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:
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
Go back to
Nickel Binding Sites List in 2pos
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
Go back to
Nickel Binding Sites List in 2pos
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: Wed Oct 9 16:54:33 2024
|