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Calcium in PDB 3zdv: Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside

Protein crystallography data

The structure of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside, PDB code: 3zdv was solved by D.Hauck, I.Joachim, B.Frommeyer, A.Varrot, B.Philipp, H.M.Moller, A.Imberty, T.E.Exner, A.Titz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.24 / 1.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.530, 76.980, 99.660, 90.00, 90.00, 90.00
R / Rfree (%) 11.46 / 14.529

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside (pdb code 3zdv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside, PDB code: 3zdv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3zdv

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Calcium binding site 1 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca199

b:9.5
occ:1.00
 OD1 A:ASP99 2.3 12.3 1.0
OD1 A:ASP101 2.3 10.7 1.0
OE2 A:GLU95 2.4 10.0 1.0
OE1 A:GLU95 2.4 8.9 1.0
OD2 A:ASP104 2.5 9.5 1.0
O3 A:MMA201 2.5 9.9 1.0
O4 A:MMA201 2.5 10.2 1.0
OD1 A:ASP104 2.7 9.0 1.0
CD A:GLU95 2.8 8.3 1.0
CG A:ASP104 2.9 9.3 1.0
C4 A:MMA201 3.3 9.3 1.0
C3 A:MMA201 3.4 9.8 1.0
CG A:ASP99 3.4 11.0 1.0
CG A:ASP101 3.4 10.2 1.0
CA A:CA200 3.7 9.3 1.0
OD2 A:ASP99 3.7 11.9 1.0
OD2 A:ASP101 4.0 10.1 1.0
O A:HOH2127 4.1 14.8 1.0
N A:ASP101 4.1 10.9 1.0
OD1 A:ASP96 4.2 11.1 1.0
CG A:GLU95 4.3 10.0 1.0
N A:TYR102 4.4 10.0 1.0
CB A:ASP104 4.4 8.8 1.0
N A:ASN100 4.5 12.0 1.0
N A:ASP96 4.5 7.8 1.0
CB A:ASP101 4.5 10.4 1.0
N A:GLY97 4.7 9.9 1.0
CA A:ASP101 4.7 10.3 1.0
OD1 A:ASN103 4.7 8.9 1.0
C2 A:MMA201 4.7 10.2 1.0
CA A:GLU95 4.7 8.7 1.0
CB A:ASP99 4.7 11.7 1.0
N A:ASP99 4.7 10.8 1.0
C5 A:MMA201 4.8 10.7 1.0
O2 A:MMA201 4.8 9.8 1.0
CB A:GLU95 4.9 9.4 1.0
C A:ASP101 5.0 10.3 1.0
C A:ASP99 5.0 12.2 1.0

Calcium binding site 2 out of 8 in 3zdv

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Calcium binding site 2 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca200

b:9.3
occ:1.00
 OD1 A:ASN103 2.3 8.9 1.0
O A:ASN21 2.3 8.5 1.0
OD1 A:ASP104 2.4 9.0 1.0
O B:GLY114 2.4 9.7 1.0
OD2 A:ASP101 2.4 10.1 1.0
O3 A:MMA201 2.5 9.9 1.0
O2 A:MMA201 2.6 9.8 1.0
OD1 A:ASP101 3.0 10.7 1.0
CG A:ASP101 3.1 10.2 1.0
CG A:ASN103 3.4 9.0 1.0
C3 A:MMA201 3.4 9.8 1.0
C B:GLY114 3.4 11.2 1.0
C2 A:MMA201 3.5 10.2 1.0
C A:ASN21 3.5 8.4 1.0
CG A:ASP104 3.6 9.3 1.0
OXT B:GLY114 3.6 13.1 1.0
CA A:CA199 3.7 9.5 1.0
ND2 A:ASN103 3.7 10.0 1.0
C4 A:MMA201 3.9 9.3 1.0
CB A:ASN21 4.1 8.9 1.0
CA A:ASP104 4.2 8.6 1.0
N A:ASP104 4.3 7.9 1.0
N A:SER22 4.4 8.9 1.0
CA A:SER22 4.4 8.8 1.0
OD2 A:ASP104 4.4 9.5 1.0
O4 A:MMA201 4.5 10.2 1.0
C A:ASN103 4.5 8.1 1.0
CB A:ASP104 4.5 8.8 1.0
OD2 A:ASP99 4.5 11.9 1.0
CA A:ASN21 4.5 9.3 1.0
O A:HOH2131 4.5 28.1 1.0
CB A:ASP101 4.5 10.4 1.0
CB A:ASN103 4.7 8.4 1.0
CB A:SER22 4.7 9.9 1.0
CA B:GLY114 4.8 12.0 1.0
O A:ASN103 4.8 8.4 1.0
C1 A:MMA201 4.8 11.3 1.0
N A:ASN103 4.9 8.8 1.0
CA A:ASN103 4.9 8.4 1.0
OD1 A:ASP99 5.0 12.3 1.0

