Cadmium in PDB 1yp7: Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water

The structure of Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water, PDB code: 1yp7 was solved by E.Barratt, R.J.Bingham, D.J.Warner, C.A.Laughton, S.E.V.Phillips, S.W.Homans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.23 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.459, 56.459, 104.071, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.6

The binding sites of Cadmium atom in the Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water (pdb code 1yp7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water, PDB code: 1yp7:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd163 b:26.6 occ:1.00 O A:HOH339 1.9 19.2 1.0 O A:HOH341 2.3 21.4 1.0 OE1 A:GLU139 2.4 23.6 1.0 OE2 A:GLU139 2.4 23.1 1.0 O A:HOH340 2.6 23.5 1.0 CD A:GLU139 2.7 23.9 1.0 CG A:GLU139 4.2 24.3 1.0 NE2 A:GLN136 4.4 22.5 1.0 OE1 A:GLN136 4.8 26.8 1.0 O A:HOH193 4.9 30.9 1.0

Cadmium binding site 2 out of 3 in the Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd164 b:37.0 occ:1.00 O A:HOH342 2.5 33.7 1.0 O A:HOH215 2.6 19.5 1.0 O A:HOH258 2.6 29.2 1.0 OG A:SER128 2.8 27.5 1.0 CB A:SER128 3.1 21.2 1.0 O A:HOH301 3.3 63.6 1.0 N A:SER128 3.9 22.9 1.0 CA A:SER128 4.1 23.6 1.0 N A:ASP129 4.4 21.4 1.0 OD1 A:ASP129 4.6 40.4 1.0 O A:HOH335 4.6 48.1 1.0 C A:SER128 4.8 23.2 1.0 CB A:SER127 5.0 19.5 1.0

Cadmium binding site 3 out of 3 in the Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd178 b:24.3 occ:1.00 OE1 A:GLN115 2.0 29.2 1.0 O A:HOH183 2.1 34.6 1.0 NE2 A:HIS104 2.3 18.9 1.0 ND1 A:HIS141 2.4 22.4 1.0 O A:HOH184 2.4 18.7 1.0 CD A:GLN115 3.0 29.3 1.0 CD2 A:HIS104 3.2 20.1 1.0 CE1 A:HIS104 3.3 19.3 1.0 CE1 A:HIS141 3.3 21.9 1.0 CG A:HIS141 3.4 21.3 1.0 CB A:HIS141 3.7 22.8 1.0 CG A:GLN115 3.8 28.8 1.0 NE2 A:GLN115 3.8 30.3 1.0 CG A:HIS104 4.3 19.6 1.0 ND1 A:HIS104 4.3 19.0 1.0 NE2 A:HIS141 4.4 21.8 1.0 CD2 A:HIS141 4.5 22.5 1.0 CA A:HIS141 4.5 23.5 1.0 O A:HIS141 4.5 27.2 1.0 CB A:GLN115 4.6 25.7 1.0 O A:HOH265 4.9 82.0 1.0 O A:HOH247 4.9 25.6 1.0

E.Barratt, R.J.Bingham, D.J.Warner, C.A.Laughton, S.E.V.Phillips, S.W.Homans. Van Der Waals Interactions Dominate Ligand-Protein Association in A Protein Binding Site Occluded From Solvent Water J.Am.Chem.Soc. V. 127 11827 2005.
ISSN: ISSN 0002-7863
PubMed: 16104761
DOI: 10.1021/JA0527525