Calcium in PDB 6q79: Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
Protein crystallography data
The structure of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution, PDB code: 6q79
was solved by
S.Baeriswyl,
A.Stocker,
J.-L.Reymond,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.63 /
2.01
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.422,
64.124,
68.960,
90.00,
104.06,
90.00
|
R / Rfree (%)
|
15.4 /
23.2
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
(pdb code 6q79). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution, PDB code: 6q79:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 6q79
Go back to
Calcium Binding Sites List in 6q79
Calcium binding site 1 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:35.4
occ:1.00
|
OD1
|
A:ASN103
|
2.3
|
29.6
|
1.0
|
O
|
A:ASN21
|
2.3
|
34.1
|
1.0
|
OD2
|
A:ASP101
|
2.3
|
33.8
|
1.0
|
O3
|
E:ZDC1
|
2.3
|
31.6
|
1.0
|
O
|
D:GLY114
|
2.5
|
34.8
|
1.0
|
OD1
|
A:ASP104
|
2.6
|
33.0
|
1.0
|
O2
|
E:ZDC1
|
2.6
|
34.1
|
1.0
|
CG
|
A:ASP101
|
3.1
|
34.3
|
1.0
|
OD1
|
A:ASP101
|
3.1
|
36.9
|
1.0
|
C3
|
E:ZDC1
|
3.3
|
31.4
|
1.0
|
CG
|
A:ASN103
|
3.4
|
30.1
|
1.0
|
C2
|
E:ZDC1
|
3.5
|
33.7
|
1.0
|
C
|
D:GLY114
|
3.5
|
36.5
|
1.0
|
C
|
A:ASN21
|
3.5
|
34.8
|
1.0
|
CA
|
A:CA302
|
3.6
|
36.0
|
1.0
|
OXT
|
D:GLY114
|
3.7
|
38.8
|
1.0
|
C4
|
E:ZDC1
|
3.8
|
33.2
|
1.0
|
CG
|
A:ASP104
|
3.8
|
35.2
|
1.0
|
ND2
|
A:ASN103
|
3.9
|
28.4
|
1.0
|
N
|
A:ASP104
|
4.1
|
30.8
|
1.0
|
CB
|
A:ASN21
|
4.1
|
29.3
|
1.0
|
CA
|
A:ASP104
|
4.1
|
33.7
|
1.0
|
OD2
|
A:ASP99
|
4.3
|
38.2
|
1.0
|
N
|
A:SER22
|
4.4
|
36.5
|
1.0
|
CA
|
A:SER22
|
4.4
|
36.6
|
1.0
|
C
|
A:ASN103
|
4.4
|
31.7
|
1.0
|
O4
|
E:ZDC1
|
4.4
|
32.6
|
1.0
|
CA
|
A:ASN21
|
4.5
|
33.2
|
1.0
|
CB
|
A:ASP101
|
4.5
|
31.4
|
1.0
|
O
|
A:HOH436
|
4.5
|
45.7
|
1.0
|
CB
|
A:ASP104
|
4.6
|
34.3
|
1.0
|
CB
|
A:SER22
|
4.6
|
37.6
|
1.0
|
CB
|
