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Cadmium in PDB 2dm5: Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor

Protein crystallography data

The structure of Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor, PDB code: 2dm5 was solved by E.Barratt, A.Bronowska, J.Vondrasek, R.Bingham, S.Phillips, S.W.Homans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.42 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.522, 53.522, 137.192, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 20

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor (pdb code 2dm5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor, PDB code: 2dm5:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 2dm5

Go back to Cadmium Binding Sites List in 2dm5
Cadmium binding site 1 out of 4 in the Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd200

b:14.9
occ:1.00
O A:HOH472 2.3 11.6 1.0
OE2 A:GLU139 2.3 14.7 1.0
O A:HOH476 2.3 18.0 1.0
O A:HOH474 2.3 15.0 1.0
OE1 A:GLU139 2.5 13.1 1.0
CD A:GLU139 2.7 14.3 1.0
CG A:GLU139 4.2 12.9 1.0
O A:HOH486 4.2 32.5 1.0
NE2 A:GLN136 4.2 11.8 1.0
O A:HOH485 4.2 32.6 1.0
O A:HOH481 4.4 27.7 1.0
OE1 A:GLN136 4.5 17.0 1.0
CD A:GLN136 4.8 12.7 1.0
O A:HOH373 4.9 27.6 1.0

Cadmium binding site 2 out of 4 in 2dm5

Go back to Cadmium Binding Sites List in 2dm5
Cadmium binding site 2 out of 4 in the Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:25.3
occ:1.00
O A:HOH415 2.2 24.7 1.0
OE1 A:GLU13 2.3 20.1 1.0
O A:HOH475 2.4 19.8 1.0
OE2 A:GLU13 2.6 50.2 1.0
CD A:GLU13 2.8 30.0 1.0
O A:HOH463 3.1 53.5 1.0
CG A:GLU13 4.3 25.9 1.0
O A:HOH365 4.6 48.4 1.0

Cadmium binding site 3 out of 4 in 2dm5

Go back to Cadmium Binding Sites List in 2dm5
Cadmium binding site 3 out of 4 in the Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:23.8
occ:0.50
O A:HOH326 2.2 18.5 1.0
ND1 A:HIS104 2.4 19.1 1.0
O A:HOH394 2.5 16.4 1.0
CE1 A:HIS104 3.0 24.0 1.0
CG A:HIS104 3.4 16.3 1.0
CD A:CD311 3.6 28.0 0.5
OG1 A:THR91 3.7 14.7 1.0
O A:HOH349 3.7 31.3 1.0
CB A:HIS104 3.9 12.8 1.0
NE2 A:HIS104 4.1 13.1 1.0
CD2 A:HIS104 4.2 16.9 1.0
NE2 A:HIS141 4.5 16.5 1.0
O A:HOH362 4.5 32.4 1.0
O A:HIS104 4.7 14.0 1.0
CB A:THR91 4.9 13.8 1.0
CG2 A:THR91 5.0 16.5 1.0
CD2 A:HIS141 5.0 17.0 1.0
C A:HIS104 5.0 12.2 1.0

Cadmium binding site 4 out of 4 in 2dm5

Go back to Cadmium Binding Sites List in 2dm5
Cadmium binding site 4 out of 4 in the Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd311

b:28.0
occ:0.50
NE2 A:HIS141 2.4 16.5 1.0
O A:HOH394 2.4 16.4 1.0
O A:HOH342 2.5 25.0 1.0
CE1 A:HIS141 3.0 15.9 1.0
CD A:CD202 3.6 23.8 0.5
CD2 A:HIS141 3.6 17.0 1.0
O A:HOH315 4.0 15.8 1.0
O A:HOH349 4.1 31.3 1.0
ND1 A:HIS141 4.3 20.2 1.0
O A:HOH442 4.5 38.5 1.0
CG A:HIS141 4.6 14.7 1.0
ND1 A:HIS104 4.8 19.1 1.0
CG A:HIS104 5.0 16.3 1.0
CB A:PRO93 5.0 17.2 1.0

Reference:

E.Barratt, A.Bronowska, J.Vondrasek, J.Cerny, R.Bingham, S.Phillips, S.W.Homans. Thermodynamic Penalty Arising From Burial of A Ligand Polar Group Within A Hydrophobic Pocket of A Protein Receptor J.Mol.Biol. V. 362 994 2006.
ISSN: ISSN 0022-2836
PubMed: 16935302
DOI: 10.1016/J.JMB.2006.07.067
Page generated: Sat Dec 12 08:16:46 2020

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