Calcium binding site 3 out of 8 in 3zdv

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Calcium binding site 3 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca199

b:9.3
occ:1.00
 OD1 B:ASP101 2.3 10.0 1.0
OD1 B:ASP99 2.4 13.0 1.0
OD2 B:ASP104 2.4 9.7 1.0
OE2 B:GLU95 2.4 9.8 1.0
OE1 B:GLU95 2.4 10.0 1.0
O4 B:MMA201 2.5 9.9 1.0
O3 B:MMA201 2.5 9.7 1.0
OD1 B:ASP104 2.6 8.0 1.0
CD B:GLU95 2.8 9.7 1.0
CG B:ASP104 2.9 8.3 1.0
C4 B:MMA201 3.3 9.8 1.0
C3 B:MMA201 3.4 10.6 1.0
CG B:ASP99 3.4 11.8 1.0
CG B:ASP101 3.4 11.0 1.0
CA B:CA200 3.7 8.9 1.0
OD2 B:ASP99 3.7 12.1 1.0
OD2 B:ASP101 4.0 10.7 1.0
O B:HOH2105 4.1 16.3 1.0
N B:ASP101 4.1 12.7 1.0
OD1 B:ASP96 4.2 11.5 1.0
CG B:GLU95 4.2 10.7 1.0
CB B:ASP104 4.4 7.9 1.0
N B:TYR102 4.4 9.8 1.0
CB B:ASP101 4.5 11.2 1.0
N B:ASP96 4.5 9.3 1.0
N B:ASN100 4.5 13.5 1.0
CA B:GLU95 4.7 8.5 1.0
CA B:ASP101 4.7 12.5 1.0
N B:GLY97 4.7 10.8 1.0
C2 B:MMA201 4.7 10.0 1.0
OD1 B:ASN103 4.7 8.7 1.0
CB B:ASP99 4.7 12.2 1.0
C5 B:MMA201 4.7 9.4 1.0
N B:ASP99 4.8 11.8 1.0
O2 B:MMA201 4.8 10.2 1.0
CB B:GLU95 4.9 9.0 1.0
C B:ASP101 5.0 10.8 1.0
CG B:ASP96 5.0 11.3 1.0

Calcium binding site 4 out of 8 in 3zdv

Go back to Calcium Binding Sites List in 3zdv
Calcium binding site 4 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca200

b:8.9
occ:1.00
 OD1 B:ASN103 2.3 8.7 1.0
OD1 B:ASP104 2.3 8.0 1.0
O B:ASN21 2.4 8.5 1.0
OD2 B:ASP101 2.4 10.7 1.0
O A:GLY114 2.4 9.1 1.0
O3 B:MMA201 2.5 9.7 1.0
O2 B:MMA201 2.5 10.2 1.0
OD1 B:ASP101 3.1 10.0 1.0
CG B:ASP101 3.1 11.0 1.0
CG B:ASN103 3.4 8.4 1.0
C A:GLY114 3.4 10.3 1.0
C3 B:MMA201 3.4 10.6 1.0
C2 B:MMA201 3.4 10.0 1.0
C B:ASN21 3.6 8.3 1.0
CG B:ASP104 3.6 8.3 1.0
OXT A:GLY114 3.6 12.1 1.0
ND2 B:ASN103 3.7 10.0 1.0
CA B:CA199 3.7 9.3 1.0
C4 B:MMA201 3.9 9.8 1.0
CA B:ASP104 4.2 7.7 1.0
CB B:ASN21 4.2 8.8 1.0
N B:ASP104 4.3 8.3 1.0
CA B:SER22 4.3 8.9 1.0
N B:SER22 4.4 8.1 1.0
OD2 B:ASP104 4.4 9.7 1.0
CB B:ASP104 4.4 7.9 1.0
C B:ASN103 4.5 8.1 1.0
O4 B:MMA201 4.5 9.9 1.0
O A:HOH2133 4.5 29.8 1.0
OD2 B:ASP99 4.5 12.1 1.0
CB B:ASP101 4.6 11.2 1.0
CA B:ASN21 4.6 7.7 1.0
CB B:SER22 4.7 9.1 1.0
CB B:ASN103 4.7 8.2 1.0
O A:HOH2068 4.7 37.1 1.0
C1 B:MMA201 4.8 10.2 1.0
O B:ASN103 4.8 8.0 1.0
CA A:GLY114 4.8 10.0 1.0
N B:ASN103 4.9 7.5 1.0
CA B:ASN103 4.9 8.1 1.0

