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Cadmium in PDB 1ihu: Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3

Enzymatic activity of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3

All present enzymatic activity of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3:
3.6.3.16;

Protein crystallography data

The structure of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3, PDB code: 1ihu 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) 25.15 / 2.15
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 73.897, 75.945, 222.607, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 26.2

Other elements in 1ihu:

The structure of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Magnesium (Mg) 2 atoms
Aluminium (Al) 1 atom
Arsenic (As) 1 atom
Chlorine (Cl) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3 (pdb code 1ihu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3, PDB code: 1ihu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 1ihu

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Cadmium binding site 1 out of 8 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3


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 in Complex with Mg-Adp-ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd600

b:54.3
occ:1.00
 O A:HOH891 3.0 38.9 1.0
O A:HOH892 3.3 5.6 0.5
CE1 A:HIS585 3.5 79.5 1.0
ND1 A:HIS585 3.8 74.8 1.0
NE2 A:HIS585 3.9 76.3 1.0
CB A:HIS586 4.2 65.1 1.0
CG A:HIS585 4.3 78.1 1.0
CD2 A:HIS585 4.3 79.9 1.0
N A:HIS586 4.9 68.2 1.0
CA A:HIS586 5.0 69.5 1.0

Cadmium binding site 2 out of 8 in 1ihu

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Cadmium binding site 2 out of 8 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3


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 in Complex with Mg-Adp-ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:57.2
occ:1.00
 O A:HOH889 1.7 23.8 1.0
O A:HOH890 2.9 38.1 1.0
OD1 A:ASP321 3.1 46.1 1.0
CG A:ASP321 4.0 36.0 1.0
OD2 A:ASP321 4.1 44.0 1.0
CB A:ASP320 4.9 36.6 1.0
O A:ALA317 4.9 38.9 1.0

Cadmium binding site 3 out of 8 in 1ihu

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Cadmium binding site 3 out of 8 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3


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 in Complex with Mg-Adp-ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd602

b:55.4
occ:1.00
 NE2 A:HIS584 2.2 35.6 1.0
O A:HOH885 2.7 48.1 1.0
CE1 A:HIS584 3.1 38.1 1.0
CD2 A:HIS584 3.2 37.8 1.0
NE2 A:HIS586 3.2 70.3 1.0
CD2 A:HIS586 3.6 69.1 1.0
ND1 A:HIS584 4.3 37.6 1.0
CG A:HIS584 4.3 42.2 1.0
CE1 A:HIS586 4.4 70.5 1.0
O A:HIS585 4.7 66.7 1.0
CG A:HIS586 4.9 67.8 1.0

Cadmium binding site 4 out of 8 in 1ihu

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Cadmium binding site 4 out of 8 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3


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 in Complex with Mg-Adp-ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd603

b:79.9
occ:1.00
 NE2 A:HIS397 2.4 47.6 1.0
O A:HOH737 2.7 37.8 1.0
O A:HOH886 3.0 47.6 1.0
CD2 A:HIS397 3.3 44.0 1.0
CE1 A:HIS397 3.4 50.8 1.0
CG A:HIS397 4.5 45.3 1.0
ND1 A:HIS397 4.5 49.0 1.0
OG1 A:THR401 4.8 57.9 1.0

Cadmium binding site 5 out of 8 in 1ihu

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Cadmium binding site 5 out of 8 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3


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 in Complex with Mg-Adp-ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd604

b:52.0
occ:0.50
 ND1 A:HIS388 2.0 33.4 1.0
OD2 A:ASP386 2.3 46.7 1.0
CE1 A:HIS388 2.9 43.0 1.0
OD1 A:ASP386 2.9 42.1 1.0
CG A:ASP386 3.0 44.5 1.0
CG A:HIS388 3.1 38.9 1.0
CB A:HIS388 3.5 34.2 1.0
NE2 A:HIS388 4.0 42.3 1.0
CD2 A:HIS388 4.2 34.0 1.0
CB A:ASP386 4.4 43.6 1.0
N A:HIS388 4.7 35.7 1.0
CA A:HIS388 4.7 32.6 1.0

Cadmium binding site 6 out of 8 in 1ihu

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Cadmium binding site 6 out of 8 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3


