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Copper in PDB 1rju: Crystal Structure of A Truncated Form of Yeast Copper Thionein

Protein crystallography data

The structure of Crystal Structure of A Truncated Form of Yeast Copper Thionein, PDB code: 1rju was solved by V.Calderone, B.Dolderer, H.J.Hartmann, H.Echner, C.Luchinat, C.Del Bianco, S.Mangani, U.Weser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.84 / 1.44
Space group P 43 3 2
Cell size a, b, c (Å), α, β, γ (°) 62.167, 62.167, 62.167, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.1

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of A Truncated Form of Yeast Copper Thionein (pdb code 1rju). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of A Truncated Form of Yeast Copper Thionein, PDB code: 1rju:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 1rju

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Copper binding site 1 out of 8 in the Crystal Structure of A Truncated Form of Yeast Copper Thionein


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 A Truncated Form of Yeast Copper Thionein within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cu37

b:9.9
occ:1.00
 SG V:CYS20 2.2 9.9 1.0
SG V:CYS3 2.2 10.6 1.0
SG V:CYS5 2.3 9.6 1.0
CU V:CU139 2.8 9.3 1.0
CU V:CU138 3.0 11.8 1.0
CU V:CU142 3.1 10.5 1.0
CB V:CYS5 3.3 9.8 1.0
CB V:CYS3 3.3 10.4 1.0
CB V:CYS20 3.3 9.8 1.0
CA V:CYS3 3.7 11.1 1.0
N V:CYS5 3.9 10.0 1.0
CU V:CU143 4.0 11.3 1.0
SG V:CYS10 4.0 9.9 1.0
SG V:CYS22 4.0 9.2 1.0
CB V:CYS10 4.0 10.1 1.0
CB V:CYS22 4.1 9.4 1.0
N V:GLN4 4.2 10.4 1.0
O V:HOH47 4.2 12.6 1.0
CA V:CYS5 4.3 9.9 1.0
C V:CYS3 4.3 11.2 1.0
O V:HOH46 4.6 11.6 1.0
CA V:CYS20 4.7 11.3 1.0
SG V:CYS16 4.8 11.9 1.0
CE1 V:HIS1 4.8 10.1 1.0
O V:CYS16 4.9 13.8 1.0
N V:CYS3 4.9 11.2 1.0
C V:GLN4 5.0 11.3 1.0

Copper binding site 2 out of 8 in 1rju

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Copper binding site 2 out of 8 in the Crystal Structure of A Truncated Form of Yeast Copper Thionein


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 A Truncated Form of Yeast Copper Thionein within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cu38

b:11.8
occ:1.00
 SG V:CYS16 2.1 11.9 1.0
SG V:CYS3 2.2 10.6 1.0
CU V:CU143 2.8 11.3 1.0
CU V:CU137 3.0 9.9 1.0
CB V:CYS3 3.0 10.4 1.0
CB V:CYS16 3.2 14.6 1.0
O V:CYS16 3.2 13.8 1.0
CB V:CYS10 3.4 10.1 1.0
NE2 V:GLN17 3.5 17.2 1.0
C V:CYS16 3.5 13.2 1.0
O V:CYS10 3.8 14.1 1.0
SG V:CYS10 3.8 9.9 1.0
CA V:CYS16 3.9 14.9 1.0
CU V:CU142 4.0 10.5 1.0
SG V:CYS20 4.0 9.9 1.0
CA V:CYS10 4.1 10.9 1.0
CB V:CYS20 4.1 9.8 1.0
N V:GLN17 4.1 14.6 1.0
CU V:CU139 4.2 9.3 1.0
C V:CYS10 4.3 11.6 1.0
CA V:CYS3 4.4 11.1 1.0
CD V:GLN17 4.4 17.6 1.0
CA V:GLN17 4.5 16.0 1.0
SG V:CYS34 4.6 11.2 1.0
N V:CYS16 4.7 16.5 1.0
O V:ASN13 4.7 16.9 1.0
SG V:CYS5 4.7 9.6 1.0
O V:HOH60 4.9 22.8 1.0
CB V:CYS5 4.9 9.8 1.0

Copper binding site 3 out of 8 in 1rju

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Copper binding site 3 out of 8 in the Crystal Structure of A Truncated Form of Yeast Copper Thionein


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 A Truncated Form of Yeast Copper Thionein within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cu39

b:9.3
occ:1.00
 SG V:CYS5 2.2 9.6 1.0
SG V:CYS10 2.3 9.9 1.0
SG V:CYS22 2.3 9.2 1.0
CU V:CU141 2.6 9.2 1.0
CU V:CU142 2.7 10.5 1.0
CU V:CU137 2.8 9.9 1.0
CU V:CU140 2.9 9.8 1.0
CB V:CYS10 3.3 10.1 1.0
CB V:CYS22 3.3 9.4 1.0
CU V:CU144 3.3 9.9 1.0
CB V:CYS5 3.3 9.8 1.0
CU V:CU143 3.3 11.3 1.0
SG V:CYS20 3.6 9.9 1.0
SG V:CYS7 4.0 9.3 1.0
SG V:CYS32 4.0 9.2 1.0
CB V:CYS34 4.0 10.1 1.0
SG V:CYS34 4.0 11.2 1.0
SG V:CYS26 4.1 9.1 1.0
CU V:CU138 4.2 11.8 1.0
CB V:CYS26 4.4 9.1 1.0
SG V:CYS3 4.5 10.6 1.0
CA V:CYS22 4.7 8.4 1.0
CA V:CYS10 4.7 10.9 1.0
CA V:CYS5 4.7 9.9 1.0
O V:CYS26 4.8 9.6 1.0

Copper binding site 4 out of 8 in 1rju

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Copper binding site 4 out of 8 in the Crystal Structure of A Truncated Form of Yeast Copper Thionein


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 A Truncated Form of Yeast Copper Thionein within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cu40

b:9.8
occ:1.00
 SG V:CYS32 2.2 9.2 1.0
SG V:CYS7 2.3 9.3 1.0
SG V:CYS10 2.3 9.9 1.0
CU V:CU144 2.6 9.9 1.0
CU V:CU141 2.7 9.2 1.0
CU V:CU139 2.9 9.3 1.0
CB V:CYS32 3.3 9.6 1.0
CB V:CYS10 3.4 10.1 1.0
CB V:CYS7 3.7 9.8 1.0
N V:CYS10 3.8 10.1 1.0
CB V:SER9 3.8 9.5 1.0
SG V:CYS26 4.0 9.1 1.0
SG V:CYS22 4.1 9.2 1.0
CB V:CYS34 4.1 10.1 1.0
CA V:CYS10 4.2 10.9 1.0
CU V:CU143 4.3 11.3 1.0
C V:SER9 4.3 11.2 1.0
OD2 V:ASP29 4.5 11.8 1.0
CA V:SER9 4.5 9.6 1.0
SG V:CYS5 4.5 9.6 1.0
CA V:CYS32 4.6 10.1 1.0
CB V:CYS5 4.7 9.8 1.0
N V:SER9 4.7 10.5 1.0
OG V:SER9 4.8 13.7 1.0
CA V:CYS7 4.9 9.3 1.0
O V:CYS26 5.0 9.6 1.0
CU V:CU142 5.0 10.5 1.0

Copper binding site 5 out of 8 in 1rju

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Copper binding site 5 out of 8 in the Crystal Structure of A Truncated Form of Yeast Copper Thionein


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of A Truncated Form of Yeast Copper Thionein within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cu41

b:9.2
occ:1.00
 SG V:CYS22 2.2 9.2 1.0
SG V:CYS26 2.3 9.1 1.0
SG V:CYS32 2.3 9.2 1.0
CU V:CU144 2.6 9.9 1.0
CU V:CU139 2.6 9.3 1.0
CU V:CU140 2.7 9.8 1.0
CB V:CYS32 3.2 9.6 1.0
CB V:CYS22 3.2 9.4 1.0
CB V:CYS26 3.5 9.1 1.0
CA V:CYS32 3.5 10.1 1.0
CD V:PRO33 3.5 10.1 1.0
N V:PRO33 3.9 9.9 1.0
SG V:CYS10 3.9 9.9 1.0
C V:CYS32 4.0 11.1 1.0
CB V:CYS34 4.0 10.1 1.0
N V:CYS34 4.0 9.6 1.0
SG V:CYS5 4.0 9.6 1.0
SG V:CYS7 4.2 9.3 1.0
CU V:CU142 4.3 10.5 1.0
CA V:CYS22 4.3 8.4 1.0
CA V:CYS34 4.6 10.6 1.0
CG V:PRO33 4.6 10.3 1.0
CA V:CYS26 4.8 8.8 1.0
O V:CYS26 4.8 9.6 1.0
N V:CYS32 4.8 11.1 1.0
CD V:PRO23 4.9 10.4 1.0
C V:PRO33 4.9 10.9 1.0
CA V:PRO33 4.9 11.7 1.0
O V:CYS32 5.0 10.1 1.0

Copper binding site 6 out of 8 in 1rju

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Copper binding site 6 out of 8 in the Crystal Structure of A Truncated Form of Yeast Copper Thionein


