Copper in PDB 5vdf: Crystal Structure of Cu(I)-Loaded Yeast ATX1: Crystal Form II
Protein crystallography data
The structure of Crystal Structure of Cu(I)-Loaded Yeast ATX1: Crystal Form II, PDB code: 5vdf
was solved by
M.Lee,
M.J.Maher,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
58.09 /
1.93
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.148,
114.385,
58.135,
90.00,
92.32,
90.00
|
R / Rfree (%)
|
19.5 /
24.2
|
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Cu(I)-Loaded Yeast ATX1: Crystal Form II
(pdb code 5vdf). 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 Cu(I)-Loaded Yeast ATX1: Crystal Form II, PDB code: 5vdf:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 5vdf
Go back to
Copper Binding Sites List in 5vdf
Copper binding site 1 out
of 4 in the Crystal Structure of Cu(I)-Loaded Yeast ATX1: Crystal Form II
 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 Cu(I)-Loaded Yeast ATX1: Crystal Form II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu101
b:20.8
occ:1.00
|
SG
|
B:CYS15
|
2.3
|
22.1
|
1.0
|
SG
|
A:CYS15
|
2.3
|
19.1
|
1.0
|
SG
|
B:CYS18
|
2.4
|
21.3
|
1.0
|
SG
|
A:CYS18
|
2.4
|
20.5
|
1.0
|
CB
|
B:CYS15
|
3.3
|
21.9
|
1.0
|
CB
|
A:CYS15
|
3.3
|
18.5
|
1.0
|
N
|
B:CYS18
|
3.5
|
21.0
|
1.0
|
N
|
A:CYS18
|
3.5
|
19.2
|
1.0
|
CB
|
A:CYS18
|
3.5
|
18.8
|
1.0
|
N
|
B:CYS15
|
3.7
|
20.5
|
1.0
|
CB
|
B:CYS18
|
3.7
|
20.4
|
1.0
|
N
|
A:CYS15
|
3.8
|
18.6
|
1.0
|
CA
|
B:CYS15
|
3.9
|
20.8
|
1.0
|
CA
|
A:CYS18
|
4.0
|
18.9
|
1.0
|
CA
|
A:CYS15
|
4.0
|
18.9
|
1.0
|
CA
|
B:CYS18
|
4.1
|
20.4
|
1.0
|
O
|
B:CYS15
|
4.2
|
20.0
|
1.0
|
C
|
B:GLY17
|
4.3
|
22.2
|
1.0
|
C
|
B:CYS15
|
4.3
|
20.6
|
1.0
|
C
|
A:GLY17
|
4.4
|
20.8
|
1.0
|
OG1
|
A:THR14
|
4.4
|
20.0
|
1.0
|
C
|
A:THR14
|
4.4
|
20.4
|
1.0
|
O
|
A:CYS15
|
4.4
|
18.3
|
1.0
|
OG1
|
B:THR14
|
4.5
|
26.8
|
1.0
|
CA
|
B:GLY17
|
4.5
|
21.9
|
1.0
|
C
|
A:CYS15
|
4.5
|
19.4
|
1.0
|
N
|
B:GLY17
|
4.6
|
21.4
|
1.0
|
C
|
B:THR14
|
4.6
|
23.0
|
1.0
|
CA
|
A:GLY17
|
4.7
|
21.6
|
1.0
|
NZ
|
B:LYS65
|
4.7
|
22.3
|
1.0
|
N
|
A:THR14
|
4.7
|
20.4
|
1.0
|
N
|
A:GLY17
|
4.8
|
21.5
|
1.0
|
N
|
B:THR14
|
4.9
|
22.1
|
1.0
|
CA
|
A:THR14
|
5.0
|
20.5
|
1.0
|
|
Copper binding site 2 out
of 4 in 5vdf
Go back to
Copper Binding Sites List in 5vdf
Copper binding site 2 out
