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Calcium in PDB 6q6x: Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution

Protein crystallography data

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution, PDB code: 6q6x 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) 47.51 / 1.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.474, 59.416, 72.060, 90.00, 106.12, 90.00
R / Rfree (%) 15.8 / 18.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution (pdb code 6q6x). 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 SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution, PDB code: 6q6x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6q6x

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Calcium binding site 1 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 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 SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:8.1
occ:1.00
 OD1 A:ASP99 2.4 12.2 1.0
OD1 A:ASP101 2.4 7.4 1.0
OD2 A:ASP104 2.4 9.8 1.0
OE2 A:GLU95 2.4 9.1 1.0
OE1 A:GLU95 2.5 9.8 1.0
O3 E:ZDC1 2.5 8.9 1.0
O4 E:ZDC1 2.5 7.3 1.0
OD1 A:ASP104 2.7 6.9 1.0
CD A:GLU95 2.8 7.2 1.0
CG A:ASP104 2.9 7.2 1.0
C4 E:ZDC1 3.3 8.4 1.0
C3 E:ZDC1 3.3 8.8 1.0
CG A:ASP99 3.4 9.6 1.0
CG A:ASP101 3.4 9.2 1.0
OD2 A:ASP99 3.6 9.3 1.0
CA A:CA302 3.8 7.9 1.0
OD2 A:ASP101 4.0 10.1 1.0
N A:ASP101 4.2 8.8 1.0
OD1 A:ASP96 4.3 9.8 1.0
CG A:GLU95 4.3 8.2 1.0
CB A:ASP104 4.4 7.9 1.0
N A:ASP96 4.5 7.2 1.0
N A:TYR102 4.5 8.5 1.0
N A:ASN100 4.6 9.9 1.0
N A:GLY97 4.6 9.2 1.0
CB A:ASP101 4.6 8.3 1.0
CA A:GLU95 4.7 7.8 1.0
C2 E:ZDC1 4.7 8.2 1.0
C5 E:ZDC1 4.7 9.0 1.0
CB A:ASP99 4.7 9.4 1.0
CA A:ASP101 4.8 7.8 1.0
OD1 A:ASN103 4.8 6.8 1.0
N A:ASP99 4.8 11.0 1.0
O2 E:ZDC1 4.8 6.6 1.0
CG A:ASP96 4.9 10.0 1.0
CB A:GLU95 4.9 8.9 1.0

Calcium binding site 2 out of 8 in 6q6x

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Calcium binding site 2 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 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 SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:7.9
occ:1.00
 OD1 A:ASN103 2.3 6.8 1.0
O A:ASN21 2.4 7.8 1.0
OD1 A:ASP104 2.4 6.9 1.0
OD2 A:ASP101 2.4 10.1 1.0
O3 E:ZDC1 2.4 8.9 1.0
O C:GLY114 2.5 9.2 1.0
O2 E:ZDC1 2.5 6.6 1.0
OD1 A:ASP101 3.1 7.4 1.0
CG A:ASP101 3.1 9.2 1.0
CG A:ASN103 3.4 8.7 1.0
C3 E:ZDC1 3.4 8.8 1.0
C C:GLY114 3.4 10.0 1.0
C2 E:ZDC1 3.4 8.2 1.0
C A:ASN21 3.6 6.7 1.0
CG A:ASP104 3.6 7.2 1.0
OXT C:GLY114 3.6 11.8 1.0
CA A:CA301 3.8 8.1 1.0
ND2 A:ASN103 3.8 7.8 1.0
C4 E:ZDC1 3.8 8.4 1.0
CA A:ASP104 4.2 6.6 1.0
N A:ASP104 4.2 6.3 1.0
CB A:ASN21 4.2 6.5 1.0
CA A:SER22 4.4 7.5 1.0
N A:SER22 4.4 7.4 1.0
C A:ASN103 4.4 7.1 1.0
OD2 A:ASP104 4.4 9.8 1.0
CB A:ASP104 4.4 7.9 1.0
O A:HOH440 4.5 19.8 1.0
O4 E:ZDC1 4.5 7.3 1.0
OD2 A:ASP99 4.5 9.3 1.0
CA A:ASN21 4.5 6.8 1.0
CB A:ASP101 4.6 8.3 1.0
CB A:SER22 4.6 9.6 1.0
CB A:ASN103 4.7 6.9 1.0
O A:ASN103 4.8 8.2 1.0
C1 E:ZDC1 4.8 9.2 1.0
CA C:GLY114 4.8 9.4 1.0
N A:ASN103 4.8 9.1 1.0
CA A:ASN103 4.9 9.4 1.0