Calcium binding site 5 out of 8 in 3zdv

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Calcium binding site 5 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca199

b:10.1
occ:1.00
 OD1 C:ASP101 2.4 10.5 1.0
OD1 C:ASP99 2.4 13.2 1.0
OE2 C:GLU95 2.4 9.8 1.0
OD2 C:ASP104 2.4 9.8 1.0
OE1 C:GLU95 2.5 10.6 1.0
O3 C:MMA201 2.5 10.4 1.0
O4 C:MMA201 2.5 11.1 1.0
OD1 C:ASP104 2.6 9.3 1.0
CD C:GLU95 2.8 9.7 1.0
CG C:ASP104 2.9 8.7 1.0
C4 C:MMA201 3.3 11.3 1.0
CG C:ASP99 3.4 12.7 1.0
C3 C:MMA201 3.4 10.8 1.0
CG C:ASP101 3.4 10.3 1.0
CA C:CA200 3.7 9.7 1.0
OD2 C:ASP99 3.7 12.9 1.0
OD2 C:ASP101 4.0 12.2 1.0
O C:HOH2100 4.1 16.8 1.0
OD1 C:ASP96 4.1 11.3 1.0
N C:ASP101 4.2 10.7 1.0
CG C:GLU95 4.3 10.4 1.0
CB C:ASP104 4.4 9.6 1.0
N C:TYR102 4.5 9.6 1.0
N C:ASN100 4.5 12.9 1.0
N C:ASP96 4.6 10.2 1.0
CB C:ASP101 4.6 12.5 1.0
CA C:GLU95 4.7 9.7 1.0
N C:GLY97 4.7 11.6 1.0
OD1 C:ASN103 4.7 9.4 1.0
C2 C:MMA201 4.7 11.4 1.0
CA C:ASP101 4.7 12.2 1.0
CB C:ASP99 4.7 12.7 1.0
C5 C:MMA201 4.8 11.9 1.0
N C:ASP99 4.8 13.3 1.0
O2 C:MMA201 4.8 10.7 1.0
CB C:GLU95 4.9 9.4 1.0
CG C:ASP96 4.9 10.6 1.0
C C:ASP101 5.0 10.7 1.0

Calcium binding site 6 out of 8 in 3zdv

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Calcium binding site 6 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca200

b:9.7
occ:1.00
 OD1 C:ASP104 2.3 9.3 1.0
OD1 C:ASN103 2.3 9.4 1.0
O C:ASN21 2.4 9.5 1.0
O D:GLY114 2.4 10.6 1.0
OD2 C:ASP101 2.4 12.2 1.0
O3 C:MMA201 2.5 10.4 1.0
O2 C:MMA201 2.5 10.7 1.0
OD1 C:ASP101 3.0 10.5 1.0
CG C:ASP101 3.0 10.3 1.0
C3 C:MMA201 3.4 10.8 1.0
C D:GLY114 3.4 11.9 1.0
CG C:ASN103 3.4 8.6 1.0
C2 C:MMA201 3.4 11.4 1.0
C C:ASN21 3.6 9.5 1.0
CG C:ASP104 3.6 8.7 1.0
OXT D:GLY114 3.7 13.0 1.0
CA C:CA199 3.7 10.1 1.0
ND2 C:ASN103 3.8 9.3 1.0
C4 C:MMA201 3.9 11.3 1.0
CB C:ASN21 4.1 9.3 1.0
CA C:ASP104 4.2 8.8 1.0
N C:ASP104 4.3 9.1 1.0
CA C:SER22 4.4 9.7 1.0
N C:SER22 4.4 10.3 1.0
OD2 C:ASP104 4.4 9.8 1.0
O4 C:MMA201 4.5 11.1 1.0
CB C:ASP104 4.5 9.6 1.0
CB C:ASP101 4.5 12.5 1.0
C C:ASN103 4.5 8.1 1.0
O C:HOH2105 4.5 20.8 1.0
CA C:ASN21 4.5 9.1 1.0
OD2 C:ASP99 4.6 12.9 1.0
CB C:SER22 4.7 9.4 1.0
CB C:ASN103 4.7 8.4 1.0
CA D:GLY114 4.8 10.7 1.0
C1 C:MMA201 4.8 11.7 1.0
O C:ASN103 4.8 9.8 1.0
N C:ASN103 4.9 9.4 1.0
CA C:ASN103 4.9 8.5 1.0
OD1 C:ASP99 5.0 13.2 1.0

