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Calcium in PDB 5may: Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)

Protein crystallography data

The structure of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl), PDB code: 5may was solved by R.Sommer, A.Imberty, A.Titz, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.59 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.089, 65.520, 109.173, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 17.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) (pdb code 5may). 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 the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl), PDB code: 5may:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5may

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Calcium binding site 1 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca200

b:9.4
occ:1.00
 OD1 A:ASN103 2.4 8.6 1.0
OD1 A:ASP104 2.4 9.1 1.0
O A:ASN21 2.4 9.4 1.0
O B:GLY114 2.4 9.4 1.0
OD2 A:ASP101 2.5 10.2 1.0
O4 A:FUL202 2.5 10.7 1.0
O3 A:FUL202 2.5 11.8 1.0
OD1 A:ASP101 3.1 10.6 1.0
CG A:ASP101 3.1 10.6 1.0
CG A:ASN103 3.4 8.5 1.0
C3 A:FUL202 3.4 11.3 1.0
C4 A:FUL202 3.4 11.0 1.0
C B:GLY114 3.4 10.9 1.0
C A:ASN21 3.6 8.2 1.0
CG A:ASP104 3.6 8.5 1.0
OXT B:GLY114 3.7 10.9 1.0
ND2 A:ASN103 3.7 8.9 1.0
CA A:CA201 3.8 10.3 1.0
C2 A:FUL202 3.9 10.7 1.0
CB A:ASN21 4.2 8.0 1.0
CA A:ASP104 4.2 7.4 1.0
N A:ASP104 4.3 7.7 1.0
O A:HOH313 4.4 19.6 1.0
CA A:SER22 4.4 9.4 1.0
OD2 A:ASP104 4.4 8.4 1.0
N A:SER22 4.4 8.4 1.0
O2 A:FUL202 4.4 10.4 1.0
C A:ASN103 4.4 7.5 1.0
CB A:ASP104 4.5 8.0 1.0
CB A:ASP101 4.5 9.4 1.0
CA A:ASN21 4.6 7.9 1.0
OD2 A:ASP99 4.6 13.2 1.0
CB A:SER22 4.7 9.6 1.0
CB A:ASN103 4.7 8.5 1.0
O A:ASN103 4.8 8.0 1.0
C5 A:FUL202 4.8 10.7 1.0
CA B:GLY114 4.8 9.4 1.0
N A:ASN103 4.9 7.9 1.0
CA A:ASN103 4.9 8.2 1.0

Calcium binding site 2 out of 8 in 5may

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Calcium binding site 2 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:10.3
occ:1.00
 OE2 A:GLU95 2.4 10.8 1.0
OD1 A:ASP99 2.4 13.2 1.0
OD1 A:ASP101 2.4 10.6 1.0
OD2 A:ASP104 2.4 8.4 1.0
O3 A:FUL202 2.5 11.8 1.0
O2 A:FUL202 2.5 10.4 1.0
OE1 A:GLU95 2.5 10.4 1.0
OD1 A:ASP104 2.7 9.1 1.0
CD A:GLU95 2.8 9.9 1.0
CG A:ASP104 2.9 8.5 1.0
C3 A:FUL202 3.3 11.3 1.0
C2 A:FUL202 3.4 10.7 1.0
CG A:ASP99 3.4 13.5 1.0
CG A:ASP101 3.5 10.6 1.0
OD2 A:ASP99 3.7 13.2 1.0
CA A:CA200 3.8 9.4 1.0
OD1 A:ASP96 4.0 10.0 1.0
OD2 A:ASP101 4.0 10.2 1.0
N A:ASP101 4.2 9.3 1.0
CG A:GLU95 4.2 8.6 1.0
CB A:ASP104 4.4 8.0 1.0
N A:ASP96 4.5 8.0 1.0
N A:ASN100 4.5 11.2 1.0
N A:TYR102 4.5 8.7 1.0
CB A:ASP101 4.6 9.4 1.0
N A:SER97 4.7 10.9 1.0
CA A:GLU95 4.7 7.7 1.0
C4 A:FUL202 4.7 11.0 1.0
OD1 A:ASN103 4.7 8.6 1.0
CB A:ASP99 4.7 13.1 1.0
CB A:SER97 4.7 15.3 1.0
CA A:ASP101 4.8 9.0 1.0
C1 A:FUL202 4.8 10.6 1.0
O4 A:FUL202 4.8 10.7 1.0
N A:ASP99 4.9 12.5 1.0
CG A:ASP96 4.9 10.1 1.0
CB A:GLU95 4.9 8.5 1.0