Calcium binding site 3 out of 8 in 6q6x

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Calcium binding site 3 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 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 SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:7.9
occ:1.00
 OD1 C:ASN103 2.3 8.5 1.0
O C:ASN21 2.4 7.8 1.0
OD1 C:ASP104 2.4 8.3 1.0
OD2 C:ASP101 2.4 8.0 1.0
O2 G:ZDC1 2.5 8.5 1.0
O A:GLY114 2.5 9.6 1.0
O3 G:ZDC1 2.5 7.3 1.0
OD1 C:ASP101 3.1 8.8 1.0
CG C:ASP101 3.1 10.1 1.0
C3 G:ZDC1 3.4 8.7 1.0
CG C:ASN103 3.4 6.7 1.0
C2 G:ZDC1 3.4 9.4 1.0
C A:GLY114 3.4 10.3 1.0
C C:ASN21 3.6 8.5 1.0
OXT A:GLY114 3.6 12.9 1.0
CG C:ASP104 3.6 8.4 1.0
CA C:CA301 3.7 8.8 1.0
ND2 C:ASN103 3.8 9.6 1.0
C4 G:ZDC1 3.8 8.3 1.0
CB C:ASN21 4.1 9.0 1.0
CA C:ASP104 4.2 8.1 1.0
N C:ASP104 4.3 7.2 1.0
CA C:SER22 4.4 7.0 1.0
N C:SER22 4.4 9.0 1.0
C C:ASN103 4.5 6.4 1.0
O4 G:ZDC1 4.5 9.7 1.0
OD2 C:ASP104 4.5 7.2 1.0
OD2 C:ASP99 4.5 10.9 1.0
CA C:ASN21 4.5 7.6 1.0
CB C:ASP104 4.5 6.7 1.0
CB C:ASP101 4.6 8.7 1.0
O C:HOH459 4.6 32.4 1.0
CB C:SER22 4.6 10.7 1.0
CB C:ASN103 4.7 6.5 1.0
C1 G:ZDC1 4.8 9.8 1.0
O C:ASN103 4.8 6.3 1.0
CA A:GLY114 4.8 12.9 1.0
N C:ASN103 4.9 6.5 1.0
CA C:ASN103 4.9 8.3 1.0
OD1 C:ASP99 5.0 11.5 1.0

Calcium binding site 4 out of 8 in 6q6x

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Calcium binding site 4 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 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 SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:9.9
occ:1.00
 OD1 B:ASP101 2.4 10.0 1.0
OE1 B:GLU95 2.4 11.3 1.0
OD1 B:ASP99 2.4 13.3 1.0
OE2 B:GLU95 2.4 11.3 1.0
OD2 B:ASP104 2.4 10.9 1.0
O3 F:ZDC1 2.5 9.9 1.0
O4 F:ZDC1 2.6 8.6 1.0
OD1 B:ASP104 2.7 7.9 1.0
CD B:GLU95 2.7 14.2 1.0
CG B:ASP104 2.9 10.7 1.0
C4 F:ZDC1 3.3 8.7 1.0
C3 F:ZDC1 3.4 8.9 1.0
CG B:ASP101 3.4 10.9 1.0
CG B:ASP99 3.4 15.8 1.0
CA B:CA302 3.7 9.3 1.0
OD2 B:ASP99 3.7 12.5 1.0
OD2 B:ASP101 3.9 10.2 1.0
O F:HOH308 4.0 14.7 1.0
N B:ASP101 4.0 9.9 1.0
OD1 B:ASP96 4.2 10.4 1.0
CG B:GLU95 4.2 11.0 1.0
N B:TYR102 4.3 9.7 1.0
CB B:ASP104 4.4 9.2 1.0
N B:ASN100 4.4 11.9 1.0
N B:ASP96 4.5 9.3 1.0
CB B:ASP101 4.5 11.9 1.0
CA B:ASP101 4.7 10.6 1.0
OD1 B:ASN103 4.7 8.4 1.0
C2 F:ZDC1 4.7 9.7 1.0
CA B:GLU95 4.7 11.0 1.0
N B:GLY97 4.7 8.9 1.0
O2 F:ZDC1 4.8 8.3 1.0
C5 F:ZDC1 4.8 9.2 1.0
CB B:ASP99 4.8 10.6 1.0
N B:ASP99 4.8 13.9 1.0
CB B:GLU95 4.9 8.9 1.0
CG B:ASP96 4.9 11.6 1.0
C B:ASP101 4.9 10.4 1.0
C B:ASP99 5.0 12.0 1.0
CA B:ASN100 5.0 13.2 1.0
C B:ASN100 5.0 13.7 1.0

