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Calcium in PDB 6y0v: Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution

Protein crystallography data

The structure of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution, PDB code: 6y0v 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) 45.06 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.14, 104.88, 52.996, 90, 93.38, 90
R / Rfree (%) 17.9 / 23.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution (pdb code 6y0v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution, PDB code: 6y0v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6y0v

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Calcium binding site 1 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:26.9
occ:1.00
 O A:ASN21 2.3 20.4 1.0
OD1 A:ASN103 2.3 22.4 1.0
OD2 A:ASP104 2.4 22.5 1.0
OD2 A:ASP101 2.4 24.3 1.0
O C:GLY114 2.5 21.8 1.0
O3 E:ZDC101 2.5 24.2 1.0
O2 E:ZDC101 2.6 22.4 1.0
OD1 A:ASP101 3.1 24.3 1.0
CG A:ASP101 3.1 23.4 1.0
CG A:ASN103 3.4 23.1 1.0
C3 E:ZDC101 3.5 25.2 1.0
C A:ASN21 3.5 21.2 1.0
C C:GLY114 3.5 21.9 1.0
C2 E:ZDC101 3.6 24.7 1.0
CG A:ASP104 3.6 22.6 1.0
OXT C:GLY114 3.7 22.6 1.0
CA A:CA302 3.7 23.4 1.0
C4 E:ZDC101 3.8 26.8 1.0
ND2 A:ASN103 3.8 24.1 1.0
CB A:ASN21 4.0 19.7 1.0
CA A:ASP104 4.1 20.4 1.0
N A:ASP104 4.2 19.7 1.0
N A:SER22 4.4 21.0 1.0
CA A:ASN21 4.4 21.3 1.0
CA A:SER22 4.4 23.2 1.0
CB A:ASP104 4.4 21.9 1.0
C A:ASN103 4.4 21.0 1.0
OD1 A:ASP104 4.5 23.1 1.0
O4 E:ZDC101 4.5 26.2 1.0
OD2 A:ASP99 4.6 33.0 1.0
CB A:ASP101 4.6 22.7 1.0
CB A:SER22 4.6 23.1 1.0
CB A:ASN103 4.7 22.8 1.0
O A:ASN103 4.8 20.7 1.0
O C:HOH440 4.8 30.1 1.0
CA C:GLY114 4.8 21.7 1.0
N A:ASN103 4.8 22.2 1.0
C1 E:ZDC101 4.9 26.5 1.0
CA A:ASN103 4.9 21.7 1.0
O5 E:ZDC101 4.9 27.3 1.0

Calcium binding site 2 out of 8 in 6y0v

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Calcium binding site 2 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:23.4
occ:1.00
 OE2 A:GLU95 2.3 23.7 1.0
OD1 A:ASP101 2.3 24.3 1.0
OE1 A:GLU95 2.4 25.9 1.0
OD1 A:ASP99 2.4 33.2 1.0
OD1 A:ASP104 2.4 23.1 1.0
O3 E:ZDC101 2.6 24.2 1.0
OD2 A:ASP104 2.6 22.5 1.0
O4 E:ZDC101 2.6 26.2 1.0
CD A:GLU95 2.6 25.0 1.0
CG A:ASP104 2.9 22.6 1.0
CG A:ASP99 3.4 33.6 1.0
CG A:ASP101 3.4 23.4 1.0
C4 E:ZDC101 3.4 26.8 1.0
C3 E:ZDC101 3.5 25.2 1.0
OD2 A:ASP99 3.7 33.0 1.0
CA A:CA301 3.7 26.9 1.0
O E:HOH203 3.9 33.3 1.0
OD2 A:ASP101 3.9 24.3 1.0
N A:ASP101 4.0 24.4 1.0
CG A:GLU95 4.1 24.2 1.0
OD1 A:ASP96 4.2 27.5 1.0
N A:ASN100 4.3 27.1 1.0
N A:TYR102 4.4 24.5 1.0
CB A:ASP104 4.4 21.9 1.0
N A:ASP96 4.5 25.9 1.0
CB A:ASP101 4.6 22.7 1.0
CA A:GLU95 4.6 24.7 1.0
N A:GLY97 4.6 28.7 1.0
CA A:ASP101 4.7 23.7 1.0
CB A:ASP99 4.8 33.4 1.0
CB A:GLU95 4.8 24.4 1.0
OD1 A:ASN103 4.8 22.4 1.0
C2 E:ZDC101 4.8 24.7 1.0
N A:ASP99 4.8 32.1 1.0
C5 E:ZDC101 4.9 29.1 1.0
C A:ASP101 4.9 23.8 1.0
C A:ASP99 4.9 28.9 1.0
CG A:ASP96 5.0 28.3 1.0
CA A:ASN100 5.0 26.7 1.0
O2 E:ZDC101 5.0 22.4 1.0
C A:ASN100 5.0 25.3 1.0
CA A:GLY97 5.0 29.8 1.0