Calcium binding site 3 out of 8 in 5may

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Calcium binding site 3 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca200

b:8.6
occ:1.00
 O B:ASN21 2.3 7.4 1.0
OD1 B:ASN103 2.4 8.8 1.0
OD1 B:ASP104 2.4 8.3 1.0
O A:GLY114 2.4 8.5 1.0
O3 B:FUL202 2.5 8.9 1.0
OD2 B:ASP101 2.5 7.6 1.0
O4 B:FUL202 2.5 9.0 1.0
OD1 B:ASP101 3.1 8.5 1.0
CG B:ASP101 3.1 8.5 1.0
CG B:ASN103 3.4 8.5 1.0
C3 B:FUL202 3.4 9.4 1.0
C4 B:FUL202 3.4 9.0 1.0
C A:GLY114 3.4 9.4 1.0
C B:ASN21 3.5 7.2 1.0
CG B:ASP104 3.6 7.3 1.0
ND2 B:ASN103 3.7 8.9 1.0
OXT A:GLY114 3.7 10.1 1.0
CA B:CA201 3.7 9.4 1.0
C2 B:FUL202 3.8 9.9 1.0
CB B:ASN21 4.1 7.3 1.0
CA B:ASP104 4.2 7.1 1.0
N B:ASP104 4.3 7.4 1.0
O B:HOH311 4.4 17.9 1.0
CA B:SER22 4.4 8.0 1.0
O2 B:FUL202 4.4 9.2 1.0
N B:SER22 4.4 7.6 1.0
OD2 B:ASP104 4.4 8.8 1.0
C B:ASN103 4.5 7.3 1.0
CB B:ASP104 4.5 7.2 1.0
CA B:ASN21 4.5 7.2 1.0
CB B:ASP101 4.6 8.3 1.0
OD2 B:ASP99 4.6 10.9 1.0
CB B:SER22 4.7 8.7 1.0
CB B:ASN103 4.7 8.5 1.0
O B:ASN103 4.7 6.7 1.0
C5 B:FUL202 4.8 9.4 1.0
CA A:GLY114 4.8 9.4 1.0
N B:ASN103 4.9 8.2 1.0
CA B:ASN103 4.9 7.9 1.0

Calcium binding site 4 out of 8 in 5may

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Calcium binding site 4 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:9.4
occ:1.00
 OD1 B:ASP101 2.3 8.5 1.0
OD1 B:ASP99 2.3 11.4 1.0
OE2 B:GLU95 2.4 8.9 1.0
OD2 B:ASP104 2.4 8.8 1.0
O3 B:FUL202 2.5 8.9 1.0
O2 B:FUL202 2.5 9.2 1.0
OE1 B:GLU95 2.5 9.0 1.0
OD1 B:ASP104 2.6 8.3 1.0
CD B:GLU95 2.8 8.9 1.0
CG B:ASP104 2.9 7.3 1.0
C2 B:FUL202 3.3 9.9 1.0
C3 B:FUL202 3.3 9.4 1.0
CG B:ASP99 3.4 11.0 1.0
CG B:ASP101 3.4 8.5 1.0
OD2 B:ASP99 3.7 10.9 1.0
CA B:CA200 3.7 8.6 1.0
OD2 B:ASP101 4.0 7.6 1.0
OD1 B:ASP96 4.0 9.3 1.0
N B:ASP101 4.2 9.2 1.0
CG B:GLU95 4.3 8.5 1.0
CB B:ASP104 4.4 7.2 1.0
N B:ASN100 4.5 10.0 1.0
N B:TYR102 4.5 8.7 1.0
N B:ASP96 4.5 7.5 1.0
CB B:ASP101 4.6 8.3 1.0
OD1 B:ASN103 4.6 8.8 1.0
C4 B:FUL202 4.6 9.0 1.0
N B:SER97 4.7 9.5 1.0
CB B:ASP99 4.7 9.9 1.0
CA B:ASP101 4.7 8.5 1.0
CA B:GLU95 4.7 7.7 1.0
C1 B:FUL202 4.8 10.4 1.0
N B:ASP99 4.8 9.9 1.0
CB B:SER97 4.8 12.6 1.0
O4 B:FUL202 4.8 9.0 1.0
CG B:ASP96 4.9 8.3 1.0
CB B:GLU95 4.9 8.7 1.0

Calcium binding site 5 out of 8 in 5may

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Calcium binding site 5 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca200

