Calcium in PDB 6q86: Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 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 2.008 Angstrom Resolution, PDB code: 6q86
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)
|
48.15 /
2.01
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.600,
55.600,
150.621,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.7 /
19
|
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 2.008 Angstrom Resolution
(pdb code 6q86). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 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 2.008 Angstrom Resolution, PDB code: 6q86:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6q86
Go back to
Calcium Binding Sites List in 6q86
Calcium binding site 1 out
of 4 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 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 2.008 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:41.0
occ:1.00
|
OD2
|
A:ASP101
|
2.1
|
44.1
|
1.0
|
O
|
A:ASN21
|
2.2
|
39.6
|
1.0
|
OD1
|
A:ASP104
|
2.3
|
43.7
|
1.0
|
OD1
|
A:ASN103
|
2.4
|
41.6
|
1.0
|
O2
|
C:ZDC1
|
2.5
|
42.4
|
1.0
|
O3
|
C:ZDC1
|
2.6
|
43.8
|
1.0
|
CG
|
A:ASP101
|
2.9
|
42.2
|
1.0
|
OD1
|
A:ASP101
|
3.0
|
43.1
|
1.0
|
C2
|
C:ZDC1
|
3.4
|
39.5
|
1.0
|
C3
|
C:ZDC1
|
3.4
|
36.2
|
1.0
|
C
|
A:ASN21
|
3.5
|
34.5
|
1.0
|
CG
|
A:ASN103
|
3.5
|
37.0
|
1.0
|
CG
|
A:ASP104
|
3.6
|
41.6
|
1.0
|
CA
|
A:CA203
|
3.7
|
42.0
|
1.0
|
C4
|
C:ZDC1
|
3.7
|
33.4
|
1.0
|
ND2
|
A:ASN103
|
4.0
|
32.7
|
1.0
|
N
|
A:ASP104
|
4.0
|
34.5
|
1.0
|
CB
|
A:ASN21
|
4.1
|
31.3
|
1.0
|
CA
|
A:ASP104
|
4.1
|
31.7
|
1.0
|
CA
|
A:SER22
|
4.3
|
38.2
|
1.0
|
CB
|
A:ASP101
|
4.3
|
43.7
|
1.0
|
C
|
A:ASN103
|
4.3
|
33.5
|
1.0
|
N
|
A:SER22
|
4.3
|
36.2
|
1.0
|
CB
|
A:ASP104
|
4.4
|
32.4
|
1.0
|
CA
|
A:ASN21
|
4.4
|
40.5
|
1.0
|
O4
|
C:ZDC1
|
4.4
|
35.0
|
1.0
|
OD2
|
A:ASP104
|
4.4
|
42.5
|
1.0
|
OD2
|
A:ASP99
|
4.5
|
48.1
|
1.0
|
CB
|
A:SER22
|
4.6
|
40.5
|
1.0
|
O
|
A:ASN103
|
4.7
|
36.8
|
1.0
|
C1
|
C:ZDC1
|
4.7
|
34.0
|
1.0
|
CB
|
A:ASN103
|
4.7
|
34.1
|
1.0
|
N
|
A:ASN103
|
4.8
|
29.6
|
1.0
|
CA
|
A:ASN103
|
4.9
|
29.4
|
1.0
|
O5
|
C:ZDC1
|
5.0
|
41.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6q86
Go back to
Calcium Binding Sites List in 6q86
Calcium binding site 2 out
