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Copper in PDB 1ws7: Crystal Structure of Mavicyanin From Cucurbita Pepo Medullosa (Zucchini)

Protein crystallography data

The structure of Crystal Structure of Mavicyanin From Cucurbita Pepo Medullosa (Zucchini), PDB code: 1ws7 was solved by Y.Xie, T.Inoue, Y.Miyamoto, H.Matsumura, K.Kataoka, K.Yamaguchi, M.Nojini, S.Suzuki, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.62 / 1.90
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 62.660, 62.660, 244.860, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 23

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Mavicyanin From Cucurbita Pepo Medullosa (Zucchini) (pdb code 1ws7). 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 Mavicyanin From Cucurbita Pepo Medullosa (Zucchini), PDB code: 1ws7:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1ws7

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Copper binding site 1 out of 4 in the Crystal Structure of Mavicyanin From Cucurbita Pepo Medullosa (Zucchini)


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 Mavicyanin From Cucurbita Pepo Medullosa (Zucchini) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1001

b:18.7
occ:1.00
ND1 A:HIS45 2.1 14.6 1.0
ND1 A:HIS91 2.1 13.8 1.0
SG A:CYS86 2.2 14.7 1.0
OE1 A:GLN96 2.6 15.8 1.0
CG A:HIS45 3.0 16.1 1.0
CE1 A:HIS91 3.0 15.8 1.0
CG A:HIS91 3.0 15.5 1.0
CE1 A:HIS45 3.1 15.8 1.0
CB A:HIS45 3.2 14.5 1.0
CB A:CYS86 3.2 12.6 1.0
CD A:GLN96 3.3 15.1 1.0
CB A:HIS91 3.4 14.9 1.0
NE2 A:GLN96 3.5 13.2 1.0
CA A:HIS45 3.6 15.8 1.0
OG1 A:THR15 3.7 24.7 1.0
O A:PHE44 3.8 17.9 1.0
CG1 A:ILE88 4.0 18.4 1.0
CD2 A:HIS45 4.1 14.9 1.0
CB A:ILE88 4.1 18.6 1.0
NE2 A:HIS91 4.1 17.7 1.0
NE2 A:HIS45 4.2 12.4 1.0
CD2 A:HIS91 4.2 15.2 1.0
N A:HIS45 4.4 15.2 1.0
C A:PHE44 4.4 18.0 1.0
CG A:GLN96 4.6 13.4 1.0
CA A:CYS86 4.6 12.7 1.0
N A:ASN46 4.7 15.4 1.0
C A:HIS45 4.7 14.9 1.0
CA A:HIS91 4.9 15.5 1.0
N A:ILE88 4.9 16.6 1.0

Copper binding site 2 out of 4 in 1ws7

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Copper binding site 2 out of 4 in the Crystal Structure of Mavicyanin From Cucurbita Pepo Medullosa (Zucchini)


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 Mavicyanin From Cucurbita Pepo Medullosa (Zucchini) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1002

b:16.2
occ:1.00
ND1 B:HIS91 2.1 15.7 1.0
ND1 B:HIS45 2.1 11.4 1.0
SG B:CYS86 2.2 12.6 1.0
OE1 B:GLN96 2.4 13.1 1.0
CG B:HIS91 3.1 14.5 1.0
CE1 B:HIS45 3.1 11.3 1.0
CE1 B:HIS91 3.1 14.0 1.0
CG B:HIS45 3.1 12.4 1.0
CD B:GLN96 3.2 13.1 1.0
CB B:CYS86 3.2 11.9 1.0
CB B:HIS91 3.4 14.4 1.0
CB B:HIS45 3.4 10.8 1.0
NE2 B:GLN96 3.4 12.5 1.0
CA B:HIS45 3.6 13.6 1.0
O B:PHE44 3.8 14.1 1.0
CB B:ILE88 3.9 18.3 1.0
CG1 B:ILE88 3.9 18.5 1.0
NE2 B:HIS45 4.2 10.6 1.0
NE2 B:HIS91 4.2 14.3 1.0
CD2 B:HIS91 4.2 14.0 1.0
CD2 B:HIS45 4.2 11.8 1.0
CG2 B:THR15 4.5 13.2 1.0
CG B:GLN96 4.5 11.2 1.0
N B:ASN46 4.5 13.6 1.0
N B:HIS45 4.6 11.9 1.0
C B:PHE44 4.6 13.3 1.0
CA B:CYS86 4.6 13.7 1.0
C B:HIS45 4.7 14.8 1.0
CG2 B:ILE88 4.7 18.9 1.0
CA B:HIS91 4.9 14.4 1.0
N B:ILE88 4.9 16.5 1.0
CB B:GLN96 5.0 12.0 1.0
CA B:ILE88 5.0 17.9 1.0

