Cadmium in PDB 1yp6: 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: 1yp6 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)	50.00 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.834, 53.834, 137.422, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22

The structure of Van Der Waals Interactions Dominate Hydrophobic Association in A Protein Binding Site Occluded From Solvent Water also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

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 1yp6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 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: 1yp6:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 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:Cd200 b:13.9 occ:1.00 O A:HOH420 2.3 12.7 1.0 OE1 A:GLU139 2.4 10.8 1.0 O A:HOH407 2.4 15.1 1.0 O A:HOH418 2.4 8.5 1.0 OE2 A:GLU139 2.5 13.2 1.0 CD A:GLU139 2.8 14.6 1.0 NE2 A:GLN136 4.2 10.5 1.0 O A:HOH237 4.2 21.4 1.0 O A:HOH238 4.3 26.5 1.0 CG A:GLU139 4.3 13.7 1.0 OE1 A:GLN136 4.5 15.2 1.0 CD A:GLN136 4.8 13.4 1.0 O A:HOH284 4.9 20.4 1.0 O A:HOH224 4.9 20.8 1.0

Cadmium binding site 2 out of 2 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:Cd201 b:24.2 occ:1.00 O A:HOH460 2.3 43.5 1.0 O A:HOH457 2.5 22.5 1.0 OE1 A:GLU13 2.5 19.7 1.0 OE2 A:GLU13 2.5 30.1 1.0 CD A:GLU13 2.8 23.9 1.0 CG A:GLU13 4.3 22.1 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