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Cadmium in PDB 1orq: X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab

Protein crystallography data

The structure of X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab, PDB code: 1orq was solved by Y.Jiang, A.Lee, J.Chen, V.Ruta, M.Cadene, B.T.Chait, R.Mackinnon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.95 / 3.20
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 189.439, 189.439, 150.479, 90.00, 90.00, 90.00
R / Rfree (%) 25.3 / 29.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab (pdb code 1orq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab, PDB code: 1orq:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 1orq

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Cadmium binding site 1 out of 7 in the X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd216

b:99.2
occ:0.25
 NH1 A:ARG62 2.2 27.4 1.0
NH2 A:ARG62 2.5 24.6 1.0
CZ A:ARG62 2.6 32.3 1.0
OE1 A:GLU82 2.8 43.9 1.0
OE2 A:GLU82 3.1 40.4 1.0
CD A:GLU82 3.3 45.3 1.0
OE1 A:GLU80 3.7 70.0 1.0
NE A:ARG62 3.8 42.0 1.0
CD A:GLU80 4.2 68.7 1.0
CG A:GLU80 4.4 66.0 1.0
CB A:GLU80 4.7 58.2 1.0
CD A:ARG62 4.7 49.9 1.0
CG A:GLU82 4.8 47.4 1.0

Cadmium binding site 2 out of 7 in 1orq

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Cadmium binding site 2 out of 7 in the X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd217

b:0.8
occ:1.00
 OD1 A:ASP168 2.6 68.9 1.0
CG A:ASP168 3.3 67.3 1.0
OD2 A:ASP168 3.4 67.9 1.0
O A:HOH219 3.6 28.5 1.0
CB A:LYS170 4.0 73.2 1.0
CE1 B:HIS169 4.4 64.9 1.0
CG A:LYS170 4.4 77.2 1.0
NE2 B:HIS169 4.7 64.4 1.0
CB A:ASP168 4.7 65.6 1.0
O B:VAL168 4.9 62.7 1.0
N A:LYS170 4.9 69.9 1.0

Cadmium binding site 3 out of 7 in 1orq

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Cadmium binding site 3 out of 7 in the X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd218

b:0.0
occ:1.00
 OE2 A:GLU17 2.6 81.8 1.0
OE1 A:GLU17 3.3 81.5 1.0
CD A:GLU17 3.4 79.9 1.0
CA A:PRO13 4.5 62.1 1.0
O A:SER12 4.5 64.0 1.0
CG A:GLU17 4.8 76.2 1.0

Cadmium binding site 4 out of 7 in 1orq

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Cadmium binding site 4 out of 7 in the X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd220

b:62.0
occ:1.00
 OD1 B:ASP178 1.9 65.7 1.0
OD2 B:ASP178 2.1 61.2 1.0
CG B:ASP178 2.3 63.5 1.0
CB B:ASP178 3.8 61.1 1.0
N B:ASP178 4.8 62.1 1.0
CA B:ASP178 4.8 59.0 1.0
O B:ASP178 5.0 56.2 1.0

Cadmium binding site 5 out of 7 in 1orq

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Cadmium binding site 5 out of 7 in the X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd7

b:1.0
occ:1.00
 OD1 C:ASP185 2.3 99.0 1.0
OD2 C:ASP185 2.7 99.2 1.0
CG C:ASP185 2.9 98.2 1.0
OG C:SER182 3.3 0.9 1.0
CB C:SER182 4.1 0.8 1.0
CB C:ASP185 4.4 95.8 1.0

Cadmium binding site 6 out of 7 in 1orq

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Cadmium binding site 6 out of 7 in the X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd8

b:0.4
occ:1.00
 CB C:CYS46 2.4 98.3 1.0
SG C:CYS46 3.4 99.4 1.0
CA C:CYS46 3.7 98.3 1.0
C C:CYS46 4.0 99.5 1.0
O C:VAL43 4.2 79.7 1.0
O C:CYS46 4.2 0.2 1.0
N C:CYS46 4.4 95.9 1.0
CA C:VAL43 4.6 78.5 1.0
N C:THR47 4.6 0.6 1.0
O C:VAL42 4.6 80.2 1.0
C C:VAL43 4.8 80.1 1.0

Cadmium binding site 7 out of 7 in 1orq

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Cadmium binding site 7 out of 7 in the X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Structure of A Voltage-Dependent Potassium Channel in Complex with An Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd9

b:0.5
occ:1.00
 CZ C:ARG133 2.4 90.5 1.0
NH1 C:ARG133 2.7 89.4 1.0
NH2 C:ARG133 2.7 90.6 1.0
NE C:ARG133 2.9 89.9 1.0
CG C:PRO95 3.6 84.4 1.0
CD C:ARG133 3.7 88.3 1.0
O C:HOH14 4.0 55.4 1.0
CD C:PRO95 4.2 82.9 1.0
CD1 C:PHE137 4.4 80.6 1.0
CE1 C:PHE137 4.4 80.0 1.0
CB C:ALA96 4.8 83.5 1.0
N C:ALA96 4.9 83.9 1.0
CB C:PRO95 5.0 83.6 1.0

Reference:

Y.Jiang, A.Lee, J.Chen, V.Ruta, M.Cadene, B.T.Chait, R.Mackinnon. X-Ray Structure of A Voltage-Dependent K+ Channel Nature V. 423 33 2003.
ISSN: ISSN 0028-0836
PubMed: 12721618
DOI: 10.1038/NATURE01580
Page generated: Fri Aug 28 12:18:16 2020
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