Nickel in PDB 2pos: Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum

The structure of Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum, PDB code: 2pos was solved by M.B.Lascombe, T.Prange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.06 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.220, 46.000, 55.730, 85.20, 71.27, 74.63
R / Rfree (%)	15 / 18.7

The structure of Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum (pdb code 2pos). 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 of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum, PDB code: 2pos:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni100 b:13.6 occ:1.00 OXT B:PHE94 1.9 18.3 1.0 O A:TRP1 2.0 12.5 1.0 O1 A:TRS2003 2.1 20.4 1.0 O2 A:TRS2003 2.1 20.1 1.0 N A:TRP1 2.1 12.6 1.0 N A:TRS2003 2.2 19.9 1.0 C A:TRS2003 2.8 21.8 1.0 C A:TRP1 2.8 12.9 1.0 C2 A:TRS2003 2.9 21.9 1.0 C1 A:TRS2003 2.9 21.6 1.0 C B:PHE94 2.9 19.4 1.0 CA A:TRP1 2.9 12.7 1.0 O B:PHE94 3.2 20.2 1.0 O B:PRO91 3.7 14.5 1.0 CB A:TRP1 3.7 13.0 1.0 N A:GLU2 4.1 13.3 1.0 CG A:GLU3 4.1 17.9 1.0 O A:HOH3062 4.2 26.3 1.0 C3 A:TRS2003 4.2 22.9 1.0 CA B:PHE94 4.3 19.5 1.0 OE2 A:GLU3 4.4 21.9 1.0 O B:HOH2014 4.5 19.1 1.0 CG A:TRP1 4.6 13.1 1.0 CD2 B:PHE94 4.6 23.2 1.0 N B:PHE94 4.6 18.2 1.0 CD A:GLU3 4.8 19.7 1.0 O3 A:TRS2003 4.8 25.1 1.0 C B:PRO91 4.8 14.1 1.0 CA A:GLU2 4.8 13.9 1.0 CD1 A:TRP1 4.8 14.6 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni100 b:14.7 occ:1.00 OXT A:PHE94 2.0 21.9 1.0 O3 B:TRS2000 2.0 19.5 1.0 O A:HOH3173 2.1 15.8 1.0 N B:TRP1 2.1 11.9 1.0 O B:TRP1 2.1 12.9 1.0 N B:TRS2000 2.2 19.4 1.0 C B:TRP1 2.9 12.7 1.0 C3 B:TRS2000 2.9 19.2 1.0 CA B:TRP1 3.0 12.6 1.0 C A:PHE94 3.0 21.8 1.0 C B:TRS2000 3.1 20.3 1.0 O A:PHE94 3.2 22.6 1.0 O A:PRO91 3.6 16.7 1.0 C2 B:TRS2000 3.7 20.7 1.0 CB B:TRP1 3.7 12.4 1.0 CG B:GLU3 4.1 13.4 1.0 N B:GLU2 4.2 12.8 1.0 O B:HOH2018 4.2 19.6 1.0 O A:HOH3049 4.2 27.2 1.0 OE2 B:GLU3 4.3 13.4 1.0 CA A:PHE94 4.4 21.3 1.0 C1 B:TRS2000 4.4 20.3 1.0 CD2 A:PHE94 4.4 23.0 1.0 CG B:TRP1 4.6 12.4 1.0 N A:PHE94 4.7 20.6 1.0 O2 B:TRS2000 4.7 21.9 1.0 CD B:GLU3 4.7 13.9 1.0 CE2 A:PHE94 4.8 23.8 1.0 C A:PRO91 4.8 16.4 1.0 CG A:PHE94 4.8 21.9 1.0 CD1 B:TRP1 4.9 13.2 1.0 CA B:GLU2 4.9 13.2 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni100 b:15.0 occ:1.00 O C:TRP1 2.0 14.6 1.0 N C:TRS2001 2.1 22.8 1.0 O C:HOH2018 2.1 19.4 1.0 O2 C:TRS2001 2.1 22.0 1.0 N C:TRP1 2.2 14.2 1.0 C C:TRP1 2.8 14.4 1.0 C2 C:TRS2001 2.9 23.0 1.0 CA C:TRP1 3.0 14.1 1.0 C C:TRS2001 3.0 23.6 1.0 C1 C:TRS2001 3.6 24.6 1.0 CB C:TRP1 3.7 13.8 1.0 CG C:GLU3 4.1 15.3 1.0 N C:GLU2 4.1 14.2 1.0 O C:HOH2158 4.2 20.9 1.0 C3 C:TRS2001 4.3 24.1 1.0 O1 C:TRS2001 4.3 26.0 1.0 OE2 C:GLU3 4.3 16.7 1.0 CG C:TRP1 4.6 13.2 1.0 CD C:GLU3 4.7 15.6 1.0 CA C:GLU2 4.8 14.3 1.0 CD1 C:TRP1 4.8 13.7 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni100 b:16.1 occ:1.00 O1 D:TRS2002 1.9 22.3 1.0 O D:TRP1 2.0 15.5 1.0 N D:TRS2002 2.2 22.5 1.0 N D:TRP1 2.2 14.9 1.0 C D:TRP1 2.8 16.0 1.0 C1 D:TRS2002 2.9 24.1 1.0 CA D:TRP1 3.0 15.4 1.0 C D:TRS2002 3.1 24.1 1.0 CB D:TRP1 3.8 15.1 1.0 C3 D:TRS2002 4.0 25.0 1.0 O3 D:TRS2002 4.1 25.4 1.0 N D:GLU2 4.1 16.4 1.0 CG D:GLU3 4.2 23.5 1.0 OE2 D:GLU3 4.2 28.1 1.0 C2 D:TRS2002 4.3 24.5 1.0 O2 D:TRS2002 4.3 26.2 1.0 CG D:TRP1 4.7 14.4 1.0 CD D:GLU3 4.8 27.1 1.0 CA D:GLU2 4.8 17.6 1.0

M.B.Lascombe, P.Retailleau, M.Ponchet, B.Industri, J.P.Blein, T.Prange. Structure of Sylvaticin, A New Alpha-Elicitin-Like Protein From Pythium Sylvaticum. Acta Crystallogr.,Sect.D V. 63 1102 2007.
ISSN: ISSN 0907-4449
PubMed: 17881828
DOI: 10.1107/S0907444907043363