A:ASN103
|
4.7
|
28.1
|
1.0
|
OD2
|
A:ASP104
|
4.7
|
37.7
|
1.0
|
O
|
A:ASN103
|
4.8
|
32.9
|
1.0
|
N
|
A:ASN103
|
4.8
|
29.7
|
1.0
|
C1
|
E:ZDC1
|
4.8
|
37.6
|
1.0
|
CA
|
D:GLY114
|
4.8
|
36.4
|
1.0
|
CA
|
A:ASN103
|
4.9
|
29.6
|
1.0
|
OD1
|
A:ASP99
|
4.9
|
40.9
|
1.0
|
|
Calcium binding site 2 out
of 8 in 6q79
Go back to
Calcium Binding Sites List in 6q79
Calcium binding site 2 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:36.0
occ:1.00
|
OD1
|
A:ASP99
|
2.3
|
40.9
|
1.0
|
O3
|
E:ZDC1
|
2.4
|
31.6
|
1.0
|
O4
|
E:ZDC1
|
2.4
|
32.6
|
1.0
|
OD1
|
A:ASP101
|
2.4
|
36.9
|
1.0
|
OD1
|
A:ASP104
|
2.5
|
33.0
|
1.0
|
OE2
|
A:GLU95
|
2.5
|
31.1
|
1.0
|
OE1
|
A:GLU95
|
2.6
|
32.9
|
1.0
|
OD2
|
A:ASP104
|
2.7
|
37.7
|
1.0
|
CD
|
A:GLU95
|
2.8
|
33.6
|
1.0
|
CG
|
A:ASP104
|
3.0
|
35.2
|
1.0
|
C4
|
E:ZDC1
|
3.2
|
33.2
|
1.0
|
C3
|
E:ZDC1
|
3.2
|
31.4
|
1.0
|
CG
|
A:ASP99
|
3.3
|
40.6
|
1.0
|
CG
|
A:ASP101
|
3.5
|
34.3
|
1.0
|
OD2
|
A:ASP99
|
3.6
|
38.2
|
1.0
|
CA
|
A:CA301
|
3.6
|
35.4
|
1.0
|
OD2
|
A:ASP101
|
3.9
|
33.8
|
1.0
|
O
|
A:HOH422
|
4.0
|
36.3
|
1.0
|
N
|
A:ASP101
|
4.2
|
34.1
|
1.0
|
OD1
|
A:ASP96
|
4.2
|
32.2
|
1.0
|
CG
|
A:GLU95
|
4.3
|
33.7
|
1.0
|
N
|
A:ASN100
|
4.4
|
41.2
|
1.0
|
CB
|
A:ASP104
|
4.5
|
34.3
|
1.0
|
N
|
A:TYR102
|
4.5
|
31.8
|
1.0
|
N
|
A:ASP96
|
4.5
|
35.9
|
1.0
|
N
|
A:GLY97
|
4.6
|
39.2
|
1.0
|
C2
|
E:ZDC1
|
4.6
|
33.7
|
1.0
|
CB
|
A:ASP99
|
4.6
|
39.1
|
1.0
|
C5
|
E:ZDC1
|
4.6
|
37.6
|
1.0
|
CB
|
A:ASP101
|
4.7
|
31.4
|
1.0
|
CA
|
A:GLU95
|
4.7
|
30.5
|
1.0
|
N
|
A:ASP99
|
4.8
|
35.1
|
1.0
|
O2
|
E:ZDC1
|
4.8
|
34.1
|
1.0
|
CA
|
A:ASP101
|
4.8
|
32.0
|
1.0
|
OD1
|
A:ASN103
|
4.9
|
29.6
|
1.0
|
CG
|
A:ASP96
|
4.9
|
34.3
|
1.0
|
C
|
A:ASP99
|
4.9
|
39.5
|
1.0
|
CB
|
A:GLU95
|
4.9
|
30.2
|
1.0
|
N
|
A:ASP104
|
5.0
|
30.8
|
1.0
|
|
Calcium binding site 3 out
of 8 in 6q79
Go back to
Calcium Binding Sites List in 6q79
