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

Protein crystallography data

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

Nickel Binding Sites:

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 2zpl

Go back to Nickel Binding Sites List in 2zpl
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 2zpl

Go back to Nickel Binding Sites List in 2zpl
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 2zpl

Go back to Nickel Binding Sites List in 2zpl
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

Reference:

K.Inaba, M.Suzuki, K.Maegawa, Y.Akiyama. Crystal Structure Analysis of Pdz-Domain A To Be Published.
Page generated: Fri Sep 25 08:18:41 2020
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