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of A Truncated Form of Yeast Copper Thionein within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cu42

b:10.5
occ:1.00
 SG V:CYS20 2.2 9.9 1.0
SG V:CYS34 2.3 11.2 1.0
SG V:CYS22 2.4 9.2 1.0
CU V:CU139 2.7 9.3 1.0
CU V:CU143 2.8 11.3 1.0
CU V:CU137 3.1 9.9 1.0
CB V:CYS34 3.2 10.1 1.0
CB V:CYS20 3.4 9.8 1.0
CB V:CYS22 3.4 9.4 1.0
N V:CYS22 3.6 9.7 1.0
CA V:CYS20 3.7 11.3 1.0
SG V:CYS10 3.7 9.9 1.0
N V:SER21 3.7 10.5 1.0
CU V:CU138 4.0 11.8 1.0
CA V:CYS34 4.0 10.6 1.0
C V:CYS20 4.1 8.8 1.0
CA V:CYS22 4.1 8.4 1.0
SG V:CYS5 4.2 9.6 1.0
CU V:CU141 4.3 9.2 1.0
SG V:CYS16 4.4 11.9 1.0
CB V:CYS16 4.4 14.6 1.0
C V:SER21 4.5 9.3 1.0
CA V:SER21 4.7 9.8 1.0
OG V:SER21 4.7 16.3 1.0
SG V:CYS3 4.8 10.6 1.0
N V:CYS34 4.9 9.6 1.0
CB V:CYS10 4.9 10.1 1.0
CU V:CU140 5.0 9.8 1.0

Copper binding site 7 out of 8 in 1rju

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Copper binding site 7 out of 8 in the Crystal Structure of A Truncated Form of Yeast Copper Thionein


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of A Truncated Form of Yeast Copper Thionein within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cu43

b:11.3
occ:1.00
 SG V:CYS16 2.2 11.9 1.0
SG V:CYS34 2.2 11.2 1.0
SG V:CYS10 2.3 9.9 1.0
CU V:CU142 2.8 10.5 1.0
CU V:CU138 2.8 11.8 1.0
CB V:CYS34 3.1 10.1 1.0
CB V:CYS16 3.1 14.6 1.0
CB V:CYS10 3.2 10.1 1.0
CU V:CU139 3.3 9.3 1.0
CA V:CYS10 3.9 10.9 1.0
CU V:CU137 4.0 9.9 1.0
CU V:CU140 4.3 9.8 1.0
SG V:CYS20 4.3 9.9 1.0
SG V:CYS22 4.4 9.2 1.0
SG V:CYS3 4.6 10.6 1.0
N V:CYS10 4.6 10.1 1.0
CA V:CYS16 4.6 14.9 1.0
CA V:CYS34 4.6 10.6 1.0
O V:SER9 4.8 14.2 1.0
ND2 V:ASN13 4.9 18.5 1.0
CB V:CYS20 5.0 9.8 1.0
O V:CYS16 5.0 13.8 1.0
C V:SER9 5.0 11.2 1.0
C V:CYS10 5.0 11.6 1.0

Copper binding site 8 out of 8 in 1rju

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Copper binding site 8 out of 8 in the Crystal Structure of A Truncated Form of Yeast Copper Thionein


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of A Truncated Form of Yeast Copper Thionein within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cu44

b:9.9
occ:1.00
 SG V:CYS26 2.1 9.1 1.0
SG V:CYS7 2.2 9.3 1.0
O V:CYS26 2.6 9.6 1.0
CU V:CU140 2.6 9.8 1.0
CU V:CU141 2.6 9.2 1.0
CB V:CYS26 3.0 9.1 1.0
CB V:CYS7 3.1 9.8 1.0
C V:CYS26 3.1 9.3 1.0
CU V:CU139 3.3 9.3 1.0
SG V:CYS32 3.6 9.2 1.0
CA V:CYS26 3.6 8.8 1.0
SG V:CYS5 3.6 9.6 1.0
CB V:CYS5 3.7 9.8 1.0
CB V:CYS32 3.8 9.6 1.0
N V:ASN27 3.9 9.0 1.0
SG V:CYS10 4.1 9.9 1.0
N V:CYS7 4.2 8.8 1.0
CA V:CYS7 4.2 9.3 1.0
O V:HOH52 4.3 16.5 1.0
SG V:CYS22 4.4 9.2 1.0
N V:SER28 4.5 9.4 1.0
O V:SER28 4.5 11.3 1.0
CA V:ASN27 4.5 9.6 1.0
CA V:CYS32 4.6 10.1 1.0
CB V:CYS10 4.6 10.1 1.0
CA V:CYS5 4.7 9.9 1.0
C V:ASN27 4.8 8.7 1.0
N V:CYS26 4.8 9.5 1.0
C V:SER28 4.9 10.8 1.0
CB V:CYS22 4.9 9.4 1.0

Reference:

V.Calderone, B.Dolderer, H.J.Hartmann, H.Echner, C.Luchinat, C.Del Bianco, S.Mangani, U.Weser. The Crystal Structure of Yeast Copper Thionein: the Solution of A Long Lasting Enigma. Proc.Natl.Acad.Sci.Usa V. 102 51 2005.
ISSN: ISSN 0027-8424
PubMed: 15613489
DOI: 10.1073/PNAS.0408254101
Page generated: Mon Jul 14 00:22:15 2025

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