Calcium binding site 7 out of 8 in 3zdv

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Calcium binding site 7 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca199

b:10.1
occ:1.00
 OD1 D:ASP99 2.3 12.2 1.0
OD1 D:ASP101 2.4 10.7 1.0
OE2 D:GLU95 2.4 10.6 1.0
OD2 D:ASP104 2.4 10.1 1.0
OE1 D:GLU95 2.5 10.5 1.0
O4 D:MMA201 2.5 10.4 1.0
O3 D:MMA201 2.5 11.4 1.0
OD1 D:ASP104 2.6 9.3 1.0
CD D:GLU95 2.8 10.5 1.0
CG D:ASP104 2.9 8.7 1.0
C4 D:MMA201 3.3 11.2 1.0
CG D:ASP99 3.4 10.8 1.0
C3 D:MMA201 3.4 10.3 1.0
CG D:ASP101 3.4 9.5 1.0
OD2 D:ASP99 3.7 14.2 1.0
CA D:CA200 3.7 9.6 1.0
OD2 D:ASP101 4.0 10.9 1.0
O D:HOH2086 4.0 18.3 1.0
OD1 D:ASP96 4.1 12.5 1.0
N D:ASP101 4.2 11.2 1.0
CG D:GLU95 4.3 9.6 1.0
CB D:ASP104 4.4 9.2 1.0
N D:TYR102 4.5 8.8 1.0
N D:ASN100 4.5 12.9 1.0
N D:ASP96 4.5 10.1 1.0
CB D:ASP101 4.5 11.0 1.0
N D:GLY97 4.7 11.1 1.0
CA D:ASP101 4.7 10.3 1.0
CB D:ASP99 4.7 12.6 1.0
OD1 D:ASN103 4.7 8.2 1.0
C2 D:MMA201 4.7 10.9 1.0
CA D:GLU95 4.8 9.2 1.0
C5 D:MMA201 4.8 11.0 1.0
O2 D:MMA201 4.8 10.9 1.0
N D:ASP99 4.8 13.7 1.0
CG D:ASP96 4.9 11.2 1.0
CB D:GLU95 4.9 10.0 1.0
C D:ASP99 5.0 13.1 1.0
C D:ASP101 5.0 9.7 1.0

Calcium binding site 8 out of 8 in 3zdv

Go back to Calcium Binding Sites List in 3zdv
Calcium binding site 8 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(2,4,6-Trimethylphenylsulfonylamido)- 6-Deoxy-Alpha-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca200

b:9.6
occ:1.00
 OD1 D:ASN103 2.3 8.2 1.0
OD1 D:ASP104 2.3 9.3 1.0
O D:ASN21 2.4 8.7 1.0
OD2 D:ASP101 2.4 10.9 1.0
O C:GLY114 2.4 10.3 1.0
O3 D:MMA201 2.5 11.4 1.0
O2 D:MMA201 2.5 10.9 1.0
OD1 D:ASP101 3.0 10.7 1.0
CG D:ASP101 3.1 9.5 1.0
CG D:ASN103 3.4 9.1 1.0
C3 D:MMA201 3.4 10.3 1.0
C C:GLY114 3.4 10.8 1.0
C2 D:MMA201 3.5 10.9 1.0
C D:ASN21 3.6 8.9 1.0
CG D:ASP104 3.6 8.7 1.0
OXT C:GLY114 3.7 12.7 1.0
CA D:CA199 3.7 10.1 1.0
ND2 D:ASN103 3.7 9.7 1.0
C4 D:MMA201 3.9 11.2 1.0
CB D:ASN21 4.2 9.5 1.0
CA D:ASP104 4.2 7.8 1.0
N D:ASP104 4.3 7.7 1.0
CA D:SER22 4.4 9.5 1.0
N D:SER22 4.4 9.4 1.0
OD2 D:ASP104 4.4 10.1 1.0
CB D:ASP104 4.5 9.2 1.0
C D:ASN103 4.5 7.9 1.0
O4 D:MMA201 4.5 10.4 1.0
O C:HOH2107 4.5 21.7 1.0
CB D:ASP101 4.5 11.0 1.0
OD2 D:ASP99 4.5 14.2 1.0
CA D:ASN21 4.5 8.8 1.0
CB D:SER22 4.7 10.8 1.0
CB D:ASN103 4.7 8.4 1.0
O D:ASN103 4.8 9.0 1.0
C1 D:MMA201 4.8 11.7 1.0
CA C:GLY114 4.8 10.0 1.0
N D:ASN103 4.9 8.9 1.0
CA D:ASN103 4.9 8.4 1.0
OD1 D:ASP99 5.0 12.2 1.0

Reference:

D.Hauck, I.Joachim, B.Frommeyer, A.Varrot, B.Philipp, H.M.Moller, A.Imberty, T.E.Exner, A.Titz. Discovery of Two Classes of Potent Glycomimetic Inhibitors of Pseudomonas Aeruginosa Lecb with Distinct Binding Modes. Acs Chem.Biol. V. 8 1775 2013.
ISSN: ISSN 1554-8929
PubMed: 23719508
DOI: 10.1021/CB400371R
Page generated: Sat Dec 12 04:36:26 2020

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