Cadmium in PDB 1dpe: Dipeptide-Binding Protein

The structure of Dipeptide-Binding Protein, PDB code: 1dpe was solved by A.V.Nickitenko, S.Trakhanov, F.A.Quiocho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.270, 79.780, 62.970, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Cadmium atom in the Dipeptide-Binding Protein (pdb code 1dpe). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Dipeptide-Binding Protein, PDB code: 1dpe:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Dipeptide-Binding Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Dipeptide-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd508 b:19.3 occ:1.00 O A:HOH697 1.6 7.5 1.0 NE2 A:HIS66 2.3 9.1 1.0 O A:HOH698 2.5 11.1 1.0 OE1 A:GLU55 2.5 17.4 1.0 OE2 A:GLU55 2.5 19.3 1.0 CD A:GLU55 2.9 18.5 1.0 CE1 A:HIS66 3.1 12.3 1.0 CD2 A:HIS66 3.4 10.3 1.0 O A:HOH937 3.7 53.9 1.0 ND1 A:HIS66 4.3 10.4 1.0 CG A:HIS66 4.4 9.9 1.0 CG A:GLU55 4.4 15.9 1.0 CE A:LYS53 4.5 15.5 1.0 O A:HOH761 4.5 28.3 1.0 NZ A:LYS53 4.7 17.8 1.0 CG2 A:THR64 4.7 10.0 1.0 O A:HOH940 4.7 36.9 1.0

Cadmium binding site 2 out of 5 in the Dipeptide-Binding Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Dipeptide-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd509 b:19.1 occ:1.00 OE1 A:GLU457 2.5 11.5 1.0 O A:HOH984 2.5 23.2 1.0 O A:HOH699 2.6 19.5 1.0 OE2 A:GLU457 2.6 15.3 1.0 CD A:GLU457 2.9 13.4 1.0 O A:HOH994 3.3 44.1 1.0 CG A:GLU457 4.4 11.2 1.0 O A:HOH700 4.8 24.4 1.0 O A:HOH701 4.8 16.1 1.0 O A:HOH888 4.9 24.4 1.0

Cadmium binding site 3 out of 5 in the Dipeptide-Binding Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Dipeptide-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd510 b:25.6 occ:1.00 O A:HOH692 2.3 15.7 1.0 O A:HOH693 2.4 31.8 1.0 O A:HOH691 2.5 23.8 1.0 NE2 A:HIS467 2.5 7.3 1.0 O A:HOH690 2.5 17.3 1.0 O A:HOH694 2.8 31.1 1.0 CE1 A:HIS467 3.4 8.5 1.0 CD2 A:HIS467 3.4 7.6 1.0 O A:HOH919 4.2 37.5 1.0 O A:HOH686 4.3 28.4 1.0 O A:GLN322 4.4 10.9 1.0 O A:HOH695 4.4 29.2 1.0 O A:HOH696 4.5 28.9 1.0 ND1 A:HIS467 4.5 7.9 1.0 CG A:HIS467 4.6 7.4 1.0 OH A:TYR287 4.7 13.4 1.0 O A:HOH684 4.8 15.5 1.0 CZ A:TYR324 4.9 12.2 1.0 CE2 A:TYR324 5.0 12.0 1.0

Cadmium binding site 4 out of 5 in the Dipeptide-Binding Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Dipeptide-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd511 b:15.8 occ:1.00 O A:HOH667 2.1 15.7 1.0 OE2 A:GLU45 2.2 11.2 1.0 NE2 A:HIS452 2.3 12.9 1.0 OE1 A:GLU45 2.6 14.8 1.0 CD A:GLU45 2.8 12.0 1.0 CD2 A:HIS452 3.1 12.7 1.0 CE1 A:HIS452 3.4 12.6 1.0 CB A:TRP315 4.2 8.7 1.0 CG A:GLU45 4.2 10.4 1.0 CG A:HIS452 4.4 13.1 1.0 O A:HOH668 4.4 24.5 1.0 ND1 A:HIS452 4.4 12.4 1.0 CG A:TRP315 4.4 7.6 1.0 O A:HOH776 4.6 21.6 1.0 CG2 A:VAL456 4.6 5.4 1.0 O A:HOH733 4.7 71.0 1.0 O A:HOH548 4.7 16.9 1.0 CD2 A:TRP315 4.8 7.5 1.0 CE3 A:TRP315 5.0 6.7 1.0

Cadmium binding site 5 out of 5 in the Dipeptide-Binding Protein


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Dipeptide-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd512 b:51.6 occ:1.00 O A:HOH707 1.9 14.6 1.0 O A:HOH708 2.6 13.0 1.0 OE1 A:GLU116 2.7 27.0 1.0 OE2 A:GLU116 3.2 26.0 1.0 CD A:GLU116 3.2 24.5 1.0 CG A:GLU116 4.7 21.7 1.0

A.V.Nickitenko, S.Trakhanov, F.A.Quiocho. 2 A Resolution Structure of Dppa, A Periplasmic Dipeptide Transport/Chemosensory Receptor. Biochemistry V. 34 16585 1995.
ISSN: ISSN 0006-2960
PubMed: 8527431
DOI: 10.1021/BI00051A006