Nickel in PDB 2zpl: Crystal Structure Analysis of Pdz Domain A

The structure of Crystal Structure Analysis of Pdz Domain A, PDB code: 2zpl was solved by K.Inaba, M.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.55 / 1.70
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	54.756, 54.756, 75.644, 90.00, 90.00, 120.00
R / Rfree (%)	15 / 17.6

The binding sites of Nickel atom in the Crystal Structure Analysis of Pdz Domain A (pdb code 2zpl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure Analysis of Pdz Domain A, PDB code: 2zpl:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure Analysis of Pdz Domain A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure Analysis of Pdz Domain A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1 b:28.2 occ:1.00 O A:HOH224 2.1 32.7 1.0 OD1 A:ASP175 2.1 25.2 1.0 O A:HOH222 2.1 28.2 1.0 O A:HOH260 2.2 30.1 1.0 CG A:ASP175 3.0 21.6 1.0 OD2 A:ASP175 3.3 26.8 1.0 O A:HOH223 3.5 56.0 1.0 O A:HOH236 4.2 22.2 1.0 CB A:ASP175 4.4 19.3 1.0 O B:GLY132 4.6 22.3 1.0 N A:ASP175 4.6 19.0 1.0 O A:ILE173 4.7 19.1 1.0 CA A:ASP175 4.7 18.8 1.0 CG B:GLU133 4.8 30.3 1.0 C A:GLY174 4.9 18.3 1.0 O A:ASP171 5.0 25.5 1.0

Nickel binding site 2 out of 3 in the Crystal Structure Analysis of Pdz Domain A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure Analysis of Pdz Domain A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni2 b:25.9 occ:1.00 O B:HOH4 1.7 27.2 1.0 N B:GLY125 1.8 26.9 1.0 O B:GLY125 2.1 23.5 1.0 O B:HOH6 2.1 30.4 1.0 NE2 A:HIS199 2.1 31.6 1.0 O B:HOH5 2.1 26.7 1.0 C B:GLY125 2.7 23.5 1.0 CA B:GLY125 2.8 24.3 1.0 CD2 A:HIS199 2.9 28.5 1.0 CE1 A:HIS199 3.2 34.5 1.0 OE1 C:GLU207 3.9 30.9 1.0 O C:ALA201 4.0 31.9 1.0 N B:SER126 4.1 23.9 1.0 CG A:HIS199 4.1 27.2 1.0 OE1 C:GLU203 4.1 30.0 1.0 ND1 A:HIS199 4.2 32.4 1.0 CD C:GLU207 4.6 33.0 1.0 CG C:GLU203 4.8 29.4 1.0 CA C:PHE202 4.8 29.4 1.0 CA B:SER126 4.9 23.2 1.0 C C:ALA201 4.9 29.1 1.0 CD C:GLU203 4.9 29.6 1.0

Nickel binding site 3 out of 3 in the Crystal Structure Analysis of Pdz Domain A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure Analysis of Pdz Domain A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni3 b:39.0 occ:1.00 NE2 C:HIS199 2.2 32.5 1.0 CD2 C:HIS199 3.0 37.6 1.0 CE1 C:HIS199 3.3 39.6 1.0 OE2 A:GLU207 4.0 27.3 1.0 CG C:HIS199 4.2 34.0 1.0 ND1 C:HIS199 4.3 34.0 1.0 O A:HOH251 4.5 43.1 1.0 CD A:GLU207 4.5 29.2 1.0 OE1 A:GLU207 4.5 36.1 1.0

K.Inaba, M.Suzuki, K.Maegawa, Y.Akiyama. Crystal Structure Analysis of Pdz-Domain A To Be Published.