Calcium binding site 3 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:37.3
occ:1.00
|
OD1
|
D:ASN103
|
2.3
|
31.9
|
1.0
|
O
|
D:ASN21
|
2.3
|
38.5
|
1.0
|
OD2
|
D:ASP101
|
2.3
|
33.2
|
1.0
|
O3
|
H:ZDC1
|
2.4
|
37.8
|
1.0
|
O2
|
H:ZDC1
|
2.4
|
39.9
|
1.0
|
OD1
|
D:ASP104
|
2.5
|
38.2
|
1.0
|
O
|
A:GLY114
|
2.6
|
44.6
|
1.0
|
CG
|
D:ASP101
|
3.1
|
34.9
|
1.0
|
OD1
|
D:ASP101
|
3.1
|
35.2
|
1.0
|
C3
|
H:ZDC1
|
3.3
|
38.8
|
1.0
|
C2
|
H:ZDC1
|
3.4
|
38.1
|
1.0
|
CG
|
D:ASN103
|
3.4
|
32.2
|
1.0
|
C
|
A:GLY114
|
3.4
|
44.9
|
1.0
|
C
|
D:ASN21
|
3.5
|
38.7
|
1.0
|
OXT
|
A:GLY114
|
3.5
|
47.8
|
1.0
|
CA
|
D:CA301
|
3.6
|
35.3
|
1.0
|
C4
|
H:ZDC1
|
3.7
|
38.0
|
1.0
|
CG
|
D:ASP104
|
3.7
|
36.8
|
1.0
|
ND2
|
D:ASN103
|
3.8
|
29.1
|
1.0
|
N
|
D:ASP104
|
4.1
|
34.3
|
1.0
|
CB
|
D:ASN21
|
4.2
|
35.9
|
1.0
|
CA
|
D:ASP104
|
4.2
|
35.8
|
1.0
|
O4
|
H:ZDC1
|
4.3
|
36.4
|
1.0
|
CA
|
D:SER22
|
4.3
|
43.4
|
1.0
|
CB
|
D:SER22
|
4.3
|
43.5
|
1.0
|
N
|
D:SER22
|
4.4
|
41.3
|
1.0
|
OD2
|
D:ASP99
|
4.4
|
44.4
|
1.0
|
C
|
D:ASN103
|
4.5
|
33.8
|
1.0
|
CB
|
D:ASP104
|
4.5
|
36.5
|
1.0
|
CA
|
D:ASN21
|
4.5
|
38.4
|
1.0
|
CB
|
D:ASP101
|
4.5
|
33.1
|
1.0
|
OD2
|
D:ASP104
|
4.6
|
34.7
|
1.0
|
CB
|
D:ASN103
|
4.7
|
31.4
|
1.0
|
C1
|
H:ZDC1
|
4.7
|
38.6
|
1.0
|
CA
|
A:GLY114
|
4.8
|
43.6
|
1.0
|
N
|
D:ASN103
|
4.9
|
34.4
|
1.0
|
O
|
D:ASN103
|
4.9
|
33.7
|
1.0
|
CA
|
D:ASN103
|
4.9
|
32.8
|
1.0
|
O5
|
H:ZDC1
|
5.0
|
38.9
|
1.0
|
C5
|
H:ZDC1
|
5.0
|
39.0
|
1.0
|
OD1
|
D:ASP99
|
5.0
|
39.8
|
1.0
|
|
Calcium binding site 4 out
of 8 in 6q79
Go back to
Calcium Binding Sites List in 6q79
Calcium binding site 4 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:0.2
occ:1.00
|
OD2
|
B:ASP101
|
2.2
|
38.2
|
1.0
|
O3
|
F:ZDC1
|
2.4
|
29.9
|
1.0
|
OD1
|
B:ASP104
|
2.4
|
32.4
|
1.0
|
O
|
B:ASN21
|
2.4
|
38.2
|
1.0
|
O
|
C:GLY114
|
2.4
|
37.1
|
1.0
|
O2
|
F:ZDC1
|
2.5
|
29.5
|
1.0
|
