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Copper in PDB 5j7d: Computationally Designed Thioredoxin DF106

Protein crystallography data

The structure of Computationally Designed Thioredoxin DF106, PDB code: 5j7d was solved by S.Horowitz, N.Johansen, J.G.Olsen, J.R.Winther, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.20 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.070, 67.950, 229.451, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 27.3

Copper Binding Sites:

The binding sites of Copper atom in the Computationally Designed Thioredoxin DF106 (pdb code 5j7d). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Computationally Designed Thioredoxin DF106, PDB code: 5j7d:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5j7d

Go back to Copper Binding Sites List in 5j7d
Copper binding site 1 out of 3 in the Computationally Designed Thioredoxin DF106


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Computationally Designed Thioredoxin DF106 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:37.8
occ:1.00
NE2 F:HIS9 2.0 41.2 1.0
NE2 A:HIS9 2.1 43.9 1.0
NE2 D:HIS9 2.2 42.2 1.0
NE2 B:HIS9 2.2 48.7 1.0
CD2 A:HIS9 2.9 40.7 1.0
CD2 F:HIS9 2.9 37.9 1.0
CE1 F:HIS9 3.0 29.2 1.0
CD2 D:HIS9 3.0 35.6 1.0
CD2 B:HIS9 3.1 43.5 1.0
CE1 A:HIS9 3.2 37.8 1.0
CE1 B:HIS9 3.2 44.4 1.0
CE1 D:HIS9 3.3 37.6 1.0
ND1 F:HIS9 4.1 41.9 1.0
CG F:HIS9 4.1 43.2 1.0
CG A:HIS9 4.1 40.8 1.0
ND1 A:HIS9 4.2 39.2 1.0
CG D:HIS9 4.3 41.5 1.0
CG B:HIS9 4.3 46.7 1.0
ND1 B:HIS9 4.3 47.3 1.0
ND1 D:HIS9 4.3 42.0 1.0

Copper binding site 2 out of 3 in 5j7d

Go back to Copper Binding Sites List in 5j7d
Copper binding site 2 out of 3 in the Computationally Designed Thioredoxin DF106


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Computationally Designed Thioredoxin DF106 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:39.3
occ:1.00
NE2 E:HIS9 2.1 50.1 1.0
NE2 C:HIS9 2.1 39.4 1.0
NE2 G:HIS9 2.1 41.4 1.0
O C:HOH313 2.2 45.0 1.0
NE2 H:HIS9 2.3 42.0 1.0
CD2 C:HIS9 2.9 38.5 1.0
CD2 G:HIS9 3.0 38.2 1.0
CD2 E:HIS9 3.0 37.3 1.0
CD2 H:HIS9 3.0 37.3 1.0
CE1 E:HIS9 3.1 35.7 1.0
CE1 C:HIS9 3.2 40.9 1.0
CE1 G:HIS9 3.2 43.7 1.0
CE1 H:HIS9 3.4 42.2 1.0
CG C:HIS9 4.1 40.2 1.0
CG E:HIS9 4.2 36.9 1.0
ND1 E:HIS9 4.2 34.0 1.0
CG G:HIS9 4.2 39.9 1.0
ND1 C:HIS9 4.2 42.8 1.0
CG H:HIS9 4.2 41.9 1.0
ND1 G:HIS9 4.3 44.8 1.0
ND1 H:HIS9 4.4 43.1 1.0
O H:HOH218 4.9 52.5 1.0

Copper binding site 3 out of 3 in 5j7d

Go back to Copper Binding Sites List in 5j7d
Copper binding site 3 out of 3 in the Computationally Designed Thioredoxin DF106


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Computationally Designed Thioredoxin DF106 within 5.0Å range:

Reference:

K.E.Johansson, N.T.Johansen, S.Christensen, S.Horowitz, J.C.Bardwell, J.G.Olsen, M.Willemoes, K.Lindorff-Larsen, J.Ferkinghoff-Borg, T.Hamelryck, J.R.Winther. Computational Redesign of Thioredoxin Is Hypersensitive Toward Minor Conformational Changes in the Backbone Template. J.Mol.Biol. V. 428 4361 2016.
ISSN: ESSN 1089-8638
PubMed: 27659562
DOI: 10.1016/J.JMB.2016.09.013
Page generated: Sun Dec 13 11:18:04 2020

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