Nickel in PDB 6o5o: Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02

The structure of Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02, PDB code: 6o5o was solved by M.Chavez, D.R.Madden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 1.75
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.724, 102.724, 80.831, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 19.9

The structure of Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02 (pdb code 6o5o). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02, PDB code: 6o5o:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:16.6 occ:0.52 N A:GLY31 2.0 15.9 1.0 O A:GLY31 2.0 18.2 1.0 C A:GLY31 2.7 21.4 1.0 CA A:GLY31 2.8 21.0 1.0 OE2 A:GLU33 3.8 26.4 1.0 N A:PRO32 4.0 18.4 1.0 O A:HOH405 4.6 27.3 1.0 CA A:PRO32 4.7 16.6 1.0 CD A:GLU33 4.8 31.7 1.0 C A:PRO32 4.9 20.3 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:21.7 occ:0.65 OE1 A:GLU141 1.8 19.7 1.0 NE2 A:HIS144 2.0 16.6 1.0 O A:HOH302 2.0 19.8 1.0 O A:HOH386 2.6 19.6 1.0 CD A:GLU141 2.7 23.8 1.0 CE1 A:HIS144 2.9 17.8 1.0 OE2 A:GLU141 3.0 22.0 1.0 CD2 A:HIS144 3.1 16.5 1.0 ND1 A:HIS144 4.1 17.4 1.0 CG A:GLU141 4.1 21.4 1.0 N A:GLY142 4.2 18.8 1.0 CG A:HIS144 4.2 16.3 1.0 O A:HOH309 4.3 29.7 1.0 CA A:GLU141 4.5 18.3 1.0 N A:ALA63 4.5 17.7 1.0 CB A:ALA63 4.7 19.2 1.0 O A:PRO61 4.8 19.4 1.0 CB A:GLU141 4.9 23.0 1.0 C A:GLU141 4.9 19.8 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:84.9 occ:1.00 NE2 A:HIS89 2.1 51.7 0.8 CE1 A:HIS89 2.7 50.8 0.8 CD2 A:HIS89 3.3 42.9 0.8 ND1 A:HIS89 4.0 52.5 0.8 O A:GLY87 4.0 42.3 0.7 CG A:HIS89 4.3 43.3 0.8 C A:GLY87 4.8 42.0 0.7 CA A:GLY87 4.9 34.9 0.7

Nickel binding site 4 out of 4 in the Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:27.0 occ:0.32 NE2 B:HIS89 2.1 62.0 0.9 O B:HOH336 2.1 35.7 0.3 O B:HOH372 2.2 43.3 0.3 CE1 B:HIS89 2.9 60.4 0.9 CD2 B:HIS89 3.1 53.1 0.9 O B:HOH369 3.6 57.3 0.6 O B:GLY87 3.9 51.7 0.7 ND1 B:HIS89 4.1 56.6 0.9 O B:HOH413 4.2 71.3 0.2 CG B:HIS89 4.2 55.6 0.9 C B:GLY87 4.9 58.6 0.7

M.Chavez, D.R.Madden. Crystal Structure of the Disabled-2 (DAB2) Dab Homology Domain in Complex with Peptide STA02 To Be Published.