OD1
|
B:ASN103
|
2.6
|
30.5
|
1.0
|
CG
|
B:ASP101
|
3.1
|
35.5
|
1.0
|
OD1
|
B:ASP101
|
3.2
|
36.8
|
1.0
|
C3
|
F:ZDC1
|
3.2
|
29.2
|
1.0
|
C2
|
F:ZDC1
|
3.3
|
27.6
|
1.0
|
C
|
C:GLY114
|
3.3
|
36.0
|
1.0
|
OXT
|
C:GLY114
|
3.5
|
34.2
|
1.0
|
CA
|
B:CA302
|
3.6
|
27.0
|
1.0
|
C
|
B:ASN21
|
3.6
|
34.8
|
1.0
|
CG
|
B:ASP104
|
3.6
|
32.3
|
1.0
|
CG
|
B:ASN103
|
3.6
|
27.5
|
1.0
|
C4
|
F:ZDC1
|
3.7
|
29.4
|
1.0
|
ND2
|
B:ASN103
|
4.1
|
25.4
|
1.0
|
CA
|
B:ASP104
|
4.2
|
28.5
|
1.0
|
N
|
B:ASP104
|
4.2
|
26.8
|
1.0
|
CB
|
B:ASN21
|
4.3
|
28.6
|
1.0
|
OD2
|
B:ASP99
|
4.3
|
31.7
|
1.0
|
CA
|
B:SER22
|
4.4
|
30.9
|
1.0
|
O4
|
F:ZDC1
|
4.4
|
29.3
|
1.0
|
N
|
B:SER22
|
4.4
|
32.3
|
1.0
|
CB
|
B:ASP104
|
4.4
|
29.9
|
1.0
|
OD2
|
B:ASP104
|
4.5
|
32.9
|
1.0
|
CB
|
B:ASP101
|
4.5
|
34.0
|
1.0
|
C
|
B:ASN103
|
4.6
|
26.1
|
1.0
|
CB
|
B:SER22
|
4.6
|
29.4
|
1.0
|
CA
|
B:ASN21
|
4.6
|
29.4
|
1.0
|
C1
|
F:ZDC1
|
4.6
|
30.5
|
1.0
|
NZ
|
F:DLY5
|
4.6
|
54.6
|
1.0
|
CA
|
C:GLY114
|
4.8
|
34.8
|
1.0
|
O5
|
F:ZDC1
|
4.8
|
30.7
|
1.0
|
O
|
B:ASN103
|
4.9
|
24.9
|
1.0
|
C5
|
F:ZDC1
|
4.9
|
31.2
|
1.0
|
CB
|
B:ASN103
|
4.9
|
23.8
|
1.0
|
N
|
B:ASN103
|
4.9
|
23.9
|
1.0
|
|
Calcium binding site 5 out
of 8 in 6q79
Go back to
Calcium Binding Sites List in 6q79
Calcium binding site 5 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca302
b:27.0
occ:1.00
|
O3
|
F:ZDC1
|
2.4
|
29.9
|
1.0
|
OD1
|
B:ASP101
|
2.4
|
36.8
|
1.0
|
OD1
|
B:ASP99
|
2.4
|
34.4
|
1.0
|
OE1
|
B:GLU95
|
2.4
|
30.0
|
1.0
|
OE2
|
B:GLU95
|
2.5
|
23.0
|
1.0
|
OD2
|
B:ASP104
|
2.5
|
32.9
|
1.0
|
OD1
|
B:ASP104
|
2.5
|
32.4
|
1.0
|
O4
|
F:ZDC1
|
2.5
|
29.3
|
1.0
|
CD
|
B:GLU95
|
2.8
|
25.8
|
1.0
|
CG
|
B:ASP104
|
2.8
|
32.3
|
1.0
|
C4
|
F:ZDC1
|
3.2
|
29.4
|
1.0
|
C3
|
F:ZDC1
|
3.3
|
29.2
|
1.0
|
CG
|
B:ASP99
|
3.3
|
32.5
|
1.0
|
CG
|
B:ASP101
|
3.4
|
35.5
|
1.0
|
OD2
|
B:ASP99
|
3.5
|
31.7
|
1.0
|
CA
|
B:CA301
