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Cadmium in PDB 1f48: Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase

Protein crystallography data

The structure of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase, PDB code: 1f48 was solved by T.Zhou, S.Radaev, B.P.Rosen, D.L.Gatti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.37 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 73.523, 75.715, 222.714, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26.3

Other elements in 1f48:

The structure of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Antimony (Sb) 4 atoms
Chlorine (Cl) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase (pdb code 1f48). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase, PDB code: 1f48:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1f48

Go back to Cadmium Binding Sites List in 1f48
Cadmium binding site 1 out of 6 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd600

b:69.1
occ:1.00
O A:HOH846 3.0 37.6 1.0
O A:HOH902 3.3 31.1 0.5
NE2 A:HIS585 3.5 93.3 1.0
CD2 A:HIS585 3.6 92.4 1.0
CE1 A:HIS585 3.8 93.5 1.0
CG A:HIS585 4.0 87.8 1.0
CB A:HIS586 4.0 77.0 1.0
ND1 A:HIS585 4.1 89.7 1.0
CA A:HIS586 4.2 78.0 1.0
N A:HIS586 4.3 81.3 1.0
CB A:HIS585 4.9 83.2 1.0

Cadmium binding site 2 out of 6 in 1f48

Go back to Cadmium Binding Sites List in 1f48
Cadmium binding site 2 out of 6 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:66.1
occ:1.00
O A:HOH909 2.6 40.9 1.0
O A:HOH719 2.9 54.1 1.0
OD1 A:ASP321 3.1 51.6 1.0
O A:HOH903 3.3 59.2 1.0
O A:HOH904 3.6 57.1 1.0
CG A:ASP321 4.1 43.6 1.0
OD2 A:ASP321 4.3 43.7 1.0
CB A:ASP320 4.6 49.8 1.0
O A:ALA317 4.7 43.6 1.0
OD2 A:ASP320 5.0 58.7 1.0

Cadmium binding site 3 out of 6 in 1f48

Go back to Cadmium Binding Sites List in 1f48
Cadmium binding site 3 out of 6 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd602

b:62.4
occ:1.00
NE2 A:HIS584 2.4 36.4 1.0
NE2 A:HIS586 3.2 76.8 1.0
O A:HOH781 3.3 60.0 1.0
CE1 A:HIS584 3.3 45.4 1.0
CD2 A:HIS584 3.4 43.8 1.0
O A:HOH761 3.5 61.0 1.0
CD2 A:HIS586 3.7 79.3 1.0
CE1 A:HIS586 4.3 79.7 1.0
ND1 A:HIS584 4.5 49.5 1.0
O A:HIS585 4.5 81.1 1.0
CG A:HIS584 4.5 48.3 1.0
CG A:HIS586 5.0 78.9 1.0

Cadmium binding site 4 out of 6 in 1f48

Go back to Cadmium Binding Sites List in 1f48
Cadmium binding site 4 out of 6 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd603

b:68.3
occ:0.50
NE2 A:HIS397 2.6 50.7 1.0
O A:HOH826 2.9 60.2 1.0
CD2 A:HIS397 3.4 52.2 1.0
CE1 A:HIS397 3.7 55.5 1.0
CG A:HIS397 4.6 53.6 1.0
ND1 A:HIS397 4.7 55.8 1.0
OE1 A:GLU168 4.8 0.7 1.0
CD A:GLU168 5.0 0.8 1.0
OE2 A:GLU168 5.0 0.8 1.0

Cadmium binding site 5 out of 6 in 1f48

Go back to Cadmium Binding Sites List in 1f48
Cadmium binding site 5 out of 6 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd604

b:58.0
occ:0.50
ND1 A:HIS388 2.5 37.4 1.0
OD2 A:ASP386 2.7 60.1 1.0
OD1 A:ASP386 2.8 58.3 1.0
CG A:ASP386 3.0 55.0 1.0
CG A:HIS388 3.3 42.5 1.0
CB A:HIS388 3.4 37.3 1.0
CE1 A:HIS388 3.5 46.3 1.0
CD2 A:HIS388 4.5 41.6 1.0
CB A:ASP386 4.5 54.0 1.0
NE2 A:HIS388 4.5 44.7 1.0
N A:HIS388 4.6 44.2 1.0
CA A:HIS388 4.6 42.6 1.0

Cadmium binding site 6 out of 6 in 1f48

Go back to Cadmium Binding Sites List in 1f48
Cadmium binding site 6 out of 6 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd605

b:0.1
occ:0.50
O A:HOH910 2.9 44.0 0.5
NE2 A:HIS520 3.1 59.8 1.0
O A:HOH786 3.3 65.6 1.0
CD2 A:HIS520 3.4 56.2 1.0
CE1 A:HIS520 4.3 62.4 1.0
CG A:HIS520 4.7 58.7 1.0
O A:GLY518 5.0 43.5 1.0

Reference:

T.Zhou, S.Radaev, B.P.Rosen, D.L.Gatti. Structure of the Arsa Atpase: the Catalytic Subunit of A Heavy Metal Resistance Pump. Embo J. V. 19 4838 2000.
ISSN: ISSN 0261-4189
PubMed: 10970874
DOI: 10.1093/EMBOJ/19.17.4838
Page generated: Sat Dec 12 08:08:59 2020

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