Calcium binding site 5 out of 8 in 6q6x

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Calcium binding site 5 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 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 SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:9.3
occ:1.00
 OD1 B:ASN103 2.3 8.4 1.0
OD1 B:ASP104 2.4 7.9 1.0
O B:ASN21 2.4 8.8 1.0
OD2 B:ASP101 2.4 10.2 1.0
O3 F:ZDC1 2.4 9.9 1.0
O2 F:ZDC1 2.4 8.3 1.0
O D:GLY114 2.5 10.3 1.0
OD1 B:ASP101 3.0 10.0 1.0
CG B:ASP101 3.1 10.9 1.0
C3 F:ZDC1 3.4 8.9 1.0
CG B:ASN103 3.4 8.4 1.0
C2 F:ZDC1 3.4 9.7 1.0
C D:GLY114 3.4 9.6 1.0
CG B:ASP104 3.6 10.7 1.0
C B:ASN21 3.6 8.9 1.0
OXT D:GLY114 3.6 12.3 1.0
CA B:CA301 3.7 9.9 1.0
ND2 B:ASN103 3.8 10.1 1.0
C4 F:ZDC1 3.8 8.7 1.0
CA B:ASP104 4.2 8.3 1.0
CB B:ASN21 4.2 7.2 1.0
N B:ASP104 4.2 7.4 1.0
OD2 B:ASP104 4.4 10.9 1.0
CA B:SER22 4.4 7.7 1.0
N B:SER22 4.4 8.0 1.0
O B:HOH422 4.5 25.4 1.0
CB B:ASP104 4.5 9.2 1.0
O4 F:ZDC1 4.5 8.6 1.0
C B:ASN103 4.5 9.4 1.0
CB B:ASP101 4.5 11.9 1.0
CA B:ASN21 4.6 8.6 1.0
OD2 B:ASP99 4.6 12.5 1.0
CB B:SER22 4.7 7.7 1.0
CB B:ASN103 4.7 7.5 1.0
C1 F:ZDC1 4.7 10.3 1.0
CA D:GLY114 4.8 10.9 1.0
N B:ASN103 4.9 8.1 1.0
O B:ASN103 4.9 7.9 1.0
CA B:ASN103 4.9 7.4 1.0

Calcium binding site 6 out of 8 in 6q6x

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Calcium binding site 6 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 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 SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:9.0
occ:1.00
 OD1 D:ASN103 2.3 9.6 1.0
O D:ASN21 2.4 10.3 1.0
OD2 D:ASP104 2.4 8.5 1.0
OD2 D:ASP101 2.4 10.5 1.0
O B:GLY114 2.4 8.9 1.0
O3 H:ZDC1 2.4 8.2 1.0
O2 H:ZDC1 2.6 9.1 1.0
OD1 D:ASP101 3.0 8.0 1.0
CG D:ASP101 3.1 10.3 1.0
CG D:ASN103 3.3 10.1 1.0
C3 H:ZDC1 3.4 10.1 1.0
C B:GLY114 3.4 10.9 1.0
C2 H:ZDC1 3.5 10.2 1.0
C D:ASN21 3.5 9.1 1.0
CG D:ASP104 3.6 7.5 1.0
OXT B:GLY114 3.7 14.2 1.0
ND2 D:ASN103 3.7 8.6 1.0
CA D:CA301 3.7 9.2 1.0
C4 H:ZDC1 3.8 10.3 1.0
CB D:ASN21 4.1 7.7 1.0
CA D:ASP104 4.2 9.2 1.0
N D:ASP104 4.2 8.3 1.0
O D:HOH423 4.4 25.8 1.0
N D:SER22 4.4 8.2 1.0
CA D:SER22 4.4 9.0 1.0
OD1 D:ASP104 4.4 9.5 1.0
C D:ASN103 4.5 7.9 1.0
O4 H:ZDC1 4.5 10.0 1.0
CB D:ASP104 4.5 10.8 1.0
CA D:ASN21 4.5 8.5 1.0
OD2 D:ASP99 4.5 10.8 1.0
CB D:ASP101 4.5 10.5 1.0
CB D:SER22 4.6 9.4 1.0
CB D:ASN103 4.7 8.8 1.0
O D:ASN103 4.8 9.0 1.0
CA B:GLY114 4.8 10.8 1.0
C1 H:ZDC1 4.8 10.3 1.0
N D:ASN103 4.9 7.1 1.0
CA D:ASN103 4.9 7.0 1.0