|
3.6
|
0.2
|
1.0
|
OD2
|
B:ASP101
|
3.8
|
38.2
|
1.0
|
N
|
B:ASP101
|
4.2
|
32.2
|
1.0
|
O
|
B:HOH438
|
4.2
|
32.1
|
1.0
|
OD1
|
B:ASP96
|
4.3
|
35.7
|
1.0
|
CG
|
B:GLU95
|
4.3
|
26.1
|
1.0
|
CB
|
B:ASP104
|
4.4
|
29.9
|
1.0
|
N
|
B:ASN100
|
4.4
|
34.4
|
1.0
|
N
|
B:TYR102
|
4.5
|
26.4
|
1.0
|
N
|
B:ASP96
|
4.5
|
28.0
|
1.0
|
N
|
B:GLY97
|
4.6
|
34.4
|
1.0
|
CB
|
B:ASP101
|
4.6
|
34.0
|
1.0
|
C2
|
F:ZDC1
|
4.6
|
27.6
|
1.0
|
C5
|
F:ZDC1
|
4.7
|
31.2
|
1.0
|
CA
|
B:GLU95
|
4.7
|
27.2
|
1.0
|
CB
|
B:ASP99
|
4.7
|
32.4
|
1.0
|
OD1
|
B:ASN103
|
4.8
|
30.5
|
1.0
|
CA
|
B:ASP101
|
4.8
|
29.8
|
1.0
|
O2
|
F:ZDC1
|
4.8
|
29.5
|
1.0
|
N
|
B:ASP99
|
4.9
|
34.5
|
1.0
|
CB
|
B:GLU95
|
4.9
|
26.6
|
1.0
|
CG
|
B:ASP96
|
4.9
|
35.7
|
1.0
|
N
|
B:ASP104
|
5.0
|
26.8
|
1.0
|
|
Calcium binding site 6 out
of 8 in 6q79
Go back to
Calcium Binding Sites List in 6q79
Calcium binding site 6 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca303
b:26.2
occ:1.00
|
OD2
|
C:ASP101
|
2.3
|
23.2
|
1.0
|
OD1
|
C:ASN103
|
2.3
|
22.4
|
1.0
|
O
|
C:ASN21
|
2.4
|
28.1
|
1.0
|
OD1
|
C:ASP104
|
2.5
|
27.4
|
1.0
|
O3
|
G:ZDC1
|
2.5
|
28.7
|
1.0
|
O
|
B:GLY114
|
2.5
|
29.1
|
1.0
|
O2
|
G:ZDC1
|
2.5
|
29.8
|
1.0
|
CG
|
C:ASP101
|
3.0
|
25.1
|
1.0
|
OD1
|
C:ASP101
|
3.1
|
25.9
|
1.0
|
CG
|
C:ASN103
|
3.3
|
25.1
|
1.0
|
C3
|
G:ZDC1
|
3.4
|
30.8
|
1.0
|
C2
|
G:ZDC1
|
3.4
|
31.6
|
1.0
|
C
|
B:GLY114
|
3.4
|
29.1
|
1.0
|
OXT
|
B:GLY114
|
3.6
|
29.8
|
1.0
|
C
|
C:ASN21
|
3.6
|
28.9
|
1.0
|
CG
|
C:ASP104
|
3.7
|
28.4
|
1.0
|
CA
|
C:CA201
|
3.7
|
29.4
|
1.0
|
ND2
|
C:ASN103
|
3.8
|
26.9
|
1.0
|
C4
|
G:ZDC1
|
3.8
|
31.8
|
1.0
|
CB
|
C:ASN21
|
4.2
|
28.7
|
1.0
|
N
|
C:ASP104
|
4.2
|
28.6
|
1.0
|
CA
|
C:ASP104
|
4.2
|
27.8
|
1.0
|
NZ
|
G:DLY5
|
4.2
|
54.3
|
1.0
|
O4
|
G:ZDC1
|
4.4
|
30.3
|
1.0
|
C
|
C:ASN103
|
4.4
|
25.6
|
1.0
|
CB
|
C:ASP101
|
4.5
|
25.0
|
1.0
|
OD2
|
C:ASP99
|
4.5
|
28.8
|
