:38:13 2024

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