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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

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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

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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

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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: Sun Dec 13 11:19:53 2020

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