of 4 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 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 2.008 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:42.0
occ:1.00
|
OE2
|
A:GLU95
|
2.2
|
48.6
|
1.0
|
OD1
|
A:ASP101
|
2.4
|
43.1
|
1.0
|
OE1
|
A:GLU95
|
2.4
|
42.0
|
1.0
|
OD2
|
A:ASP104
|
2.4
|
42.5
|
1.0
|
O3
|
C:ZDC1
|
2.4
|
43.8
|
1.0
|
OD1
|
A:ASP99
|
2.4
|
49.9
|
1.0
|
O4
|
C:ZDC1
|
2.5
|
35.0
|
1.0
|
CD
|
A:GLU95
|
2.6
|
38.7
|
1.0
|
OD1
|
A:ASP104
|
2.6
|
43.7
|
1.0
|
CG
|
A:ASP104
|
2.9
|
41.6
|
1.0
|
C4
|
C:ZDC1
|
3.2
|
33.4
|
1.0
|
CG
|
A:ASP101
|
3.3
|
42.2
|
1.0
|
C3
|
C:ZDC1
|
3.3
|
36.2
|
1.0
|
CG
|
A:ASP99
|
3.4
|
49.2
|
1.0
|
OD2
|
A:ASP99
|
3.6
|
48.1
|
1.0
|
CA
|
A:CA202
|
3.7
|
41.0
|
1.0
|
OD2
|
A:ASP101
|
3.8
|
44.1
|
1.0
|
OD1
|
A:ASP96
|
4.0
|
49.5
|
1.0
|
N
|
A:ASP101
|
4.0
|
46.2
|
1.0
|
CG
|
A:GLU95
|
4.1
|
39.6
|
1.0
|
CB
|
A:ASP104
|
4.4
|
32.4
|
1.0
|
N
|
A:TYR102
|
4.4
|
36.3
|
1.0
|
N
|
A:ASN100
|
4.4
|
41.6
|
1.0
|
CB
|
A:ASP101
|
4.4
|
43.7
|
1.0
|
N
|
A:ASP96
|
4.5
|
39.9
|
1.0
|
N
|
A:GLY97
|
4.5
|
36.5
|
1.0
|
CA
|
A:GLU95
|
4.6
|
38.2
|
1.0
|
C2
|
C:ZDC1
|
4.6
|
39.5
|
1.0
|
C5
|
C:ZDC1
|
4.6
|
42.7
|
1.0
|
CA
|
A:ASP101
|
4.7
|
44.0
|
1.0
|
O2
|
C:ZDC1
|
4.7
|
42.4
|
1.0
|
CG
|
A:ASP96
|
4.8
|
44.7
|
1.0
|
CB
|
A:GLU95
|
4.8
|
35.6
|
1.0
|
CB
|
A:ASP99
|
4.8
|
51.1
|
1.0
|
N
|
A:ASP99
|
4.9
|
52.7
|
1.0
|
OD1
|
A:ASN103
|
4.9
|
41.6
|
1.0
|
C
|
A:ASP101
|
4.9
|
42.0
|
1.0
|
N
|
A:ASP104
|
5.0
|
34.5
|
1.0
|
CA
|
A:GLY97
|
5.0
|
38.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6q86
Go back to
Calcium Binding Sites List in 6q86
Calcium binding site 3 out
of 4 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 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 2.008 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:43.7
occ:1.00
|
OD2
|
B:ASP104
|
2.2
|
57.5
|
1.0
|
OE2
|
B:GLU95
|
2.3
|
40.5
|
1.0
|
OD1
|
B:ASP101
|
2.3
|
48.8
|
1.0
|
OD1
|
B:ASP99
|
2.4
|
51.7
|
1.0
|
O3
|
D:ZDC1
|
2.4
|
53.3
|
1.0
|
OE1
|
B:GLU95
|
2.4
|
35.8
|
1.0
|
OD1
|
B:ASP104
|
2.5
|
42.8
|
1.0
|
CG
|
B:ASP104
|
2.7
|
50.5
|
1.0
|
CD
|
B:GLU95
|
2.7
|
34.6
|
1.0
|
O4
|
D:ZDC1
|
2.8
|
46.8
|
1.0
|
CG
|
B:ASP99
|
3.3
|
48.9
|
1.0
|
CG
|
B:ASP101
|
3.3
|
39.0
|
1.0
|
C3
|
D:ZDC1
|
3.4
|
46.9
|
1.0
|
OD2
|
B:ASP99
|
3.5
|
50.0
|
1.0
|
C4
|
D:ZDC1
|
3.5
|
46.4
|
1.0
|
CA
|
B:CA203
|
3.7
|
47.4
|
1.0
|
OD2
|
B:ASP101
|
3.8
|
43.8
|
1.0
|