of 4 in the Crystal Structure of Cu(I)-Loaded Yeast ATX1: Crystal Form II
 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 Cu(I)-Loaded Yeast ATX1: Crystal Form II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu101
b:21.1
occ:1.00
|
SG
|
C:CYS15
|
2.3
|
21.0
|
1.0
|
SG
|
D:CYS15
|
2.3
|
22.1
|
1.0
|
SG
|
C:CYS18
|
2.4
|
21.8
|
1.0
|
SG
|
D:CYS18
|
2.4
|
21.9
|
1.0
|
CB
|
C:CYS15
|
3.4
|
20.5
|
1.0
|
CB
|
D:CYS15
|
3.5
|
21.8
|
1.0
|
N
|
D:CYS18
|
3.5
|
20.4
|
1.0
|
N
|
C:CYS18
|
3.5
|
20.6
|
1.0
|
CB
|
C:CYS18
|
3.6
|
20.3
|
1.0
|
N
|
D:CYS15
|
3.7
|
23.5
|
1.0
|
CB
|
D:CYS18
|
3.7
|
21.3
|
1.0
|
N
|
C:CYS15
|
3.8
|
19.9
|
1.0
|
CA
|
C:CYS18
|
4.0
|
20.3
|
1.0
|
CA
|
D:CYS15
|
4.0
|
22.2
|
1.0
|
CA
|
C:CYS15
|
4.1
|
21.1
|
1.0
|
CA
|
D:CYS18
|
4.1
|
21.1
|
1.0
|
O
|
D:CYS15
|
4.2
|
21.0
|
1.0
|
C
|
D:GLY17
|
4.2
|
22.3
|
1.0
|
C
|
D:CYS15
|
4.3
|
21.7
|
1.0
|
OG1
|
D:THR14
|
4.4
|
30.7
|
1.0
|
C
|
C:GLY17
|
4.4
|
21.4
|
1.0
|
CA
|
D:GLY17
|
4.4
|
22.9
|
1.0
|
O
|
C:CYS15
|
4.5
|
20.9
|
1.0
|
C
|
C:THR14
|
4.5
|
21.5
|
1.0
|
C
|
C:CYS15
|
4.5
|
22.0
|
1.0
|
OG1
|
C:THR14
|
4.5
|
22.9
|
1.0
|
N
|
D:GLY17
|
4.6
|
21.9
|
1.0
|
NZ
|
D:LYS65
|
4.6
|
22.4
|
1.0
|
C
|
D:THR14
|
4.6
|
27.3
|
1.0
|
CA
|
C:GLY17
|
4.7
|
21.8
|
1.0
|
N
|
C:THR14
|
4.8
|
20.6
|
1.0
|
N
|
D:THR14
|
4.8
|
24.9
|
1.0
|
N
|
C:GLY17
|
4.9
|
22.3
|
1.0
|
|
Copper binding site 3 out
of 4 in 5vdf
Go back to
Copper Binding Sites List in 5vdf
Copper binding site 3 out
of 4 in the Crystal Structure of Cu(I)-Loaded Yeast ATX1: Crystal Form II
 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 Cu(I)-Loaded Yeast ATX1: Crystal Form II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cu101
b:23.9
occ:1.00
|
SG
|
E:CYS15
|
2.3
|
23.4
|
1.0
|
SG
|
F:CYS18
|
2.3
|
25.7
|
1.0
|
SG
|
E:CYS18
|
2.3
|
24.6
|
1.0
|
SG
|
F:CYS15
|
2.4
|
24.8
|
1.0
|
CB
|
E:CYS15
|
3.3
|
22.5
|
1.0
|
CB
|
F:CYS15
|
3.4
|
22.8
|
1.0
|
N
|
E:CYS18
|
3.5
|
24.0
|
1.0
|
N
|
F:CYS18
|
3.5
|
24.3
|
1.0
|
CB
|
E:CYS18
|
3.6
|
24.5
|
1.0
|
CB
|
F:CYS18
|
3.6
|
24.9
|
1.0
|
N
|
F:CYS15
|
3.8
|
23.0
|
1.0
|
N
|
E:CYS15
|
3.8
|
22.9
|
1.0
|
CA
|
E:CYS18
|
4.0
|
23.7
|
1.0
|
CA
|
F:CYS18
|
4.0
|
24.9
|
1.0
|
CA
|
E:CYS15
|
4.0
|
23.5
|
1.0
|
CA
|
F:CYS15
|
4.0
|
22.7
|
1.0
|
O
|
E:CYS15
|
4.3
|
23.6
|
1.0
|
C
|
F:GLY17
|
4.3
|
25.0
|
1.0
|
C
|
E:GLY17
|