Calcium binding site 7 out of 8 in 6q6x

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Calcium binding site 7 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 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 SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:8.8
occ:1.00
 OD1 C:ASP101 2.4 8.8 1.0
OE1 C:GLU95 2.4 8.4 1.0
OD1 C:ASP99 2.4 11.5 1.0
OD2 C:ASP104 2.4 7.2 1.0
OE2 C:GLU95 2.5 9.4 1.0
O3 G:ZDC1 2.5 7.3 1.0
O4 G:ZDC1 2.6 9.7 1.0
OD1 C:ASP104 2.6 8.3 1.0
CD C:GLU95 2.7 8.7 1.0
CG C:ASP104 2.9 8.4 1.0
C4 G:ZDC1 3.3 8.3 1.0
C3 G:ZDC1 3.4 8.7 1.0
CG C:ASP99 3.4 16.7 1.0
CG C:ASP101 3.4 10.1 1.0
OD2 C:ASP99 3.7 10.9 1.0
CA A:CA303 3.7 7.9 1.0
OD2 C:ASP101 4.0 8.0 1.0
O C:HOH479 4.0 15.2 1.0
N C:ASP101 4.1 9.5 1.0
OD1 C:ASP96 4.2 10.2 1.0
CG C:GLU95 4.2 9.1 1.0
CB C:ASP104 4.4 6.7 1.0
N C:TYR102 4.4 7.9 1.0
N C:ASN100 4.5 10.7 1.0
N C:ASP96 4.5 7.5 1.0
CB C:ASP101 4.6 8.7 1.0
N C:GLY97 4.6 9.7 1.0
CA C:GLU95 4.7 7.0 1.0
OD1 C:ASN103 4.7 8.5 1.0
C2 G:ZDC1 4.7 9.4 1.0
CA C:ASP101 4.7 7.2 1.0
C5 G:ZDC1 4.8 8.9 1.0
CB C:ASP99 4.8 13.7 1.0
O2 G:ZDC1 4.8 8.5 1.0
N C:ASP99 4.8 11.9 1.0
CG C:ASP96 4.9 10.5 1.0
CB C:GLU95 4.9 7.2 1.0
C C:ASP101 5.0 8.0 1.0
C C:ASP99 5.0 14.9 1.0

Calcium binding site 8 out of 8 in 6q6x

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Calcium binding site 8 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 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 SB6 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.525 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:9.2
occ:1.00
 OD1 D:ASP99 2.4 11.7 1.0
OD1 D:ASP101 2.4 8.0 1.0
OD1 D:ASP104 2.4 9.5 1.0
OE1 D:GLU95 2.4 12.5 1.0
OE2 D:GLU95 2.5 8.3 1.0
O4 H:ZDC1 2.5 10.0 1.0
O3 H:ZDC1 2.6 8.2 1.0
OD2 D:ASP104 2.6 8.5 1.0
CD D:GLU95 2.8 9.6 1.0
CG D:ASP104 2.9 7.5 1.0
C4 H:ZDC1 3.3 10.3 1.0
CG D:ASP99 3.4 11.2 1.0
C3 H:ZDC1 3.4 10.1 1.0
CG D:ASP101 3.4 10.3 1.0
OD2 D:ASP99 3.7 10.8 1.0
CA B:CA303 3.7 9.0 1.0
OD2 D:ASP101 4.0 10.5 1.0
O D:HOH431 4.0 15.8 1.0
N D:ASP101 4.1 10.1 1.0
OD1 D:ASP96 4.2 11.3 1.0
CG D:GLU95 4.3 7.8 1.0
N D:TYR102 4.4 7.2 1.0
CB D:ASP104 4.4 10.8 1.0
N D:ASN100 4.4 9.8 1.0
N D:ASP96 4.5 9.0 1.0
CB D:ASP101 4.6 10.5 1.0
N D:GLY97 4.6 10.4 1.0
CA D:GLU95 4.7 7.7 1.0
CB D:ASP99 4.7 10.4 1.0
C5 H:ZDC1 4.7 10.4 1.0
CA D:ASP101 4.7 8.7 1.0
C2 H:ZDC1 4.8 10.2 1.0
N D:ASP99 4.8 11.4 1.0
OD1 D:ASN103 4.8 9.6 1.0
CB D:GLU95 4.9 7.7 1.0
CG D:ASP96 4.9 12.6 1.0
O2 H:ZDC1 4.9 9.1 1.0
C D:ASP99 4.9 11.9 1.0
C D:ASP101 5.0 9.0 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 13:19:13 2024

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