1.0
|
CE
|
G:DLY5
|
4.5
|
57.1
|
1.0
|
CA
|
C:SER22
|
4.5
|
28.4
|
1.0
|
CB
|
C:ASP104
|
4.5
|
27.4
|
1.0
|
N
|
C:SER22
|
4.5
|
28.6
|
1.0
|
OD2
|
C:ASP104
|
4.5
|
28.9
|
1.0
|
CA
|
C:ASN21
|
4.6
|
28.7
|
1.0
|
CB
|
C:SER22
|
4.6
|
27.2
|
1.0
|
CB
|
C:ASN103
|
4.7
|
22.7
|
1.0
|
C1
|
G:ZDC1
|
4.8
|
34.1
|
1.0
|
CA
|
B:GLY114
|
4.8
|
27.9
|
1.0
|
O
|
C:ASN103
|
4.8
|
23.0
|
1.0
|
N
|
C:ASN103
|
4.8
|
24.1
|
1.0
|
CA
|
C:ASN103
|
4.9
|
23.1
|
1.0
|
|
Calcium binding site 7 out
of 8 in 6q79
Go back to
Calcium Binding Sites List in 6q79
Calcium binding site 7 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca201
b:29.4
occ:1.00
|
O4
|
G:ZDC1
|
2.4
|
30.3
|
1.0
|
OD1
|
C:ASP99
|
2.4
|
31.9
|
1.0
|
OD1
|
C:ASP101
|
2.4
|
25.9
|
1.0
|
OE1
|
C:GLU95
|
2.5
|
32.4
|
1.0
|
OE2
|
C:GLU95
|
2.5
|
32.1
|
1.0
|
O3
|
G:ZDC1
|
2.5
|
28.7
|
1.0
|
OD2
|
C:ASP104
|
2.5
|
28.9
|
1.0
|
OD1
|
C:ASP104
|
2.6
|
27.4
|
1.0
|
CD
|
C:GLU95
|
2.8
|
31.3
|
1.0
|
CG
|
C:ASP104
|
2.9
|
28.4
|
1.0
|
C4
|
G:ZDC1
|
3.2
|
31.8
|
1.0
|
C3
|
G:ZDC1
|
3.3
|
30.8
|
1.0
|
CG
|
C:ASP99
|
3.4
|
29.7
|
1.0
|
CG
|
C:ASP101
|
3.4
|
25.1
|
1.0
|
OD2
|
C:ASP99
|
3.6
|
28.8
|
1.0
|
CA
|
B:CA303
|
3.7
|
26.2
|
1.0
|
OD2
|
C:ASP101
|
3.9
|
23.2
|
1.0
|
O
|
C:HOH423
|
4.1
|
31.6
|
1.0
|
N
|
C:ASP101
|
4.1
|
28.4
|
1.0
|
OD1
|
C:ASP96
|
4.2
|
31.2
|
1.0
|
CG
|
C:GLU95
|
4.3
|
28.6
|
1.0
|
N
|
C:ASN100
|
4.4
|
28.9
|
1.0
|
N
|
C:TYR102
|
4.4
|
27.8
|
1.0
|
CB
|
C:ASP104
|
4.4
|
27.4
|
1.0
|
N
|
C:GLY97
|
4.5
|
31.6
|
1.0
|
N
|
C:ASP96
|
4.5
|
26.9
|
1.0
|
CB
|
C:ASP101
|
4.6
|
25.0
|
1.0
|
C5
|
G:ZDC1
|
4.6
|
32.2
|
1.0
|
C2
|
G:ZDC1
|
4.7
|
31.6
|
1.0
|
CA
|
C:GLU95
|
4.7
|
25.2
|
1.0
|
CA
|
C:ASP101
|
4.8
|
26.4
|
1.0
|
CB
|
C:ASP99
|
4.8
|
27.1
|
1.0
|
O2
|
G:ZDC1
|
4.8
|
29.8
|
1.0
|
N
|
C:ASP99
|
4.8
|
32.3
|
1.0
|
OD1
|
C:ASN103
|
4.8
|
22.4
|
1.0
|
CG
|
C:ASP96
|
4.9
|
32.6
|
1.0
|
CB
|
C:GLU95
