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

Protein crystallography data

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

Other elements in 2pos:

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

Chlorine (Cl) 1 atom

Nickel Binding Sites:

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 2pos

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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 2pos

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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 2pos

Go back to Nickel Binding Sites List in 2pos
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 2pos

Go back to Nickel Binding Sites List in 2pos
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

Reference:

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
Page generated: Thu Oct 29 06:17:46 2020
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