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Cadmium in PDB 1zne: Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex

Protein crystallography data

The structure of Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex, PDB code: 1zne was solved by R.Malham, S.Johnstone, R.J.Bingham, E.Barratt, S.E.Phillips, C.A.Laughton, S.W.Homans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.60 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.228, 53.228, 137.060, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex (pdb code 1zne). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex, PDB code: 1zne:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1zne

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Cadmium binding site 1 out of 5 in the Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd200

b:20.1
occ:1.00
OE1 A:GLU139 2.4 15.7 1.0
O A:HOH319 2.4 16.1 1.0
O A:HOH320 2.4 23.4 1.0
OE2 A:GLU139 2.5 15.4 1.0
O A:HOH213 2.5 17.9 1.0
CD A:GLU139 2.8 17.3 1.0
NE2 A:GLN136 4.2 13.4 1.0
O A:HOH289 4.3 39.6 1.0
CG A:GLU139 4.3 15.2 1.0
O A:HOH242 4.4 28.4 1.0
OE1 A:GLN136 4.5 17.0 1.0
CD A:GLN136 4.8 15.9 1.0

Cadmium binding site 2 out of 5 in 1zne

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Cadmium binding site 2 out of 5 in the Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:37.0
occ:1.00
O A:HOH323 1.9 27.1 1.0
O A:HOH324 2.3 20.6 1.0
OE1 A:GLU13 2.4 31.7 1.0
O A:HOH322 2.5 22.1 1.0
OE2 A:GLU13 2.7 38.0 1.0
CD A:GLU13 2.9 32.7 1.0
CG A:GLU13 4.3 30.1 1.0
O A:HOH433 4.8 56.1 1.0
O A:HOH260 4.8 51.0 1.0

Cadmium binding site 3 out of 5 in 1zne

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Cadmium binding site 3 out of 5 in the Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd199

b:31.2
occ:0.50
O A:HOH446 2.3 24.3 1.0
ND1 A:HIS104 2.5 19.8 1.0
O A:HOH445 2.5 18.0 1.0
CE1 A:HIS104 3.2 20.5 1.0
CG A:HIS104 3.4 18.8 1.0
CD A:CD198 3.5 34.7 0.5
OG1 A:THR91 3.7 17.5 1.0
O A:HOH296 3.7 34.7 1.0
CB A:HIS104 3.8 16.2 1.0
O A:HOH442 4.1 46.5 1.0
NE2 A:HIS104 4.2 17.9 1.0
CD2 A:HIS104 4.3 18.4 1.0
NE2 A:HIS141 4.5 20.5 1.0
O A:HOH249 4.6 43.0 1.0
O A:HIS104 4.8 16.0 1.0
CD2 A:HIS141 4.9 19.2 1.0
CB A:THR91 4.9 16.9 1.0

Cadmium binding site 4 out of 5 in 1zne

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Cadmium binding site 4 out of 5 in the Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd198

b:34.7
occ:0.50
O A:HOH447 2.4 28.8 1.0
NE2 A:HIS141 2.5 20.5 1.0
O A:HOH445 2.5 18.0 1.0
CE1 A:HIS141 3.2 17.4 1.0
O A:HOH296 3.3 34.7 1.0
CD A:CD199 3.5 31.2 0.5
CD2 A:HIS141 3.6 19.2 1.0
O A:HOH212 4.1 19.9 1.0
ND1 A:HIS141 4.4 20.4 1.0
CG A:HIS141 4.7 18.8 1.0
ND1 A:HIS104 4.8 19.8 1.0
CB A:PRO93 4.9 17.8 1.0
O A:HOH442 4.9 46.5 1.0
CG A:HIS104 5.0 18.8 1.0

Cadmium binding site 5 out of 5 in 1zne

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Cadmium binding site 5 out of 5 in the Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Strong Solute-Solute Dispersive Interactions in A Protein- Ligand Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:53.7
occ:1.00
O A:HOH414 2.4 30.0 1.0
OD2 A:ASP98 2.6 28.5 1.0
O A:HOH448 2.6 31.0 1.0
CG A:ASP98 3.7 29.1 1.0
O A:HOH230 4.0 29.3 1.0
O A:ASP96 4.1 22.4 1.0
CB A:ASP98 4.2 26.0 1.0
OD2 A:ASP96 4.3 18.9 1.0
N A:GLU1 4.6 52.2 1.0
O A:HOH428 4.6 38.5 1.0
O A:HOH280 4.6 8.7 1.0
OE2 A:GLU1 4.7 67.0 1.0
OD1 A:ASP98 4.7 31.2 1.0
O A:HOH294 4.7 28.1 1.0
CG A:ASP96 4.8 20.4 1.0
CB A:ASP96 4.8 17.6 1.0
ND2 A:ASN99 4.8 23.5 1.0

Reference:

R.Malham, S.Johnstone, R.J.Bingham, E.Barratt, S.E.Phillips, C.A.Laughton, S.W.Homans. Strong Solute-Solute Dispersive Interactions in A Protein-Ligand Complex. J.Am.Chem.Soc. V. 127 17061 2005.
ISSN: ISSN 0002-7863
PubMed: 16316253
DOI: 10.1021/JA055454G
Page generated: Fri Aug 28 12:45:19 2020
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