Nickel in PDB 4oi6: Crystal Structure Analysis of Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2)

The structure of Crystal Structure Analysis of Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2), PDB code: 4oi6 was solved by M.Lu, Yong-Liang Jiang, S.Wang, W.Cheng, Rong-Guang Zhang, Marie-Joellevirolle, Y.Chen, Cong-Zhao Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.54 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.330, 67.140, 35.090, 90.00, 94.98, 90.00
R / Rfree (%)	17.1 / 21.6

The binding sites of Nickel atom in the Crystal Structure Analysis of Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2) (pdb code 4oi6). 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 Analysis of Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2), PDB code: 4oi6:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure Analysis of Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2)


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 Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:17.2 occ:0.86 O A:HOH243 2.1 16.1 1.0 OE1 A:GLU74 2.1 12.8 1.0 O A:HOH244 2.2 13.8 1.0 O A:HOH245 2.2 18.8 1.0 OE2 A:GLU74 2.3 14.1 1.0 CD A:GLU74 2.5 13.3 1.0 O B:HOH246 3.5 17.0 1.0 O B:HOH247 3.8 17.0 1.0 NE2 A:HIS76 3.9 12.9 1.0 O A:HOH234 3.9 15.9 1.0 CG A:GLU74 4.0 14.1 1.0 NH2 A:ARG9 4.2 16.2 1.0 CE1 A:HIS76 4.6 12.9 1.0 CB A:GLU74 4.7 12.6 1.0 CD2 A:HIS76 4.9 12.1 1.0 O A:HOH227 5.0 15.5 1.0

Nickel binding site 2 out of 4 in the Crystal Structure Analysis of Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2)


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 Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni102 b:21.1 occ:0.82 OXT B:ALA82 2.1 11.0 0.7 O A:HOH240 2.1 11.7 0.8 NE2 A:HIS23 2.2 14.3 1.0 O B:HOH241 2.2 15.4 0.9 O A:HOH239 2.3 13.4 0.8 CD2 A:HIS23 3.0 14.0 1.0 C B:ALA82 3.0 11.2 1.0 O B:ALA82 3.2 10.5 0.9 CE1 A:HIS23 3.3 13.0 1.0 O A:GLU38 4.2 13.1 1.0 CG A:HIS23 4.2 13.8 1.0 ND1 A:HIS23 4.3 13.8 1.0 CA B:ALA82 4.4 13.6 1.0 O A:PHE37 4.5 13.1 1.0 CD1 A:LEU27 4.6 11.9 1.0 C A:GLU38 4.9 14.2 1.0 CB B:ALA82 5.0 12.6 1.0

Nickel binding site 3 out of 4 in the Crystal Structure Analysis of Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2)


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 Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:16.1 occ:0.83 O7 B:CIT103 2.1 13.6 0.8 O4 B:CIT103 2.1 11.8 0.8 OD2 B:ASP43 2.1 12.8 1.0 OG B:SER46 2.2 13.4 1.0 O6 B:CIT103 2.2 14.0 0.8 ND1 A:HIS76 2.3 12.1 1.0 C6 B:CIT103 2.9 13.1 0.8 C3 B:CIT103 2.9 13.4 0.8 CG B:ASP43 3.1 11.5 1.0 C5 B:CIT103 3.1 13.9 0.8 CE1 A:HIS76 3.2 12.9 1.0 CG A:HIS76 3.3 10.8 1.0 CB B:SER46 3.3 13.6 1.0 OD1 B:ASP43 3.4 10.3 1.0 C4 B:CIT103 3.6 14.4 0.8 CB A:HIS76 3.6 9.1 1.0 O B:HOH220 3.8 16.2 1.0 O1 B:CIT103 3.9 13.2 0.8 O B:HOH245 3.9 14.6 1.0 O B:HOH233 4.1 11.2 0.7 CA A:HIS76 4.1 11.4 1.0 O5 B:CIT103 4.1 15.7 0.8 N B:SER46 4.2 12.8 1.0 O3 B:CIT103 4.2 10.4 0.8 C2 B:CIT103 4.3 14.5 0.8 CA B:SER46 4.3 13.2 1.0 NE2 A:HIS76 4.4 12.9 1.0 CD2 A:HIS76 4.4 12.1 1.0 CB B:ASP43 4.5 9.6 1.0 C1 B:CIT103 4.5 15.3 0.8 N A:GLU77 4.7 10.3 1.0 C A:HIS76 4.9 10.0 1.0

Nickel binding site 4 out of 4 in the Crystal Structure Analysis of Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure Analysis of Nickel-Bound Form SCO4226 From Streptomyces Coelicolor A3(2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni102 b:15.7 occ:0.98 OE2 B:GLU38 2.1 12.6 1.0 NE2 B:HIS3 2.1 11.2 1.0 O B:HOH242 2.1 14.4 1.0 O B:HOH227 2.2 10.6 1.0 O B:HOH234 2.2 11.4 1.0 CD B:GLU38 3.0 11.8 1.0 CE1 B:HIS3 3.0 12.7 1.0 CD2 B:HIS3 3.1 12.0 1.0 OE1 B:GLU38 3.2 12.8 1.0 ND1 B:HIS3 4.2 12.2 1.0 CG B:HIS3 4.3 12.2 1.0 CG B:GLU38 4.4 12.2 1.0 CB B:GLU54 4.5 12.9 1.0 CG B:GLU54 4.6 13.5 1.0 O A:HOH208 4.6 18.9 1.0

M.Lu, Y.L.Jiang, S.Wang, H.Jin, R.G.Zhang, M.J.Virolle, Y.Chen, C.Z.Zhou. Streptomyces Coelicolor SCO4226 Is A Nickel Binding Protein. Plos One V. 9 09660 2014.
ISSN: ESSN 1932-6203
PubMed: 25285530
DOI: 10.1371/JOURNAL.PONE.0109660