CG
|
B:GLU95
|
4.2
|
34.7
|
1.0
|
N
|
B:ASP101
|
4.2
|
48.5
|
1.0
|
CB
|
B:ASP104
|
4.2
|
42.7
|
1.0
|
OD1
|
B:ASP96
|
4.2
|
49.0
|
1.0
|
N
|
B:TYR102
|
4.3
|
36.3
|
1.0
|
N
|
B:ASP96
|
4.5
|
50.5
|
1.0
|
N
|
B:ASN100
|
4.5
|
42.5
|
1.0
|
N
|
B:GLY97
|
4.5
|
44.0
|
1.0
|
CB
|
B:ASP101
|
4.5
|
40.9
|
1.0
|
CA
|
B:GLU95
|
4.6
|
35.5
|
1.0
|
CB
|
B:ASP99
|
4.7
|
48.3
|
1.0
|
C2
|
D:ZDC1
|
4.7
|
46.0
|
1.0
|
CA
|
B:ASP101
|
4.8
|
36.1
|
1.0
|
OD1
|
B:ASN103
|
4.8
|
40.2
|
1.0
|
N
|
B:ASP104
|
4.8
|
41.6
|
1.0
|
CG
|
B:ASP96
|
4.8
|
52.3
|
1.0
|
O2
|
D:ZDC1
|
4.8
|
46.5
|
1.0
|
CB
|
B:GLU95
|
4.8
|
33.8
|
1.0
|
N
|
B:ASP99
|
4.9
|
51.6
|
1.0
|
C5
|
D:ZDC1
|
4.9
|
46.5
|
1.0
|
C
|
B:ASP101
|
4.9
|
42.8
|
1.0
|
CA
|
B:ASP104
|
5.0
|
44.9
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6q86
Go back to
Calcium Binding Sites List in 6q86
Calcium binding site 4 out
of 4 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 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 2.008 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:47.4
occ:1.00
|
OD1
|
B:ASP104
|
2.3
|
42.8
|
1.0
|
OD1
|
B:ASN103
|
2.3
|
40.2
|
1.0
|
OD2
|
B:ASP101
|
2.3
|
43.8
|
1.0
|
O
|
B:ASN21
|
2.3
|
45.1
|
1.0
|
O2
|
D:ZDC1
|
2.5
|
46.5
|
1.0
|
O3
|
D:ZDC1
|
2.5
|
53.3
|
1.0
|
CG
|
B:ASP101
|
3.1
|
39.0
|
1.0
|
OD1
|
B:ASP101
|
3.2
|
48.8
|
1.0
|
CG
|
B:ASN103
|
3.4
|
40.1
|
1.0
|
C3
|
D:ZDC1
|
3.4
|
46.9
|
1.0
|
C2
|
D:ZDC1
|
3.4
|
46.0
|
1.0
|
CG
|
B:ASP104
|
3.5
|
50.5
|
1.0
|
C
|
B:ASN21
|
3.5
|
46.3
|
1.0
|
CA
|
B:CA202
|
3.7
|
43.7
|
1.0
|
C4
|
D:ZDC1
|
3.8
|
46.4
|
1.0
|
ND2
|
B:ASN103
|
3.8
|
42.1
|
1.0
|
O
|
B:HOH309
|
4.0
|
40.6
|
1.0
|
CB
|
B:ASN21
|
4.1
|
53.9
|
1.0
|
N
|
B:ASP104
|
4.1
|
41.6
|
1.0
|
CA
|
B:ASP104
|
4.1
|
44.9
|
1.0
|
OD2
|
B:ASP99
|
4.2
|
50.0
|
1.0
|
OD2
|
B:ASP104
|
4.3
|
57.5
|
1.0
|
CB
|
B:ASP104
|
4.4
|
42.7
|
1.0
|
C
|
B:ASN103
|
4.4
|
40.3
|
1.0
|
N
|
B:SER22
|
4.4
|
48.6
|
1.0
|
CA
|
B:ASN21
|
4.4
|
50.0
|
1.0
|
CA
|
B:SER22
|
4.4
|
49.7
|
1.0
|
CB
|
B:ASP101
|
4.5
|
40.9
|
1.0
|
O4
|
D:ZDC1
|
4.5
|
46.8
|
1.0
|
CB
|
B:ASN103
|
4.7
|
37.8
|
1.0
|
CB
|
B:SER22
|
4.7
|
49.1
|
1.0
|
C1
|
D:ZDC1
|
4.7
|
46.5
|
1.0
|
O
|
B:ASN103
|
4.7
|
46.9
|
1.0
|
N
|
B:ASN103
|
4.8
|
46.4
|
1.0
|
CA
|
B:ASN103
|
4.9
|
37.9
|
1.0
|
O5
|
D:ZDC1
|
5.0
|
44.7
|
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
|