4.3
|
26.5
|
1.0
|
C
|
E:CYS15
|
4.4
|
25.4
|
1.0
|
OG1
|
E:THR14
|
4.4
|
26.0
|
1.0
|
O
|
F:CYS15
|
4.4
|
20.9
|
1.0
|
C
|
F:CYS15
|
4.4
|
23.6
|
1.0
|
OG1
|
F:THR14
|
4.4
|
33.6
|
1.0
|
C
|
E:THR14
|
4.5
|
24.8
|
1.0
|
CA
|
F:GLY17
|
4.6
|
25.0
|
1.0
|
CA
|
E:GLY17
|
4.6
|
27.8
|
1.0
|
NZ
|
E:LYS65
|
4.7
|
32.0
|
1.0
|
N
|
F:GLY17
|
4.8
|
25.1
|
1.0
|
N
|
E:GLY17
|
4.8
|
29.4
|
1.0
|
C
|
F:THR14
|
4.8
|
25.1
|
1.0
|
N
|
E:THR14
|
4.8
|
25.8
|
1.0
|
NZ
|
F:LYS65
|
4.8
|
31.6
|
1.0
|
|
Copper binding site 4 out
of 4 in 5vdf
Go back to
Copper Binding Sites List in 5vdf
Copper binding site 4 out
of 4 in the Crystal Structure of Cu(I)-Loaded Yeast ATX1: Crystal Form II
 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 Cu(I)-Loaded Yeast ATX1: Crystal Form II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cu101
b:22.4
occ:1.00
|
SG
|
H:CYS15
|
2.2
|
23.0
|
1.0
|
SG
|
G:CYS18
|
2.3
|
25.2
|
1.0
|
SG
|
G:CYS15
|
2.3
|
24.9
|
1.0
|
SG
|
H:CYS18
|
2.3
|
22.9
|
1.0
|
CB
|
H:CYS15
|
3.4
|
23.0
|
1.0
|
CB
|
G:CYS15
|
3.5
|
24.0
|
1.0
|
N
|
G:CYS18
|
3.5
|
24.9
|
1.0
|
N
|
H:CYS18
|
3.5
|
25.2
|
1.0
|
CB
|
H:CYS18
|
3.5
|
24.8
|
1.0
|
CB
|
G:CYS18
|
3.6
|
24.4
|
1.0
|
N
|
H:CYS15
|
3.7
|
22.9
|
1.0
|
N
|
G:CYS15
|
3.8
|
25.6
|
1.0
|
CA
|
H:CYS18
|
4.0
|
24.7
|
1.0
|
CA
|
G:CYS18
|
4.0
|
23.6
|
1.0
|
CA
|
H:CYS15
|
4.0
|
22.9
|
1.0
|
CA
|
G:CYS15
|
4.1
|
24.4
|
1.0
|
OG1
|
G:THR14
|
4.2
|
32.5
|
1.0
|
C
|
H:THR14
|
4.4
|
23.5
|
1.0
|
C
|
G:GLY17
|
4.4
|
26.8
|
1.0
|
O
|
G:CYS15
|
4.4
|
21.3
|
1.0
|
C
|
H:GLY17
|
4.4
|
26.6
|
1.0
|
O
|
H:CYS15
|
4.4
|
22.9
|
1.0
|
C
|
G:CYS15
|
4.5
|
24.9
|
1.0
|
C
|
H:CYS15
|
4.5
|
24.1
|
1.0
|
OG1
|
H:THR14
|
4.5
|
24.4
|
1.0
|
CA
|
G:GLY17
|
4.6
|
25.5
|
1.0
|
NZ
|
H:LYS65
|
4.7
|
30.7
|
1.0
|
CA
|
H:GLY17
|
4.7
|
26.4
|
1.0
|
N
|
H:THR14
|
4.7
|
23.6
|
1.0
|
C
|
G:THR14
|
4.8
|
29.4
|
1.0
|
N
|
G:GLY17
|
4.8
|
25.3
|
1.0
|
N
|
H:GLY17
|
4.9
|
26.2
|
1.0
|
N
|
G:THR14
|
4.9
|
28.6
|
1.0
|
O
|
H:THR14
|
4.9
|
22.9
|
1.0
|
CA
|
H:THR14
|
5.0
|
24.2
|
1.0
|
|
Reference:
M.Lee,
N.D.G.Cooray,
M.J.Maher.
The Crystal Structures of A Copper-Bound Metallochaperone From Saccharomyces Cerevisiae. J. Inorg. Biochem. V. 177 368 2017.
ISSN: ISSN 1873-3344
PubMed: 28865724
DOI: 10.1016/J.JINORGBIO.2017.08.009
Page generated: Wed Jul 31 05:15:02 2024
|