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:
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
|