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Cadmium in PDB 2xq7: Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+)

Protein crystallography data

The structure of Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+), PDB code: 2xq7 was solved by R.J.C.Hilf, C.Bertozzi, I.Zimmermann, A.Reiter, D.Trauner, R.Dutzler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.20 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.314, 128.310, 164.374, 90.00, 104.04, 90.00
R / Rfree (%) 24.2 / 26.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+) (pdb code 2xq7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+), PDB code: 2xq7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 2xq7

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Cadmium binding site 1 out of 5 in the Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1317

b:0.6
occ:1.00
OE1 C:GLU221 2.3 0.1 0.5
OE1 E:GLU221 2.4 0.1 0.5
OE1 A:GLU221 2.4 0.1 0.5
OE1 D:GLU221 2.7 0.1 0.5
OE1 B:GLU221 2.9 0.1 0.5
CD C:GLU221 3.4 0.5 0.5
CD A:GLU221 3.4 0.5 0.5
CD E:GLU221 3.5 0.5 0.5
CD D:GLU221 3.8 0.5 0.5
OE2 A:GLU221 3.8 0.1 0.5
OE2 C:GLU221 3.8 0.1 0.5
CD B:GLU221 3.9 0.5 0.5
OE2 E:GLU221 4.0 0.1 0.5
CG C:GLU221 4.1 0.4 0.5
CG E:GLU221 4.1 0.4 0.5
OE2 D:GLU221 4.2 0.1 0.5
CG A:GLU221 4.3 0.4 0.5
OE2 B:GLU221 4.4 0.1 0.5
CG D:GLU221 4.4 0.4 0.5
CD A:CD1318 4.5 0.4 1.0
CG C:GLU221 4.6 0.8 0.5
CG E:GLU221 4.6 0.8 0.5
CG B:GLU221 4.6 0.4 0.5
CB E:GLU221 4.6 0.0 0.5
CB C:GLU221 4.6 0.0 0.5
CB E:GLU221 4.7 0.8 0.5
CB C:GLU221 4.7 0.8 0.5
CG A:GLU221 4.7 0.8 0.5
OE2 E:GLU221 4.8 80.2 0.5
OE2 C:GLU221 4.8 80.2 0.5
CB A:GLU221 4.9 0.0 0.5
CD C:GLU221 4.9 88.7 0.5
CB A:GLU221 4.9 0.8 0.5
CD E:GLU221 4.9 88.7 0.5
CG D:GLU221 5.0 0.8 0.5
OE2 D:GLU221 5.0 80.2 0.5
CB D:GLU221 5.0 0.0 0.5

Cadmium binding site 2 out of 5 in 2xq7

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Cadmium binding site 2 out of 5 in the Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1318

b:0.4
occ:1.00
OE2 E:GLU221 2.5 80.2 0.5
OE2 C:GLU221 2.5 80.2 0.5
OE2 A:GLU221 2.7 80.2 0.5
OE2 D:GLU221 2.8 80.2 0.5
OE2 B:GLU221 2.9 80.2 0.5
CD C:GLU221 3.2 88.7 0.5
CD E:GLU221 3.2 88.7 0.5
CD A:GLU221 3.3 88.7 0.5
CD D:GLU221 3.6 88.7 0.5
OE1 C:GLU221 3.7 81.7 0.5
CD B:GLU221 3.7 88.7 0.5
OE1 A:GLU221 3.8 81.7 0.5
OE1 E:GLU221 3.8 81.7 0.5
OE1 D:GLU221 4.1 81.7 0.5
CG C:GLU221 4.1 0.4 0.5
CG A:GLU221 4.1 0.4 0.5
CG E:GLU221 4.1 0.4 0.5
OG1 E:THR225 4.2 96.3 1.0
OG1 C:THR225 4.2 96.3 1.0
OE1 B:GLU221 4.3 81.7 0.5
OE1 A:GLU221 4.3 0.1 0.5
OE1 C:GLU221 4.4 0.1 0.5
OG1 D:THR225 4.4 96.3 1.0
CG D:GLU221 4.4 0.4 0.5
OE1 E:GLU221 4.5 0.1 0.5
CG B:GLU221 4.5 0.4 0.5
CD A:CD1317 4.5 0.6 1.0
OG1 A:THR225 4.6 96.3 1.0
OG1 B:THR225 4.6 96.3 1.0
OE1 B:GLU221 4.7 0.1 0.5
OE1 D:GLU221 4.7 0.1 0.5

Cadmium binding site 3 out of 5 in 2xq7

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Cadmium binding site 3 out of 5 in the Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1319

b:0.1
occ:1.00
OE2 A:GLU74 3.7 0.4 1.0
CD A:GLU74 4.2 0.8 1.0
O E:VAL88 4.2 91.6 1.0
CG A:GLU74 4.5 0.8 1.0
CB E:ASP87 4.9 0.6 1.0
OE1 A:GLU74 4.9 0.1 1.0

Cadmium binding site 4 out of 5 in 2xq7

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Cadmium binding site 4 out of 5 in the Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1317

b:0.9
occ:1.00
OE2 C:GLU74 3.6 0.4 1.0
CD C:GLU74 4.1 0.8 1.0
O B:VAL88 4.3 91.6 1.0
CG C:GLU74 4.4 0.8 1.0
CB B:ASP87 4.6 0.6 1.0
OD2 B:ASP87 4.8 0.3 1.0
CB C:GLU74 4.9 0.2 1.0
OE1 C:GLU74 4.9 0.1 1.0

Cadmium binding site 5 out of 5 in 2xq7

Go back to Cadmium Binding Sites List in 2xq7
Cadmium binding site 5 out of 5 in the Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Pentameric Ligand Gated Ion Channel Glic in Complex with Cadmium Ion (CD2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1318

b:0.1
occ:1.00
OE2 D:GLU74 3.6 0.4 1.0
O C:VAL88 4.0 91.6 1.0
CD D:GLU74 4.1 0.8 1.0
CB C:ASP87 4.2 0.6 1.0
CG D:GLU74 4.4 0.8 1.0
OD2 C:ASP87 4.6 0.3 1.0
CG C:ASP87 4.8 0.8 1.0
CB D:GLU74 4.8 0.2 1.0
N C:VAL88 4.8 91.0 1.0
C C:ASP87 4.9 91.5 1.0
C C:VAL88 4.9 84.0 1.0
OE1 D:GLU74 4.9 0.1 1.0

Reference:

R.J.C.Hilf, C.Bertozzi, I.Zimmermann, A.Reiter, D.Trauner, R.Dutzler. Structural Basis of Open Channel Block in A Prokaryotic Pentameric Ligand-Gated Ion Channel Nat.Struct.Mol.Biol. V. 17 1330 2010.
ISSN: ISSN 1545-9993
PubMed: 21037567
DOI: 10.1038/NSMB.1933
Page generated: Fri Aug 28 13:16:16 2020
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