Calcium binding site 3 out of 8 in 6y0v

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Calcium binding site 3 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:22.1
occ:1.00
 OD1 B:ASN103 2.3 20.2 1.0
O B:ASN21 2.3 18.0 1.0
O3 B:ZDC303 2.4 24.1 1.0
OD2 B:ASP101 2.4 16.7 1.0
OD2 B:ASP104 2.4 19.2 1.0
O2 B:ZDC303 2.4 21.4 1.0
O D:GLY114 2.5 25.4 1.0
OD1 B:ASP101 3.0 14.5 1.0
CG B:ASP101 3.1 16.0 1.0
C3 B:ZDC303 3.3 24.1 1.0
C2 B:ZDC303 3.4 23.3 1.0
CG B:ASN103 3.4 18.8 1.0
C D:GLY114 3.5 22.9 1.0
C B:ASN21 3.5 19.6 1.0
CG B:ASP104 3.7 19.1 1.0
OXT D:GLY114 3.7 21.5 1.0
C4 B:ZDC303 3.7 24.1 1.0
CA B:CA302 3.7 20.2 1.0
ND2 B:ASN103 3.9 17.2 1.0
CB B:ASN21 4.1 17.2 1.0
CA B:ASP104 4.2 15.9 1.0
N B:ASP104 4.2 15.7 1.0
N B:SER22 4.4 20.8 1.0
CA B:SER22 4.4 22.0 1.0
O4 B:ZDC303 4.4 22.7 1.0
OD2 B:ASP99 4.4 27.2 1.0
C B:ASN103 4.4 16.6 1.0
CA B:ASN21 4.5 19.3 1.0
CB B:ASP104 4.5 17.4 1.0
CB B:ASP101 4.5 16.9 1.0
OD1 B:ASP104 4.5 20.9 1.0
CB B:SER22 4.5 21.5 1.0
CB B:ASN103 4.7 18.7 1.0
C1 B:ZDC303 4.7 24.1 1.0
O B:ASN103 4.8 15.3 1.0
CA D:GLY114 4.9 21.8 1.0
N B:ASN103 4.9 18.8 1.0
CA B:ASN103 4.9 17.7 1.0

Calcium binding site 4 out of 8 in 6y0v

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Calcium binding site 4 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:20.2
occ:1.00
 OD1 B:ASP101 2.3 14.5 1.0
OD1 B:ASP99 2.4 23.9 1.0
OD1 B:ASP104 2.4 20.9 1.0
OE2 B:GLU95 2.5 23.4 1.0
OE1 B:GLU95 2.5 22.6 1.0
O4 B:ZDC303 2.5 22.7 1.0
O3 B:ZDC303 2.5 24.1 1.0
OD2 B:ASP104 2.6 19.2 1.0
CD B:GLU95 2.8 22.6 1.0
CG B:ASP104 2.9 19.1 1.0
C4 B:ZDC303 3.3 24.1 1.0
CG B:ASP99 3.4 25.2 1.0
CG B:ASP101 3.4 16.0 1.0
C3 B:ZDC303 3.4 24.1 1.0
OD2 B:ASP99 3.6 27.2 1.0
CA B:CA301 3.7 22.1 1.0
OD2 B:ASP101 3.9 16.7 1.0
N B:ASP101 4.0 19.0 1.0
OD2 B:ASP96 4.0 30.6 1.0
O B:HOH449 4.1 25.8 1.0
CG B:GLU95 4.3 22.0 1.0
N B:ASN100 4.4 23.9 1.0
CB B:ASP104 4.4 17.4 1.0
N B:TYR102 4.4 20.0 1.0
N B:GLY97 4.5 24.2 1.0
N B:ASP96 4.5 21.1 1.0
CB B:ASP101 4.5 16.9 1.0
CA B:ASP101 4.7 18.0 1.0
CA B:GLU95 4.7 20.4 1.0
CB B:ASP99 4.7 24.6 1.0
C2 B:ZDC303 4.7 23.3 1.0
C5 B:ZDC303 4.8 26.1 1.0
OD1 B:ASN103 4.8 20.2 1.0
N B:ASP99 4.8 26.5 1.0
O2 B:ZDC303 4.8 21.4 1.0
CG B:ASP96 4.9 30.2 1.0
CB B:GLU95 4.9 21.1 1.0
C B:ASP101 4.9 19.4 1.0
C B:ASP99 4.9 24.4 1.0
CA B:GLY97 5.0 25.0 1.0
C B:ASN100 5.0 21.8 1.0
CA B:ASN100 5.0 23.9 1.0

