Nickel in PDB 2pr0: 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: 2pr0 was solved by M.B.Lascombe, T.Prange, P.Retailleau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.90 / 1.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.692, 25.974, 68.349, 90.00, 99.69, 90.00
R / Rfree (%)	19.4 / 18.6

The binding sites of Nickel atom in the Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum (pdb code 2pr0). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Sylvaticin, A New Secreted Protein From Pythium Sylvaticum, PDB code: 2pr0:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 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:Ni252 b:13.9 occ:1.00 O B:PHE194 1.8 16.7 1.0 O3 A:TRS202 1.9 22.6 1.0 O A:TRP1 2.0 16.5 1.0 N A:TRP1 2.1 20.9 1.0 O A:HOH359 2.2 27.5 1.0 C3 A:TRS202 2.7 33.6 1.0 C A:TRP1 2.7 8.4 1.0 C B:PHE194 2.8 37.4 1.0 CA A:TRP1 2.9 15.3 1.0 OXT B:PHE194 3.2 41.5 1.0 C2 A:TRS202 3.7 41.7 1.0 O B:PRO191 3.7 33.2 1.0 C A:TRS202 3.7 20.2 1.0 CB A:TRP1 3.8 13.7 1.0 O2 A:TRS202 3.9 29.7 1.0 N A:GLU2 4.0 17.9 1.0 O B:HOH285 4.1 27.5 1.0 C1 A:TRS202 4.1 41.3 1.0 CA B:PHE194 4.2 45.2 1.0 OE2 A:GLU3 4.4 27.1 1.0 CG A:GLU3 4.4 23.5 1.0 CG A:TRP1 4.6 14.9 1.0 N B:PHE194 4.7 34.3 1.0 CA A:GLU2 4.7 20.9 1.0 C B:PRO191 4.8 29.0 1.0 CD A:GLU3 4.9 36.4 1.0 CB B:PHE194 4.9 49.5 1.0 CD1 A:TRP1 4.9 13.0 1.0

Nickel binding site 2 out of 2 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:Ni251 b:12.8 occ:1.00 OXT A:PHE94 1.9 17.4 1.0 O2 B:TRS201 2.0 17.8 1.0 N B:TRS201 2.1 20.2 1.0 O B:TRP101 2.1 13.1 1.0 N B:TRP101 2.2 14.8 1.0 O A:HOH355 2.2 20.5 1.0 C B:TRS201 2.7 20.2 1.0 C2 B:TRS201 2.8 16.1 1.0 C B:TRP101 2.8 7.8 1.0 C A:PHE94 2.9 16.5 1.0 CA B:TRP101 3.0 13.8 1.0 O A:PHE94 3.3 12.5 1.0 C1 B:TRS201 3.6 19.4 1.0 O A:PRO91 3.7 20.0 1.0 CB B:TRP101 3.8 14.2 1.0 O1 B:TRS201 4.0 19.1 1.0 N B:GLU102 4.1 16.6 1.0 O B:HOH268 4.1 24.8 1.0 CA A:PHE94 4.2 17.5 1.0 C3 B:TRS201 4.3 21.5 1.0 OE2 B:GLU103 4.3 24.9 1.0 CG B:GLU103 4.4 20.7 1.0 O3 B:TRS201 4.6 27.6 1.0 CG B:TRP101 4.7 10.1 1.0 N A:PHE94 4.7 22.2 1.0 CB A:PHE94 4.7 16.9 1.0 C A:PRO91 4.8 17.6 1.0 CA B:GLU102 4.8 15.0 1.0 CD B:GLU103 4.9 27.4 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