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Cadmium in PDB 1ij2: GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position

Protein crystallography data

The structure of GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position, PDB code: 1ij2 was solved by D.L.Akey, V.N.Malashkevich, P.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.763, 46.332, 51.359, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 27.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position (pdb code 1ij2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position, PDB code: 1ij2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1ij2

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Cadmium binding site 1 out of 5 in the GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:27.1
occ:0.65
CD A:CD202 0.0 27.1 0.7
CD A:CD202 2.0 39.1 0.3
ND1 A:HIS18 2.4 27.9 1.0
O A:HOH237 2.5 49.9 1.0
CE1 A:HIS18 3.1 29.5 1.0
CG A:HIS18 3.5 24.7 1.0
CB A:HIS18 3.9 24.0 1.0
CA A:HIS18 4.1 20.1 1.0
NE2 A:HIS18 4.4 28.0 1.0
OE2 A:GLU22 4.4 35.1 1.0
CD2 A:HIS18 4.5 29.7 1.0
O A:HIS18 4.7 20.4 1.0
O A:HOH217 4.7 39.5 1.0
C A:HIS18 4.8 21.4 1.0
ND2 A:ASN21 4.8 26.1 1.0

Cadmium binding site 2 out of 5 in 1ij2

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Cadmium binding site 2 out of 5 in the GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:39.1
occ:0.35
CD A:CD202 0.0 39.1 0.3
CD A:CD202 2.0 27.1 0.7
ND1 A:HIS18 2.7 27.9 1.0
CE1 A:HIS18 3.5 29.5 1.0
CG A:HIS18 3.6 24.7 1.0
CB A:HIS18 4.0 24.0 1.0
NE2 A:HIS18 4.5 28.0 1.0
O A:HOH237 4.5 49.9 1.0
CD2 A:HIS18 4.5 29.7 1.0
CA A:HIS18 4.7 20.1 1.0

Cadmium binding site 3 out of 5 in 1ij2

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Cadmium binding site 3 out of 5 in the GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:25.6
occ:1.00
O B:HOH243 2.2 38.1 1.0
NE2 B:HIS18 2.3 21.4 1.0
OE2 B:GLU22 2.4 30.2 1.0
O B:HOH241 2.5 41.5 1.0
O B:HOH203 2.5 26.0 1.0
CD2 B:HIS18 3.3 24.8 1.0
CE1 B:HIS18 3.3 26.6 1.0
CD B:GLU22 3.4 26.2 1.0
CG B:GLU22 3.8 22.7 1.0
NZ C:LYS27 4.0 27.8 1.0
O C:HOH213 4.3 36.1 1.0
ND1 B:HIS18 4.4 22.6 1.0
CG B:HIS18 4.4 20.5 1.0
O C:HOH219 4.4 36.6 1.0
OE1 B:GLU22 4.5 30.9 1.0
O C:HOH212 4.6 32.2 1.0

Cadmium binding site 4 out of 5 in 1ij2

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Cadmium binding site 4 out of 5 in the GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd203

b:28.9
occ:0.77
CD C:CD203 0.0 28.9 0.8
CD C:CD203 2.1 37.2 0.2
ND1 C:HIS18 2.4 29.7 1.0
O C:HOH237 2.6 51.0 1.0
CE1 C:HIS18 3.2 26.7 1.0
CG C:HIS18 3.5 27.2 1.0
CB C:HIS18 3.9 20.5 1.0
CA C:HIS18 4.1 16.2 1.0
NE2 C:HIS18 4.3 29.2 1.0
OE1 C:GLU22 4.5 31.7 1.0
CD2 C:HIS18 4.5 26.4 1.0
ND2 C:ASN21 4.7 33.5 1.0
O C:HIS18 4.7 15.8 1.0
O C:HOH220 4.8 54.5 1.0
C C:HIS18 4.9 18.7 1.0
O C:HOH225 5.0 38.0 1.0

Cadmium binding site 5 out of 5 in 1ij2

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Cadmium binding site 5 out of 5 in the GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of GCN4-Pvtl Coiled-Coil Trimer with Threonine at the A(16) Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd203

b:37.2
occ:0.23
CD C:CD203 0.0 37.2 0.2
CD C:CD203 2.1 28.9 0.8
ND1 C:HIS18 2.8 29.7 1.0
O C:HOH220 3.0 54.5 1.0
CE1 C:HIS18 3.5 26.7 1.0
CG C:HIS18 3.5 27.2 1.0
CB C:HIS18 3.9 20.5 1.0
O C:HOH237 4.0 51.0 1.0
NE2 C:HIS18 4.3 29.2 1.0
CD2 C:HIS18 4.4 26.4 1.0
CA C:HIS18 4.7 16.2 1.0

Reference:

D.L.Akey, V.N.Malashkevich, P.S.Kim. Buried Polar Residues in Coiled-Coil Interfaces. Biochemistry V. 40 6352 2001.
ISSN: ISSN 0006-2960
PubMed: 11371197
DOI: 10.1021/BI002829W
Page generated: Wed Oct 28 09:53:34 2020
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