|
4.9
|
26.9
|
1.0
|
CA
|
C:GLY97
|
5.0
|
33.3
|
1.0
|
C
|
C:ASP99
|
5.0
|
30.6
|
1.0
|
|
Calcium binding site 8 out
of 8 in 6q79
Go back to
Calcium Binding Sites List in 6q79
Calcium binding site 8 out
of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca301
b:35.3
occ:1.00
|
O4
|
H:ZDC1
|
2.3
|
36.4
|
1.0
|
OD1
|
D:ASP99
|
2.3
|
39.8
|
1.0
|
OD1
|
D:ASP101
|
2.4
|
35.2
|
1.0
|
O3
|
H:ZDC1
|
2.5
|
37.8
|
1.0
|
OE2
|
D:GLU95
|
2.5
|
30.9
|
1.0
|
OD1
|
D:ASP104
|
2.6
|
38.2
|
1.0
|
OE1
|
D:GLU95
|
2.6
|
33.5
|
1.0
|
OD2
|
D:ASP104
|
2.7
|
34.7
|
1.0
|
CD
|
D:GLU95
|
2.9
|
33.9
|
1.0
|
CG
|
D:ASP104
|
3.0
|
36.8
|
1.0
|
C4
|
H:ZDC1
|
3.2
|
38.0
|
1.0
|
CG
|
D:ASP99
|
3.3
|
42.1
|
1.0
|
CG
|
D:ASP101
|
3.3
|
34.9
|
1.0
|
C3
|
H:ZDC1
|
3.3
|
38.8
|
1.0
|
OD2
|
D:ASP99
|
3.5
|
44.4
|
1.0
|
CA
|
A:CA303
|
3.6
|
37.3
|
1.0
|
OD2
|
D:ASP101
|
3.7
|
33.2
|
1.0
|
O
|
D:HOH430
|
3.8
|
42.6
|
1.0
|
N
|
D:ASP101
|
4.1
|
37.0
|
1.0
|
OD1
|
D:ASP96
|
4.1
|
45.0
|
1.0
|
CG
|
D:GLU95
|
4.4
|
34.0
|
1.0
|
N
|
D:TYR102
|
4.4
|
33.6
|
1.0
|
CB
|
D:ASP101
|
4.5
|
33.1
|
1.0
|
CB
|
D:ASP104
|
4.5
|
36.5
|
1.0
|
N
|
D:ASN100
|
4.5
|
39.6
|
1.0
|
C5
|
H:ZDC1
|
4.6
|
39.0
|
1.0
|
N
|
D:ASP96
|
4.6
|
37.7
|
1.0
|
C2
|
H:ZDC1
|
4.7
|
38.1
|
1.0
|
CB
|
D:ASP99
|
4.7
|
41.1
|
1.0
|
N
|
D:GLY97
|
4.7
|
38.3
|
1.0
|
CA
|
D:ASP101
|
4.7
|
33.5
|
1.0
|
OD1
|
D:ASN103
|
4.7
|
31.9
|
1.0
|
O2
|
H:ZDC1
|
4.7
|
39.9
|
1.0
|
N
|
D:ASP99
|
4.8
|
43.7
|
1.0
|
CA
|
D:GLU95
|
4.8
|
36.0
|
1.0
|
C
|
D:ASP101
|
4.9
|
35.0
|
1.0
|
|
Reference:
S.Baeriswyl,
B.H.Gan,
T.N.Siriwardena,
R.Visini,
M.Robadey,
S.Javor,
A.Stocker,
T.Darbre,
J.L.Reymond.
X-Ray Crystal Structures of Short Antimicrobial Peptides As Pseudomonas Aeruginosa Lectin B Complexes. Acs Chem.Biol. V. 14 758 2019.
ISSN: ESSN 1554-8937
PubMed: 30830745
DOI: 10.1021/ACSCHEMBIO.9B00047
Page generated: Tue Jul 16 13:43:16 2024
|