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 in Complex with Mg-Adp-ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd594

b:32.1
occ:1.00
 SG A:CYS422 2.6 30.7 1.0
SG A:CYS113 2.6 30.8 1.0
CL A:CL597 2.6 27.5 1.0
SG A:CYS172 2.6 27.4 1.0
O A:HOH703 2.7 25.1 1.0
CB A:CYS422 3.4 34.8 1.0
CB A:CYS113 3.5 24.6 1.0
CB A:CYS172 3.7 25.6 1.0
CD A:CD595 3.7 28.9 1.0
CB A:SER420 3.8 32.1 1.0
O A:HOH715 3.8 23.2 1.0
O A:HOH882 4.0 47.8 1.0
OG A:SER420 4.1 36.5 1.0
CD A:CD596 4.3 30.8 1.0
N A:CYS113 4.4 25.5 1.0
N A:CYS422 4.5 28.7 1.0
CA A:CYS113 4.6 28.6 1.0
CA A:CYS422 4.6 33.2 1.0
O A:HOH740 4.8 33.2 1.0
CL A:CL598 5.0 27.9 1.0

Cadmium binding site 7 out of 8 in 1ihu

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Cadmium binding site 7 out of 8 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd595

b:28.9
occ:1.00
 NE2 A:HIS453 2.4 26.9 1.0
O A:HOH883 2.4 28.1 1.0
CL A:CL598 2.5 27.9 1.0
SG A:CYS172 2.5 27.4 1.0
CL A:CL597 2.7 27.5 1.0
CE1 A:HIS453 3.3 17.7 1.0
CD2 A:HIS453 3.3 22.2 1.0
O A:HOH715 3.4 23.2 1.0
CB A:CYS172 3.5 25.6 1.0
CD A:CD594 3.7 32.1 1.0
CA A:GLY111 4.0 19.3 1.0
CA A:CYS172 4.1 28.6 1.0
CD2 A:LEU457 4.2 36.9 1.0
N A:GLY111 4.3 24.6 1.0
O A:GLN108 4.4 29.3 1.0
ND1 A:HIS453 4.4 27.4 1.0
O A:HOH882 4.4 47.8 1.0
CG A:HIS453 4.5 27.2 1.0
CB A:CYS113 4.5 24.6 1.0
O A:SER171 4.5 34.4 1.0
C A:GLY111 4.8 23.9 1.0
N A:CYS172 4.8 30.3 1.0
C A:SER171 4.9 39.9 1.0

Cadmium binding site 8 out of 8 in 1ihu

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Cadmium binding site 8 out of 8 in the Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of the Escherichia Coli Arsenite-Translocating Atpase in Complex with Mg-Adp-ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd596

b:30.8
occ:1.00
 O A:HOH881 2.2 22.2 1.0
NE2 A:HIS148 2.4 28.4 1.0
OG A:SER420 2.4 36.5 1.0
CL A:CL599 2.4 61.4 1.0
SG A:CYS113 2.5 30.8 1.0
CD2 A:HIS148 3.2 23.7 1.0
CB A:SER420 3.4 32.1 1.0
CE1 A:HIS148 3.4 28.2 1.0
CB A:CYS113 3.5 24.6 1.0
O A:HOH712 3.5 28.6 1.0
CD1 A:LEU152 4.0 26.2 1.0
OD1 A:ASP417 4.2 37.9 1.0
CA A:SER420 4.2 27.8 1.0
CB A:CYS172 4.2 25.6 1.0
O A:HOH713 4.3 29.0 1.0
CD A:CD594 4.3 32.1 1.0
CG A:HIS148 4.4 29.2 1.0
ND1 A:HIS148 4.5 24.2 1.0
CA A:CYS113 4.5 28.6 1.0
O A:CYS172 4.9 30.6 1.0
O A:ASP417 4.9 22.3 1.0
N A:SER420 5.0 31.9 1.0

Reference:

T.Zhou, S.Radaev, B.P.Rosen, D.L.Gatti. Conformational Changes in Four Regions of the Escherichia Coli Arsa Atpase Link Atp Hydrolysis to Ion Translocation. J.Biol.Chem. V. 276 30414 2001.
ISSN: ISSN 0021-9258
PubMed: 11395509
DOI: 10.1074/JBC.M103671200
Page generated: Fri Jul 19 13:32:06 2024

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