Atomistry » Copper » PDB 1rju-1tl4 » 1rju
Atomistry »
  Copper »
    PDB 1rju-1tl4 »
      1rju »

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

Go back to Copper Binding Sites List in 1rju
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

Go back to Copper Binding Sites List in 1rju
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

Go back to Copper Binding Sites List in 1rju
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

Go back to Copper Binding Sites List in 1rju
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

Go back to Copper Binding Sites List in 1rju
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

Go back to Copper Binding Sites List in 1rju
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

Go back to Copper Binding Sites List in 1rju
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

Go back to Copper Binding Sites List in 1rju
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: Sun Dec 13 11:01:44 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy