Calcium in PDB 5ngq: Bicyclic Antimicrobial Peptides
Protein crystallography data
The structure of Bicyclic Antimicrobial Peptides, PDB code: 5ngq
was solved by
I.Di Bonaventura,
X.Jin,
R.Visini,
G.Michaud,
M.Robadey,
T.Koehler,
C.Vandelden,
A.Stocker,
T.Darbre,
J.-L.Reymond,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.23 /
1.17
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.708,
45.875,
88.218,
90.00,
94.21,
90.00
|
|
R / Rfree (%)
|
13.2 /
15.7
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Bicyclic Antimicrobial Peptides
(pdb code 5ngq). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Bicyclic Antimicrobial Peptides, PDB code: 5ngq:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 5ngq
Go back to
Calcium Binding Sites List in 5ngq
Calcium binding site 1 out
of 8 in the Bicyclic Antimicrobial Peptides
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Bicyclic Antimicrobial Peptides within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:12.9
occ:1.00
|
OD1
|
A:ASP101
|
2.4
|
12.2
|
1.0
|
|
OD1
|
A:ASP99
|
2.4
|
16.4
|
1.0
|
|
OD2
|
A:ASP104
|
2.4
|
12.5
|
1.0
|
|
OE2
|
A:GLU95
|
2.4
|
13.9
|
1.0
|
|
O3
|
G:ZDC201
|
2.4
|
13.9
|
1.0
|
|
OE1
|
A:GLU95
|
2.5
|
13.2
|
1.0
|
|
O4
|
G:ZDC201
|
2.5
|
13.8
|
1.0
|
|
OD1
|
A:ASP104
|
2.7
|
12.1
|
1.0
|
|
CD
|
A:GLU95
|
2.8
|
13.7
|
1.0
|
|
CG
|
A:ASP104
|
2.9
|
11.5
|
1.0
|
|
C4
|
G:ZDC201
|
3.3
|
12.6
|
1.0
|
|
C3
|
G:ZDC201
|
3.3
|
12.8
|
1.0
|
|
CG
|
A:ASP99
|
3.4
|
15.3
|
1.0
|
|
CG
|
A:ASP101
|
3.4
|
12.3
|
1.0
|
|
OD2
|
A:ASP99
|
3.7
|
16.4
|
1.0
|
|
CA
|
A:CA302
|
3.7
|
11.4
|
1.0
|
|
OD2
|
A:ASP101
|
4.0
|
13.4
|
1.0
|
|
O
|
A:HOH454
|
4.1
|
24.9
|
1.0
|
|
N
|
A:ASP101
|
4.2
|
14.6
|
1.0
|
|
CG
|
A:GLU95
|
4.2
|
14.1
|
1.0
|
|
OD1
|
A:ASP96
|
4.3
|
15.1
|
1.0
|
|
CB
|
A:ASP104
|
4.4
|
10.3
|
1.0
|
|
N
|
A:TYR102
|
4.4
|
11.5
|
1.0
|
|
N
|
A:ASP96
|
4.5
|
13.1
|
1.0
|
|
N
|
A:ASN100
|
4.5
|
15.5
|
1.0
|
|
CB
|
A:ASP101
|
4.6
|
13.9
|
1.0
|
|
N
|
A:GLY97
|
4.6
|
14.5
|
1.0
|
|
C2
|
G:ZDC201
|
4.7
|
13.5
|
1.0
|
|
CA
|
A:GLU95
|
4.7
|
12.4
|
1.0
|
|
CA
|
A:ASP101
|
4.7
|
13.6
|
1.0
|
|
OD1
|
A:ASN103
|
4.7
|
10.5
|
1.0
|
|
C5
|
G:ZDC201
|
4.7
|
14.3
|
1.0
|
|
CB
|
A:ASP99
|
4.7
|
16.9
|
1.0
|
|
N
|
A:ASP99
|
4.8
|
17.1
|
1.0
|
|
O2
|
G:ZDC201
|
4.8
|
12.2
|
1.0
|
|
CB
|
A:GLU95
|
4.9
|
12.7
|
1.0
|
|
CG
|
A:ASP96
|
4.9
|
14.1
|
1.0
|
|
C
|
A:ASP101
|
5.0
|
12.3
|
1.0
|
|
Calcium binding site 2 out
of 8 in 5ngq
Go back to
Calcium Binding Sites List in 5ngq
Calcium binding site 2 out
of 8 in the Bicyclic Antimicrobial Peptides
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Bicyclic Antimicrobial Peptides within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:11.4
occ:1.00
|
OD1
|
A:ASN103
|
2.3
|
10.5
|
1.0
|
|
OD1
|
A:ASP104
|
2.4
|
12.1
|
1.0
|
|
O
|
A:ASN21
|
2.4
|
11.7
|
1.0
|
|
OD2
|
A:ASP101
|
2.4
|
13.4
|
1.0
|
|
O
|
C:GLY114
|
2.4
|
12.5
|
1.0
|
|
O3
|
G:ZDC201
|
2.5
|
13.9
|
1.0
|
|
O2
|
G:ZDC201
|
2.5
|
12.2
|
1.0
|
|
OD1
|
A:ASP101
|
3.0
|
12.2
|
1.0
|
|
CG
|
A:ASP101
|
3.1
|
12.3
|
1.0
|
|
C3
|
G:ZDC201
|
3.4
|
12.8
|
1.0
|
|
CG
|
A:ASN103
|
3.4
|
10.1
|
1.0
|
|
C2
|
G:ZDC201
|
3.4
|
13.5
|
1.0
|
|
C
|
C:GLY114
|
3.4
|
12.8
|
1.0
|
|
C
|
A:ASN21
|
3.6
|
10.1
|
1.0
|
|
CG
|
A:ASP104
|
3.6
|
11.5
|
1.0
|
|
OXT
|
C:GLY114
|
3.7
|
14.6
|
1.0
|
|
CA
|
A:CA301
|
3.7
|
12.9
|
1.0
|
|
ND2
|
A:ASN103
|
3.8
|
11.4
|
1.0
|
|
C4
|
G:ZDC201
|
3.8
|
12.6
|
1.0
|
|
CB
|
A:ASN21
|
4.1
|
10.4
|
1.0
|
|
CA
|
A:ASP104
|
4.2
|
10.3
|
1.0
|
|
N
|
A:ASP104
|
4.3
|
10.2
|
1.0
|
|
CA
|
A:SER22
|
4.4
|
12.0
|
1.0
|
|
N
|
A:SER22
|
4.4
|
10.9
|
1.0
|
|
OD2
|
A:ASP104
|
4.4
|
12.5
|
1.0
|
|
C
|
A:ASN103
|
4.5
|
10.9
|
1.0
|
|
O4
|
G:ZDC201
|
4.5
|
13.8
|
1.0
|
|
CB
|
A:ASP104
|
4.5
|
10.3
|
1.0
|
|
O
|
A:HOH428
|
4.5
|
23.0
|
1.0
|
|
CB
|
A:ASP101
|
4.5
|
13.9
|
1.0
|
|
CA
|
A:ASN21
|
4.5
|
10.7
|
1.0
|
|
OD2
|
A:ASP99
|
4.5
|
16.4
|
1.0
|
|
CB
|
A:SER22
|
4.7
|
12.6
|
1.0
|
|
CB
|
A:ASN103
|
4.7
|
10.8
|
1.0
|
|
C1
|
G:ZDC201
|
4.8
|
13.5
|
1.0
|
|
O
|
A:ASN103
|
4.8
|
10.2
|
1.0
|
|
CA
|
C:GLY114
|
4.8
|
13.2
|
1.0
|
|
N
|
A:ASN103
|
4.9
|
11.1
|
1.0
|
|
CA
|
A:ASN103
|
4.9
|
10.9
|
1.0
|
|
Calcium binding site 3 out
of 8 in 5ngq
Go back to
Calcium Binding Sites List in 5ngq
Calcium binding site 3 out
of 8 in the Bicyclic Antimicrobial Peptides
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Bicyclic Antimicrobial Peptides within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:11.3
occ:1.00
|
OD1
|
B:ASP99
|
2.4
|
13.8
|
1.0
|
|
OD1
|
B:ASP101
|
2.4
|
11.9
|
1.0
|
|
OD2
|
B:ASP104
|
2.4
|
11.6
|
1.0
|
|
OE2
|
B:GLU95
|
2.4
|
12.1
|
1.0
|
|
O3
|
H:ZDC201
|
2.4
|
12.0
|
1.0
|
|
OE1
|
B:GLU95
|
2.5
|
11.7
|
1.0
|
|
O4
|
H:ZDC201
|
2.5
|
11.8
|
1.0
|
|
OD1
|
B:ASP104
|
2.6
|
10.4
|
1.0
|
|
CD
|
B:GLU95
|
2.8
|
11.2
|
1.0
|
|
CG
|
B:ASP104
|
2.9
|
10.4
|
1.0
|
|
C4
|
H:ZDC201
|
3.3
|
11.9
|
1.0
|
|
C3
|
H:ZDC201
|
3.4
|
11.6
|
1.0
|
|
CG
|
B:ASP99
|
3.4
|
14.4
|
1.0
|
|
CG
|
B:ASP101
|
3.4
|
11.7
|
1.0
|
|
OD2
|
B:ASP99
|
3.7
|
14.7
|
1.0
|
|
CA
|
B:CA302
|
3.7
|
10.4
|
1.0
|
|
OD2
|
B:ASP101
|
4.0
|
11.6
|
1.0
|
|
O
|
B:HOH460
|
4.1
|
19.3
|
1.0
|
|
N
|
B:ASP101
|
4.1
|
12.2
|
1.0
|
|
CG
|
B:GLU95
|
4.2
|
12.0
|
1.0
|
|
OD1
|
B:ASP96
|
4.3
|
12.5
|
1.0
|
|
CB
|
B:ASP104
|
4.4
|
10.1
|
1.0
|
|
N
|
B:TYR102
|
4.4
|
10.9
|
1.0
|
|
N
|
B:ASN100
|
4.5
|
14.0
|
1.0
|
|
N
|
B:ASP96
|
4.5
|
11.1
|
1.0
|
|
CB
|
B:ASP101
|
4.6
|
12.6
|
1.0
|
|
N
|
B:GLY97
|
4.7
|
13.3
|
1.0
|
|
C2
|
H:ZDC201
|
4.7
|
12.4
|
1.0
|
|
CA
|
B:ASP101
|
4.7
|
11.8
|
1.0
|
|
CA
|
B:GLU95
|
4.7
|
11.0
|
1.0
|
|
CB
|
B:ASP99
|
4.7
|
14.9
|
1.0
|
|
OD1
|
B:ASN103
|
4.7
|
10.3
|
1.0
|
|
C5
|
H:ZDC201
|
4.8
|
13.1
|
1.0
|
|
O2
|
H:ZDC201
|
4.8
|
11.3
|
1.0
|
|
N
|
B:ASP99
|
4.8
|
16.2
|
1.0
|
|
CG
|
B:ASP96
|
4.9
|
11.6
|
1.0
|
|
CB
|
B:GLU95
|
4.9
|
11.0
|
1.0
|
|
C
|
B:ASP101
|
5.0
|
11.2
|
1.0
|
|
C
|
B:ASP99
|
5.0
|
14.1
|
1.0
|
|
Calcium binding site 4 out
of 8 in 5ngq
Go back to
Calcium Binding Sites List in 5ngq
Calcium binding site 4 out
of 8 in the Bicyclic Antimicrobial Peptides
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Bicyclic Antimicrobial Peptides within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca302
b:10.4
occ:1.00
|
OD1
|
B:ASN103
|
2.4
|
10.3
|
1.0
|
|
OD1
|
B:ASP104
|
2.4
|
10.4
|
1.0
|
|
O
|
B:ASN21
|
2.4
|
9.7
|
1.0
|
|
OD2
|
B:ASP101
|
2.4
|
11.6
|
1.0
|
|
O
|
D:GLY114
|
2.4
|
10.9
|
1.0
|
|
O2
|
H:ZDC201
|
2.5
|
11.3
|
1.0
|
|
O3
|
H:ZDC201
|
2.5
|
12.0
|
1.0
|
|
OD1
|
B:ASP101
|
3.0
|
11.9
|
1.0
|
|
CG
|
B:ASP101
|
3.1
|
11.7
|
1.0
|
|
C3
|
H:ZDC201
|
3.4
|
11.6
|
1.0
|
|
CG
|
B:ASN103
|
3.4
|
9.4
|
1.0
|
|
C2
|
H:ZDC201
|
3.4
|
12.4
|
1.0
|
|
C
|
D:GLY114
|
3.4
|
11.9
|
1.0
|
|
C
|
B:ASN21
|
3.6
|
10.3
|
1.0
|
|
CG
|
B:ASP104
|
3.6
|
10.4
|
1.0
|
|
OXT
|
D:GLY114
|
3.7
|
13.6
|
1.0
|
|
CA
|
B:CA301
|
3.7
|
11.3
|
1.0
|
|
ND2
|
B:ASN103
|
3.8
|
11.7
|
1.0
|
|
C4
|
H:ZDC201
|
3.8
|
11.9
|
1.0
|
|
CB
|
B:ASN21
|
4.2
|
9.7
|
1.0
|
|
CA
|
B:ASP104
|
4.2
|
9.3
|
1.0
|
|
N
|
B:ASP104
|
4.3
|
9.5
|
1.0
|
|
CA
|
B:SER22
|
4.4
|
10.6
|
1.0
|
|
N
|
B:SER22
|
4.4
|
10.4
|
1.0
|
|
OD2
|
B:ASP104
|
4.4
|
11.6
|
1.0
|
|
C
|
B:ASN103
|
4.5
|
9.2
|
1.0
|
|
O
|
B:HOH423
|
4.5
|
23.2
|
1.0
|
|
O4
|
H:ZDC201
|
4.5
|
11.8
|
1.0
|
|
CB
|
B:ASP104
|
4.5
|
10.1
|
1.0
|
|
CB
|
B:ASP101
|
4.5
|
12.6
|
1.0
|
|
OD2
|
B:ASP99
|
4.5
|
14.7
|
1.0
|
|
CA
|
B:ASN21
|
4.5
|
10.0
|
1.0
|
|
CB
|
B:SER22
|
4.6
|
11.2
|
1.0
|
|
CB
|
B:ASN103
|
4.7
|
10.4
|
1.0
|
|
C1
|
H:ZDC201
|
4.8
|
13.2
|
1.0
|
|
O
|
B:ASN103
|
4.8
|
9.4
|
1.0
|
|
CA
|
D:GLY114
|
4.8
|
12.4
|
1.0
|
|
N
|
B:ASN103
|
4.9
|
9.6
|
1.0
|
|
CA
|
B:ASN103
|
4.9
|
9.7
|
1.0
|
|
Calcium binding site 5 out
of 8 in 5ngq
Go back to
Calcium Binding Sites List in 5ngq
Calcium binding site 5 out
of 8 in the Bicyclic Antimicrobial Peptides
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Bicyclic Antimicrobial Peptides within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca201
b:11.5
occ:1.00
|
OD1
|
C:ASN103
|
2.4
|
10.5
|
1.0
|
|
OD1
|
C:ASP104
|
2.4
|
11.1
|
1.0
|
|
O
|
C:ASN21
|
2.4
|
11.3
|
1.0
|
|
OD2
|
C:ASP101
|
2.4
|
13.5
|
1.0
|
|
O
|
A:GLY114
|
2.4
|
12.1
|
1.0
|
|
O2
|
E:ZDC301
|
2.5
|
13.3
|
1.0
|
|
O3
|
E:ZDC301
|
2.5
|
13.3
|
1.0
|
|
OD1
|
C:ASP101
|
3.0
|
12.9
|
1.0
|
|
CG
|
C:ASP101
|
3.1
|
12.8
|
1.0
|
|
C3
|
E:ZDC301
|
3.4
|
12.3
|
1.0
|
|
CG
|
C:ASN103
|
3.4
|
10.9
|
1.0
|
|
C
|
A:GLY114
|
3.4
|
12.8
|
1.0
|
|
C2
|
E:ZDC301
|
3.4
|
13.0
|
1.0
|
|
C
|
C:ASN21
|
3.6
|
11.0
|
1.0
|
|
CG
|
C:ASP104
|
3.6
|
11.6
|
1.0
|
|
OXT
|
A:GLY114
|
3.7
|
14.6
|
1.0
|
|
CA
|
C:CA202
|
3.7
|
12.8
|
1.0
|
|
C4
|
E:ZDC301
|
3.8
|
14.1
|
1.0
|
|
ND2
|
C:ASN103
|
3.8
|
11.5
|
1.0
|
|
CB
|
C:ASN21
|
4.2
|
10.6
|
1.0
|
|
CA
|
C:ASP104
|
4.2
|
9.5
|
1.0
|
|
N
|
C:ASP104
|
4.3
|
10.2
|
1.0
|
|
CA
|
C:SER22
|
4.4
|
11.3
|
1.0
|
|
N
|
C:SER22
|
4.4
|
11.9
|
1.0
|
|
O4
|
E:ZDC301
|
4.5
|
13.4
|
1.0
|
|
OD2
|
C:ASP104
|
4.5
|
12.4
|
1.0
|
|
O
|
C:HOH433
|
4.5
|
24.6
|
1.0
|
|
CB
|
C:ASP104
|
4.5
|
11.0
|
1.0
|
|
C
|
C:ASN103
|
4.5
|
10.0
|
1.0
|
|
CB
|
C:ASP101
|
4.5
|
13.6
|
1.0
|
|
CA
|
C:ASN21
|
4.5
|
10.5
|
1.0
|
|
OD2
|
C:ASP99
|
4.6
|
17.6
|
1.0
|
|
CB
|
C:SER22
|
4.7
|
11.7
|
1.0
|
|
CB
|
C:ASN103
|
4.7
|
10.9
|
1.0
|
|
C1
|
E:ZDC301
|
4.8
|
13.1
|
1.0
|
|
O
|
C:ASN103
|
4.8
|
9.6
|
1.0
|
|
CA
|
A:GLY114
|
4.8
|
13.1
|
1.0
|
|
N
|
C:ASN103
|
4.8
|
10.4
|
1.0
|
|
CA
|
C:ASN103
|
4.9
|
10.3
|
1.0
|
|
O5
|
E:ZDC301
|
5.0
|
12.9
|
1.0
|
|
OD1
|
C:ASP99
|
5.0
|
17.9
|
1.0
|
|
Calcium binding site 6 out
of 8 in 5ngq
Go back to
Calcium Binding Sites List in 5ngq
Calcium binding site 6 out
of 8 in the Bicyclic Antimicrobial Peptides
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Bicyclic Antimicrobial Peptides within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca202
b:12.8
occ:1.00
|
OD1
|
C:ASP99
|
2.3
|
17.9
|
1.0
|
|
OD1
|
C:ASP101
|
2.4
|
12.9
|
1.0
|
|
OE2
|
C:GLU95
|
2.4
|
14.8
|
1.0
|
|
O3
|
E:ZDC301
|
2.4
|
13.3
|
1.0
|
|
OD2
|
C:ASP104
|
2.4
|
12.4
|
1.0
|
|
OE1
|
C:GLU95
|
2.5
|
14.3
|
1.0
|
|
O4
|
E:ZDC301
|
2.5
|
13.4
|
1.0
|
|
OD1
|
C:ASP104
|
2.6
|
11.1
|
1.0
|
|
CD
|
C:GLU95
|
2.8
|
13.8
|
1.0
|
|
CG
|
C:ASP104
|
2.9
|
11.6
|
1.0
|
|
C4
|
E:ZDC301
|
3.3
|
14.1
|
1.0
|
|
C3
|
E:ZDC301
|
3.4
|
12.3
|
1.0
|
|
CG
|
C:ASP99
|
3.4
|
18.4
|
1.0
|
|
CG
|
C:ASP101
|
3.4
|
12.8
|
1.0
|
|
OD2
|
C:ASP99
|
3.7
|
17.6
|
1.0
|
|
CA
|
C:CA201
|
3.7
|
11.5
|
1.0
|
|
OD2
|
C:ASP101
|
4.0
|
13.5
|
1.0
|
|
O
|
C:HOH474
|
4.0
|
21.3
|
1.0
|
|
N
|
C:ASP101
|
4.1
|
15.0
|
1.0
|
|
OD1
|
C:ASP96
|
4.2
|
15.7
|
1.0
|
|
CG
|
C:GLU95
|
4.3
|
13.8
|
1.0
|
|
CB
|
C:ASP104
|
4.4
|
11.0
|
1.0
|
|
N
|
C:TYR102
|
4.4
|
12.8
|
1.0
|
|
N
|
C:ASN100
|
4.5
|
17.8
|
1.0
|
|
N
|
C:ASP96
|
4.5
|
12.7
|
1.0
|
|
CB
|
C:ASP101
|
4.6
|
13.6
|
1.0
|
|
N
|
C:GLY97
|
4.7
|
16.1
|
1.0
|
|
CA
|
C:ASP101
|
4.7
|
14.0
|
1.0
|
|
C2
|
E:ZDC301
|
4.7
|
13.0
|
1.0
|
|
CA
|
C:GLU95
|
4.7
|
13.2
|
1.0
|
|
CB
|
C:ASP99
|
4.7
|
18.5
|
1.0
|
|
C5
|
E:ZDC301
|
4.7
|
14.5
|
1.0
|
|
OD1
|
C:ASN103
|
4.8
|
10.5
|
1.0
|
|
N
|
C:ASP99
|
4.8
|
18.8
|
1.0
|
|
O2
|
E:ZDC301
|
4.8
|
13.3
|
1.0
|
|
CB
|
C:GLU95
|
4.9
|
13.8
|
1.0
|
|
C
|
C:ASP101
|
4.9
|
12.6
|
1.0
|
|
CG
|
C:ASP96
|
5.0
|
14.7
|
1.0
|
|
C
|
C:ASP99
|
5.0
|
18.0
|
1.0
|
|
Calcium binding site 7 out
of 8 in 5ngq
Go back to
Calcium Binding Sites List in 5ngq
Calcium binding site 7 out
of 8 in the Bicyclic Antimicrobial Peptides
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Bicyclic Antimicrobial Peptides within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:15.1
occ:1.00
|
OD1
|
D:ASN103
|
2.3
|
13.7
|
1.0
|
|
OD1
|
D:ASP104
|
2.4
|
15.0
|
1.0
|
|
O
|
D:ASN21
|
2.4
|
15.2
|
1.0
|
|
O
|
B:GLY114
|
2.4
|
16.2
|
1.0
|
|
OD2
|
D:ASP101
|
2.4
|
16.1
|
1.0
|
|
O2
|
F:ZDC201
|
2.5
|
17.3
|
1.0
|
|
O3
|
F:ZDC201
|
2.5
|
16.8
|
1.0
|
|
OD1
|
D:ASP101
|
3.0
|
15.7
|
1.0
|
|
CG
|
D:ASP101
|
3.1
|
14.2
|
1.0
|
|
CG
|
D:ASN103
|
3.4
|
13.2
|
1.0
|
|
C3
|
F:ZDC201
|
3.4
|
17.2
|
1.0
|
|
C
|
B:GLY114
|
3.4
|
18.0
|
1.0
|
|
C2
|
F:ZDC201
|
3.4
|
18.1
|
1.0
|
|
C
|
D:ASN21
|
3.6
|
14.6
|
1.0
|
|
CG
|
D:ASP104
|
3.6
|
14.1
|
1.0
|
|
OXT
|
B:GLY114
|
3.7
|
19.7
|
1.0
|
|
CA
|
D:CA202
|
3.7
|
15.8
|
1.0
|
|
C4
|
F:ZDC201
|
3.8
|
17.4
|
1.0
|
|
ND2
|
D:ASN103
|
3.8
|
13.6
|
1.0
|
|
CB
|
D:ASN21
|
4.1
|
15.0
|
1.0
|
|
CA
|
D:ASP104
|
4.2
|
13.4
|
1.0
|
|
N
|
D:ASP104
|
4.3
|
13.0
|
1.0
|
|
CA
|
D:SER22
|
4.4
|
17.5
|
1.0
|
|
OD2
|
D:ASP104
|
4.4
|
15.3
|
1.0
|
|
N
|
D:SER22
|
4.5
|
15.4
|
1.0
|
|
C
|
D:ASN103
|
4.5
|
12.2
|
1.0
|
|
O4
|
F:ZDC201
|
4.5
|
18.3
|
1.0
|
|
OD2
|
D:ASP99
|
4.5
|
20.1
|
1.0
|
|
CB
|
D:ASP104
|
4.5
|
12.8
|
1.0
|
|
CA
|
D:ASN21
|
4.5
|
14.3
|
1.0
|
|
CB
|
D:ASP101
|
4.6
|
16.0
|
1.0
|
|
O
|
D:HOH451
|
4.6
|
28.6
|
1.0
|
|
CB
|
D:SER22
|
4.7
|
17.6
|
1.0
|
|
CB
|
D:ASN103
|
4.7
|
13.6
|
1.0
|
|
C1
|
F:ZDC201
|
4.8
|
18.9
|
1.0
|
|
CA
|
B:GLY114
|
4.8
|
17.7
|
1.0
|
|
O
|
D:ASN103
|
4.8
|
12.9
|
1.0
|
|
N
|
D:ASN103
|
4.8
|
12.2
|
1.0
|
|
CA
|
D:ASN103
|
4.9
|
12.7
|
1.0
|
|
OD1
|
D:ASP99
|
5.0
|
20.6
|
1.0
|
|
Calcium binding site 8 out
of 8 in 5ngq
Go back to
Calcium Binding Sites List in 5ngq
Calcium binding site 8 out
of 8 in the Bicyclic Antimicrobial Peptides
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Bicyclic Antimicrobial Peptides within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca202
b:15.8
occ:1.00
|
OD1
|
D:ASP99
|
2.3
|
20.6
|
1.0
|
|
OD1
|
D:ASP101
|
2.4
|
15.7
|
1.0
|
|
OD2
|
D:ASP104
|
2.4
|
15.3
|
1.0
|
|
OE2
|
D:GLU95
|
2.4
|
16.9
|
1.0
|
|
O3
|
F:ZDC201
|
2.5
|
16.8
|
1.0
|
|
OE1
|
D:GLU95
|
2.5
|
15.9
|
1.0
|
|
O4
|
F:ZDC201
|
2.5
|
18.3
|
1.0
|
|
OD1
|
D:ASP104
|
2.6
|
15.0
|
1.0
|
|
CD
|
D:GLU95
|
2.8
|
15.9
|
1.0
|
|
CG
|
D:ASP104
|
2.9
|
14.1
|
1.0
|
|
C4
|
F:ZDC201
|
3.3
|
17.4
|
1.0
|
|
CG
|
D:ASP99
|
3.3
|
19.6
|
1.0
|
|
C3
|
F:ZDC201
|
3.4
|
17.2
|
1.0
|
|
CG
|
D:ASP101
|
3.4
|
14.2
|
1.0
|
|
OD2
|
D:ASP99
|
3.6
|
20.1
|
1.0
|
|
CA
|
D:CA201
|
3.7
|
15.1
|
1.0
|
|
OD2
|
D:ASP101
|
4.0
|
16.1
|
1.0
|
|
O
|
D:HOH475
|
4.0
|
26.3
|
1.0
|
|
N
|
D:ASP101
|
4.1
|
16.5
|
1.0
|
|
OD1
|
D:ASP96
|
4.2
|
17.8
|
1.0
|
|
CG
|
D:GLU95
|
4.3
|
15.8
|
1.0
|
|
CB
|
D:ASP104
|
4.4
|
12.8
|
1.0
|
|
N
|
D:TYR102
|
4.4
|
13.8
|
1.0
|
|
N
|
D:ASN100
|
4.5
|
19.3
|
1.0
|
|
N
|
D:ASP96
|
4.6
|
15.2
|
1.0
|
|
CB
|
D:ASP101
|
4.6
|
16.0
|
1.0
|
|
N
|
D:GLY97
|
4.6
|
17.9
|
1.0
|
|
C2
|
F:ZDC201
|
4.7
|
18.1
|
1.0
|
|
CA
|
D:ASP101
|
4.7
|
15.4
|
1.0
|
|
CB
|
D:ASP99
|
4.7
|
20.4
|
1.0
|
|
CA
|
D:GLU95
|
4.7
|
14.3
|
1.0
|
|
OD1
|
D:ASN103
|
4.7
|
13.7
|
1.0
|
|
C5
|
F:ZDC201
|
4.8
|
18.4
|
1.0
|
|
N
|
D:ASP99
|
4.8
|
22.9
|
1.0
|
|
O2
|
F:ZDC201
|
4.8
|
17.3
|
1.0
|
|
CA
|
D:GLY97
|
4.9
|
19.9
|
1.0
|
|
CB
|
D:GLU95
|
4.9
|
14.1
|
1.0
|
|
C
|
D:ASP101
|
5.0
|
14.0
|
1.0
|
|
CG
|
D:ASP96
|
5.0
|
17.4
|
1.0
|
|
Reference:
I.Di Bonaventura,
X.Jin,
R.Visini,
D.Probst,
S.Javor,
B.H.Gan,
G.Michaud,
A.Natalello,
S.M.Doglia,
T.Kohler,
C.Van Delden,
A.Stocker,
T.Darbre,
J.L.Reymond.
Chemical Space Guided Discovery of Antimicrobial Bridged Bicyclic Peptides Against Pseudomonas Aeruginosa and Its Biofilms. Chem Sci V. 8 6784 2017.
ISSN: ISSN 2041-6520
PubMed: 29147502
DOI: 10.1039/C7SC01314K
Page generated: Mon Jul 15 09:03:08 2024
|
