Nickel in PDB 3set: Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form I)

The structure of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form I), PDB code: 3set was solved by M.Zhao, A.B.Soriaga, A.Laganowsky, M.R.Sawaya, D.Cascio, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.90 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.940, 62.270, 89.710, 90.00, 109.03, 90.00
R / Rfree (%)	23.2 / 28.2

The binding sites of Nickel atom in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form I) (pdb code 3set). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form I), PDB code: 3set:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form I)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni373 b:16.7 occ:1.00 O C:HIS40 2.2 9.2 1.0 OE1 A:GLU222 2.2 18.0 1.0 O A:HOH396 2.3 13.7 1.0 ND1 C:HIS40 2.3 20.8 1.0 O A:HOH394 2.4 13.8 1.0 CE1 A:HIS216 2.4 20.9 1.0 CD A:GLU222 3.1 13.5 1.0 ND1 A:HIS216 3.2 22.8 1.0 CG C:HIS40 3.3 17.7 1.0 CE1 C:HIS40 3.3 22.2 1.0 C C:HIS40 3.3 13.4 1.0 OE2 A:GLU222 3.4 11.2 1.0 NE2 A:HIS216 3.5 24.2 1.0 CB C:HIS40 3.5 14.6 1.0 CA C:HIS40 3.9 14.1 1.0 O A:HOH420 4.0 19.9 1.0 O C:HOH391 4.2 13.5 1.0 NE2 C:HIS40 4.4 22.9 1.0 N C:PRO41 4.4 13.0 1.0 CD2 C:HIS40 4.4 22.1 1.0 CG A:HIS216 4.4 20.6 1.0 CG A:GLU222 4.5 11.7 1.0 CD2 A:HIS216 4.6 19.1 1.0 N C:HIS40 4.6 13.5 1.0 CA C:PRO41 4.6 13.4 1.0 C C:PRO41 4.7 16.6 1.0 OD1 C:ASP42 4.8 28.8 1.0 N C:ASP42 4.8 15.8 1.0

Nickel binding site 2 out of 2 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form I)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni373 b:12.2 occ:1.00 O A:HIS40 2.2 4.2 1.0 OE1 C:GLU222 2.2 7.0 1.0 ND1 A:HIS40 2.2 14.6 1.0 O A:HOH395 2.2 7.1 1.0 NE2 C:HIS216 2.3 8.3 1.0 O C:HOH397 2.4 13.2 1.0 CD2 C:HIS216 3.1 12.1 1.0 CD C:GLU222 3.1 12.4 1.0 CE1 A:HIS40 3.2 15.9 1.0 CG A:HIS40 3.2 12.9 1.0 C A:HIS40 3.3 4.0 1.0 OE2 C:GLU222 3.3 8.5 1.0 CE1 C:HIS216 3.4 10.5 1.0 CB A:HIS40 3.6 7.9 1.0 O C:HOH377 3.9 5.1 1.0 CA A:HIS40 4.0 5.3 1.0 O A:HOH487 4.0 7.5 1.0 CG C:HIS216 4.3 12.6 1.0 NE2 A:HIS40 4.3 18.3 1.0 N A:PRO41 4.4 7.7 1.0 CD2 A:HIS40 4.4 17.1 1.0 ND1 C:HIS216 4.4 12.3 1.0 CG C:GLU222 4.5 12.7 1.0 CA A:PRO41 4.6 11.0 1.0 C A:PRO41 4.6 8.6 1.0 N A:HIS40 4.6 6.2 1.0 OD1 A:ASP42 4.7 32.0 1.0 N A:ASP42 4.9 4.5 1.0 O A:PRO41 4.9 11.7 1.0

A.Laganowsky, M.Zhao, A.B.Soriaga, M.R.Sawaya, D.Cascio, T.O.Yeates. An Approach to Crystallizing Proteins By Metal-Mediated Synthetic Symmetrization. Protein Sci. V. 20 1876 2011.
ISSN: ISSN 0961-8368
PubMed: 21898649
DOI: 10.1002/PRO.727