Copper binding site 3 out of 4 in 1ws7

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Copper binding site 3 out of 4 in the Crystal Structure of Mavicyanin From Cucurbita Pepo Medullosa (Zucchini)


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 Mavicyanin From Cucurbita Pepo Medullosa (Zucchini) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1003

b:16.2
occ:1.00
ND1 C:HIS91 2.0 15.6 1.0
ND1 C:HIS45 2.1 12.8 1.0
SG C:CYS86 2.2 12.5 1.0
OE1 C:GLN96 2.4 13.0 1.0
CE1 C:HIS91 3.0 14.5 1.0
CG C:HIS91 3.0 15.1 1.0
CE1 C:HIS45 3.1 10.8 1.0
CG C:HIS45 3.1 13.0 1.0
CD C:GLN96 3.1 12.1 1.0
CB C:CYS86 3.2 11.2 1.0
NE2 C:GLN96 3.3 12.7 1.0
CB C:HIS91 3.3 14.4 1.0
CB C:HIS45 3.4 12.4 1.0
CA C:HIS45 3.6 13.8 1.0
O C:PHE44 3.8 14.2 1.0
CB C:ILE88 3.9 16.8 1.0
CG1 C:ILE88 3.9 16.2 1.0
NE2 C:HIS91 4.1 14.8 1.0
CD2 C:HIS91 4.1 14.8 1.0
NE2 C:HIS45 4.2 10.9 1.0
CD2 C:HIS45 4.2 12.6 1.0
CG C:GLN96 4.5 11.1 1.0
CG2 C:THR15 4.5 12.0 1.0
C C:PHE44 4.6 13.9 1.0
N C:ASN46 4.6 13.5 1.0
N C:HIS45 4.6 13.1 1.0
CA C:CYS86 4.6 13.8 1.0
CG2 C:ILE88 4.7 17.2 1.0
C C:HIS45 4.7 14.4 1.0
CA C:HIS91 4.8 15.2 1.0
N C:ILE88 4.9 15.1 1.0
CB C:GLN96 5.0 11.8 1.0
CA C:ILE88 5.0 16.8 1.0
C C:CYS86 5.0 14.2 1.0

Copper binding site 4 out of 4 in 1ws7

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Copper binding site 4 out of 4 in the Crystal Structure of Mavicyanin From Cucurbita Pepo Medullosa (Zucchini)


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 Mavicyanin From Cucurbita Pepo Medullosa (Zucchini) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1004

b:18.3
occ:1.00
ND1 D:HIS45 2.0 13.9 1.0
ND1 D:HIS91 2.2 14.8 1.0
SG D:CYS86 2.2 14.6 1.0
OE1 D:GLN96 2.5 15.8 1.0
CG D:HIS45 2.9 15.9 1.0
CE1 D:HIS45 3.1 14.6 1.0
CG D:HIS91 3.1 16.4 1.0
CE1 D:HIS91 3.1 15.4 1.0
CB D:HIS45 3.1 15.0 1.0
CB D:CYS86 3.2 11.8 1.0
CD D:GLN96 3.2 15.5 1.0
CB D:HIS91 3.4 16.0 1.0
NE2 D:GLN96 3.4 12.5 1.0
CA D:HIS45 3.6 16.0 1.0
OG1 D:THR15 3.7 23.3 1.0
O D:PHE44 3.8 17.7 1.0
CG1 D:ILE88 4.0 18.1 1.0
CD2 D:HIS45 4.1 15.1 1.0
NE2 D:HIS45 4.1 13.0 1.0
CB D:ILE88 4.2 18.3 1.0
NE2 D:HIS91 4.2 16.8 1.0
CD2 D:HIS91 4.2 16.2 1.0
N D:HIS45 4.4 15.2 1.0
C D:PHE44 4.4 17.3 1.0
CG D:GLN96 4.6 14.1 1.0
CA D:CYS86 4.6 13.0 1.0
N D:ASN46 4.7 15.0 1.0
C D:HIS45 4.7 15.0 1.0
CA D:HIS91 4.9 15.6 1.0
N D:ILE88 4.9 16.2 1.0

Reference:

Y.Xie, T.Inoue, Y.Miyamoto, H.Matsumura, K.Kataoka, K.Yamaguchi, M.Nojini, S.Suzuki, Y.Kai. Structural Reorganization of the Copper Binding Site Involving THR15 of Mavicyanin From Cucurbita Pepo Medullosa (Zucchini) Upon Reduction. J.Biochem.(Tokyo) V. 137 455 2005.
ISSN: ISSN 0021-924X
PubMed: 15858169
DOI: 10.1093/JB/MVI062
Page generated: Wed Oct 28 14:17:54 2020
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