Calcium binding site 5 out of 8 in 6y0v

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Calcium binding site 5 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:20.5
occ:1.00
 OD1 C:ASP101 2.3 18.6 1.0
OE2 C:GLU95 2.4 18.1 1.0
OE1 C:GLU95 2.5 17.0 1.0
OD1 C:ASP99 2.5 23.5 1.0
OD2 C:ASP104 2.5 17.7 1.0
O3 G:ZDC101 2.5 20.4 1.0
O4 G:ZDC101 2.5 20.4 1.0
OD1 C:ASP104 2.7 17.7 1.0
CD C:GLU95 2.7 17.9 1.0
CG C:ASP104 2.9 17.5 1.0
C4 G:ZDC101 3.3 21.4 1.0
C3 G:ZDC101 3.4 20.8 1.0
CG C:ASP101 3.4 19.4 1.0
CG C:ASP99 3.5 23.3 1.0
CA C:CA302 3.7 21.4 1.0
OD2 C:ASP99 3.7 21.6 1.0
OD2 C:ASP101 4.0 20.0 1.0
N C:ASP101 4.0 20.1 1.0
OD1 C:ASP96 4.1 17.6 1.0
O C:HOH431 4.2 27.5 1.0
CG C:GLU95 4.2 17.8 1.0
N C:ASN100 4.3 23.8 1.0
N C:TYR102 4.4 18.1 1.0
CB C:ASP104 4.4 17.4 1.0
N C:ASP96 4.5 18.4 1.0
N C:GLY97 4.6 20.4 1.0
CB C:ASP101 4.6 19.1 1.0
CA C:GLU95 4.7 18.8 1.0
CA C:ASP101 4.7 19.4 1.0
C2 G:ZDC101 4.7 20.1 1.0
C5 G:ZDC101 4.8 22.7 1.0
CB C:ASP99 4.8 23.6 1.0
OD1 C:ASN103 4.8 19.0 1.0
N C:ASP99 4.8 25.0 1.0
CB C:GLU95 4.9 18.7 1.0
CA C:ASN100 4.9 23.7 1.0
CG C:ASP96 4.9 18.3 1.0
C C:ASP99 4.9 23.7 1.0
O2 G:ZDC101 4.9 19.7 1.0
C C:ASP101 4.9 18.8 1.0
C C:ASN100 5.0 22.1 1.0

Calcium binding site 6 out of 8 in 6y0v

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Calcium binding site 6 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:21.4
occ:1.00
 O3 G:ZDC101 2.3 20.4 1.0
OD1 C:ASP104 2.4 17.7 1.0
OD2 C:ASP101 2.4 20.0 1.0
O C:ASN21 2.4 19.4 1.0
OD1 C:ASN103 2.4 19.0 1.0
O A:GLY114 2.5 22.4 1.0
O2 G:ZDC101 2.5 19.7 1.0
OD1 C:ASP101 3.0 18.6 1.0
CG C:ASP101 3.1 19.4 1.0
C3 G:ZDC101 3.3 20.8 1.0
C2 G:ZDC101 3.4 20.1 1.0
C A:GLY114 3.4 20.8 1.0
CG C:ASN103 3.5 18.7 1.0
C C:ASN21 3.6 19.5 1.0
OXT A:GLY114 3.6 19.8 1.0
CG C:ASP104 3.6 17.5 1.0
C4 G:ZDC101 3.7 21.4 1.0
CA C:CA301 3.7 20.5 1.0
ND2 C:ASN103 4.0 20.3 1.0
CB C:ASN21 4.2 17.8 1.0
CA C:ASP104 4.2 17.2 1.0
N C:ASP104 4.2 16.8 1.0
O4 G:ZDC101 4.3 20.4 1.0
CA C:SER22 4.4 21.6 1.0
N C:SER22 4.4 20.7 1.0
OD2 C:ASP104 4.4 17.7 1.0
CB C:ASP104 4.5 17.4 1.0
CB C:ASP101 4.5 19.1 1.0
C C:ASN103 4.5 16.2 1.0
CA C:ASN21 4.5 19.1 1.0
OD2 C:ASP99 4.5 21.6 1.0
CB C:SER22 4.6 21.8 1.0
O C:HOH432 4.7 44.6 1.0
C1 G:ZDC101 4.7 19.4 1.0
CA A:GLY114 4.8 18.7 1.0
CB C:ASN103 4.8 17.4 1.0
O C:ASN103 4.8 15.4 1.0
N C:ASN103 4.9 15.8 1.0
O5 G:ZDC101 5.0 21.1 1.0
C5 G:ZDC101 5.0 22.7 1.0

