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

The structure of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II), PDB code: 3sex 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)	63.66 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.560, 67.500, 191.440, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.8

The structure of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) also contains other interesting chemical elements:

Iodine

(I)

26 atoms

The binding sites of Nickel atom in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) (pdb code 3sex). 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 II), PDB code: 3sex:
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 II)


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni384 b:10.1 occ:1.00 O C:HOH423 2.2 5.5 1.0 O A:HIS40 2.2 5.7 1.0 NE2 C:HIS216 2.2 9.7 1.0 ND1 A:HIS40 2.2 7.6 1.0 OE2 C:GLU222 2.2 13.1 1.0 O C:HOH413 2.3 9.1 1.0 CD2 C:HIS216 3.0 10.4 1.0 CG A:HIS40 3.1 9.1 1.0 CD C:GLU222 3.2 12.2 1.0 CE1 A:HIS40 3.2 11.0 1.0 CE1 C:HIS216 3.2 11.6 1.0 C A:HIS40 3.3 8.9 1.0 CB A:HIS40 3.4 6.9 1.0 OE1 C:GLU222 3.4 11.1 1.0 CA A:HIS40 3.9 6.6 1.0 O A:HOH393 4.0 11.3 1.0 O C:HOH405 4.1 8.0 1.0 CG C:HIS216 4.2 10.2 1.0 ND1 C:HIS216 4.3 7.8 1.0 CD2 A:HIS40 4.3 9.1 1.0 NE2 A:HIS40 4.3 9.1 1.0 O A:HOH589 4.3 13.9 1.0 N A:PRO41 4.4 8.7 1.0 O A:HOH650 4.4 31.0 1.0 C A:PRO41 4.5 10.5 1.0 CG C:GLU222 4.5 12.5 1.0 CA A:PRO41 4.6 9.6 1.0 N A:HIS40 4.7 8.9 1.0 O A:PRO41 4.7 11.2 1.0 N A:ASP42 4.8 7.6 1.0 CA A:GLY14 4.8 7.2 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni385 b:10.4 occ:1.00 O C:HIS40 2.1 12.4 1.0 OE2 A:GLU222 2.2 4.5 1.0 ND1 C:HIS40 2.2 9.0 1.0 NE2 A:HIS216 2.2 5.9 1.0 O A:HOH414 2.3 11.4 1.0 O C:HOH398 2.4 9.8 1.0 CD2 A:HIS216 3.1 5.3 1.0 CD A:GLU222 3.1 8.6 1.0 CE1 C:HIS40 3.2 14.6 1.0 CG C:HIS40 3.2 9.5 1.0 C C:HIS40 3.2 12.3 1.0 CE1 A:HIS216 3.3 8.8 1.0 OE1 A:GLU222 3.4 8.6 1.0 CB C:HIS40 3.4 7.9 1.0 CA C:HIS40 3.9 8.7 1.0 O A:HOH432 4.1 9.5 1.0 O C:HOH448 4.2 11.7 1.0 CG A:HIS216 4.2 7.1 1.0 NE2 C:HIS40 4.3 12.4 1.0 ND1 A:HIS216 4.3 9.6 1.0 CD2 C:HIS40 4.3 12.0 1.0 N C:PRO41 4.3 14.2 1.0 O C:HOH551 4.3 13.1 1.0 CG A:GLU222 4.5 11.3 1.0 C C:PRO41 4.5 12.3 1.0 N C:HIS40 4.6 9.2 1.0 O C:HOH556 4.6 34.5 1.0 CA C:PRO41 4.6 12.1 1.0 O C:PRO41 4.7 12.7 1.0 N C:ASP42 4.7 10.2 1.0 CA C:GLY14 4.8 10.8 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