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Cadmium in PDB 3die: Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant

Protein crystallography data

The structure of Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant, PDB code: 3die was solved by S.Martinez-Rodriguez, R.Loris, J.Messens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.20 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.703, 84.451, 34.699, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant (pdb code 3die). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant, PDB code: 3die:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3die

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Cadmium binding site 1 out of 4 in the Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd105

b:11.0
occ:0.40
OE1 A:GLU40 2.3 30.7 1.0
OE2 A:GLU40 2.4 29.6 1.0
CD A:GLU40 2.7 26.6 1.0
O A:HOH159 4.1 58.6 1.0
CG A:GLU40 4.2 25.3 1.0
O A:HOH133 4.3 33.7 1.0
CA A:PRO37 4.7 28.9 1.0
CB A:PRO37 4.8 29.2 1.0
N A:PRO37 4.9 28.7 1.0

Cadmium binding site 2 out of 4 in 3die

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Cadmium binding site 2 out of 4 in the Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd106

b:11.3
occ:0.50
OD2 A:ASP80 2.2 32.0 1.0
O A:HOH191 2.4 17.9 1.0
O A:HOH109 2.5 14.8 1.0
OD1 A:ASP80 2.6 32.6 1.0
CG A:ASP80 2.8 30.9 1.0
O A:HOH129 4.0 47.1 1.0
CB A:ASP80 4.3 28.8 1.0
O A:HOH174 4.4 50.8 1.0
N B:GLY18 4.5 27.0 1.0
CE A:LYS79 4.5 35.1 1.0
CA B:GLY18 4.7 26.4 1.0
NZ A:LYS79 4.7 38.1 1.0
CG A:LYS79 4.8 30.7 1.0
O A:HOH140 4.9 50.7 1.0

Cadmium binding site 3 out of 4 in 3die

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Cadmium binding site 3 out of 4 in the Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd107

b:27.4
occ:0.70
O A:HOH188 1.6 25.6 1.0
O A:HOH187 2.2 39.8 1.0
OXT A:LEU104 2.4 31.7 1.0
O A:LEU104 2.4 31.2 1.0
C A:LEU104 2.8 30.7 1.0
O A:HOH160 3.8 55.5 1.0
O A:HOH140 3.9 50.7 1.0
CA A:LEU104 4.3 30.5 1.0
O A:HOH152 4.3 47.8 1.0

Cadmium binding site 4 out of 4 in 3die

Go back to Cadmium Binding Sites List in 3die
Cadmium binding site 4 out of 4 in the Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Domain Swapping of Staphylococcus Aureus Thioredoxin W28A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd105

b:26.1
occ:0.40
O B:HOH198 2.0 43.7 1.0
OE2 B:GLU47 2.1 34.0 1.0
OE1 B:GLU47 2.5 39.4 1.0
CD B:GLU47 2.6 35.1 1.0
CG B:GLU47 4.0 33.0 1.0
O B:HOH187 4.4 41.2 1.0
CB B:GLU47 4.9 32.9 1.0

Reference:

A.Garcia-Pino, S.Martinez-Rodriguez, K.Wahni, L.Wyns, R.Loris, J.Messens. Coupling of Domain Swapping to Kinetic Stability in A Thioredoxin Mutant J.Mol.Biol. V. 385 1590 2009.
ISSN: ISSN 0022-2836
PubMed: 19071139
DOI: 10.1016/J.JMB.2008.11.040
Page generated: Fri Aug 28 13:33:24 2020
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