Calcium binding site 7 out of 8 in 6y0v

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Calcium binding site 7 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:23.5
occ:1.00
 OD1 D:ASP101 2.3 19.2 1.0
OD1 D:ASP99 2.4 29.1 1.0
O3 H:ZDC101 2.5 22.6 1.0
OE2 D:GLU95 2.5 21.5 1.0
OD2 D:ASP104 2.5 20.2 1.0
OE1 D:GLU95 2.5 21.9 1.0
O4 H:ZDC101 2.5 21.9 1.0
OD1 D:ASP104 2.5 18.0 1.0
CD D:GLU95 2.8 21.7 1.0
CG D:ASP104 2.9 19.0 1.0
CG D:ASP99 3.3 28.5 1.0
C4 H:ZDC101 3.3 23.8 1.0
CG D:ASP101 3.4 19.6 1.0
C3 H:ZDC101 3.4 23.6 1.0
OD2 D:ASP99 3.6 28.2 1.0
CA D:CA302 3.6 25.9 1.0
OD2 D:ASP101 3.9 20.5 1.0
N D:ASP101 4.1 20.4 1.0
OD1 D:ASP96 4.1 28.1 1.0
CG D:GLU95 4.3 20.6 1.0
N D:ASN100 4.4 25.0 1.0
N D:TYR102 4.4 18.8 1.0
CB D:ASP104 4.4 18.2 1.0
O D:HOH435 4.4 38.6 1.0
CB D:ASP101 4.6 18.8 1.0
N D:ASP96 4.6 22.9 1.0
N D:GLY97 4.6 25.1 1.0
OD1 D:ASN103 4.7 20.4 1.0
CA D:ASP101 4.7 19.1 1.0
CB D:ASP99 4.7 27.3 1.0
CA D:GLU95 4.7 21.1 1.0
C2 H:ZDC101 4.8 22.6 1.0
C5 H:ZDC101 4.8 25.7 1.0
N D:ASP99 4.8 28.6 1.0
C D:ASP101 4.9 19.3 1.0
O2 H:ZDC101 4.9 20.5 1.0
CB D:GLU95 5.0 20.6 1.0
CA D:ASN100 5.0 24.2 1.0
C D:ASP99 5.0 25.6 1.0
CG D:ASP96 5.0 27.1 1.0
N D:ASP104 5.0 17.9 1.0

Calcium binding site 8 out of 8 in 6y0v

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Calcium binding site 8 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:25.9
occ:1.00
 OD1 D:ASN103 2.3 20.4 1.0
O D:ASN21 2.4 17.5 1.0
OD1 D:ASP104 2.4 18.0 1.0
OD2 D:ASP101 2.4 20.5 1.0
O3 H:ZDC101 2.5 22.6 1.0
O B:GLY114 2.5 21.5 1.0
O2 H:ZDC101 2.6 20.5 1.0
OD1 D:ASP101 3.0 19.2 1.0
CG D:ASP101 3.0 19.6 1.0
C3 H:ZDC101 3.4 23.6 1.0
CG D:ASN103 3.4 20.3 1.0
C B:GLY114 3.5 21.6 1.0
C2 H:ZDC101 3.5 22.6 1.0
C D:ASN21 3.5 18.4 1.0
CG D:ASP104 3.6 19.0 1.0
CA D:CA301 3.6 23.5 1.0
OXT B:GLY114 3.7 22.1 1.0
C4 H:ZDC101 3.7 23.8 1.0
ND2 D:ASN103 3.9 19.3 1.0
CB D:ASN21 4.1 17.3 1.0
CA D:ASP104 4.1 18.5 1.0
N D:ASP104 4.2 17.9 1.0
O4 H:ZDC101 4.3 21.9 1.0
N D:SER22 4.4 19.7 1.0
CA D:SER22 4.4 20.8 1.0
OD2 D:ASP99 4.4 28.2 1.0
C D:ASN103 4.4 19.7 1.0
CB D:ASP104 4.5 18.2 1.0
CA D:ASN21 4.5 18.5 1.0
OD2 D:ASP104 4.5 20.2 1.0
CB D:ASP101 4.5 18.8 1.0
CB D:SER22 4.7 20.4 1.0
CB D:ASN103 4.7 19.9 1.0
O D:ASN103 4.8 20.3 1.0
C1 H:ZDC101 4.8 23.6 1.0
N D:ASN103 4.8 20.3 1.0
CA B:GLY114 4.9 20.8 1.0
CA D:ASN103 4.9 20.4 1.0

Reference:

S.Baeriswyl, A.Stocker, J.-L.Reymond. Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution To Be Published.
Page generated: Tue Jul 16 18:20:45 2024

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