b:12.0
occ:1.00
 O C:ASN21 2.3 8.9 1.0
OD1 C:ASP104 2.3 11.9 1.0
OD1 C:ASN103 2.3 9.9 1.0
O4 C:FUL202 2.4 14.1 1.0
OD2 C:ASP101 2.5 14.7 1.0
O D:GLY114 2.5 12.5 1.0
O3 C:FUL202 2.5 15.2 1.0
OD1 C:ASP101 3.1 15.1 1.0
CG C:ASP101 3.1 15.4 1.0
C3 C:FUL202 3.4 13.9 1.0
CG C:ASN103 3.4 10.4 1.0
C4 C:FUL202 3.4 14.8 1.0
C D:GLY114 3.5 14.0 1.0
C C:ASN21 3.5 9.6 1.0
CG C:ASP104 3.6 11.0 1.0
OXT D:GLY114 3.7 15.0 1.0
CA C:CA201 3.7 14.3 1.0
ND2 C:ASN103 3.8 9.9 1.0
C2 C:FUL202 3.9 13.3 1.0
CA C:ASP104 4.1 9.5 1.0
CB C:ASN21 4.2 9.3 1.0
N C:ASP104 4.2 9.2 1.0
CA C:SER22 4.3 9.8 1.0
N C:SER22 4.4 9.6 1.0
OD2 C:ASP104 4.4 11.1 1.0
CB C:ASP104 4.4 10.4 1.0
O C:HOH317 4.4 22.6 1.0
C C:ASN103 4.4 9.4 1.0
O2 C:FUL202 4.5 15.0 1.0
CA C:ASN21 4.5 9.4 1.0
CB C:ASP101 4.5 14.5 1.0
OD2 C:ASP99 4.5 15.5 1.0
CB C:SER22 4.6 9.1 1.0
CB C:ASN103 4.7 10.2 1.0
O C:ASN103 4.7 9.1 1.0
C5 C:FUL202 4.8 13.9 1.0
CA D:GLY114 4.8 12.8 1.0
N C:ASN103 4.9 9.9 1.0
CA C:ASN103 4.9 9.5 1.0

Calcium binding site 6 out of 8 in 5may

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Calcium binding site 6 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:14.3
occ:1.00
 OD1 C:ASP99 2.3 15.3 1.0
OD1 C:ASP101 2.4 15.1 1.0
OD2 C:ASP104 2.4 11.1 1.0
OE2 C:GLU95 2.4 15.3 1.0
O3 C:FUL202 2.5 15.2 1.0
OE1 C:GLU95 2.5 14.3 1.0
O2 C:FUL202 2.5 15.0 1.0
OD1 C:ASP104 2.6 11.9 1.0
CD C:GLU95 2.8 14.2 1.0
CG C:ASP104 2.9 11.0 1.0
C2 C:FUL202 3.3 13.3 1.0
CG C:ASP99 3.3 15.6 1.0
C3 C:FUL202 3.4 13.9 1.0
CG C:ASP101 3.4 15.4 1.0
OD2 C:ASP99 3.7 15.5 1.0
CA C:CA200 3.7 12.0 1.0
OD2 C:ASP101 4.0 14.7 1.0
OD1 C:ASP96 4.0 13.5 1.0
O C:HOH381 4.0 25.1 1.0
N C:ASP101 4.1 16.2 1.0
CG C:GLU95 4.3 13.5 1.0
CB C:ASP104 4.4 10.4 1.0
N C:ASP96 4.5 11.5 1.0
N C:ASN100 4.5 16.9 1.0
CB C:ASP101 4.6 14.5 1.0
N C:TYR102 4.6 11.8 1.0
OD1 C:ASN103 4.7 9.9 1.0
CA C:GLU95 4.7 10.5 1.0
CB C:ASP99 4.7 16.6 1.0
C4 C:FUL202 4.7 14.8 1.0
N C:SER97 4.7 14.7 1.0
CA C:ASP101 4.7 14.0 1.0
C1 C:FUL202 4.8 14.8 1.0
O4 C:FUL202 4.8 14.1 1.0
N C:ASP99 4.8 18.4 1.0
CG C:ASP96 4.9 13.2 1.0
CB C:GLU95 4.9 11.7 1.0
CB C:SER97 4.9 18.7 1.0

Calcium binding site 7 out of 8 in 5may

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Calcium binding site 7 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca200

b:16.9
occ:1.00
 O D:ASN21 2.3 12.8 1.0
OD1 D:ASN103 2.3 14.2 1.0
OD1 D:ASP104 2.3 13.4 1.0
O3 D:FUL202 2.4 12.7 0.7
O4 D:FUL202 2.4 12.8 0.7
OD2 D:ASP101 2.5 21.6 1.0
O C:GLY114 2.5 16.6 1.0
OD1 D:ASP101 3.1 21.3 1.0
CG D:ASP101 3.2 24.3 1.0
CG D:ASN103 3.4 12.7 1.0
C3 D:FUL202 3.4 12.9 0.7
C4 D:FUL202 3.4 12.2 0.7
C C:GLY114 3.5 17.1 1.0
C D:ASN21 3.5 12.4 1.0
CG D:ASP104 3.5 14.0 1.0
OXT C:GLY114 3.6 18.0 1.0
ND2 D:ASN103 3.8 12.4 1.0
CA D:CA201 3.8 21.4 1.0
C2 D:FUL202 3.9 13.1 0.7
CB D:ASN21 4.1 10.8 1.0
CA D:ASP104 4.1 12.1 1.0
N D:ASP104 4.2 11.6 1.0
C D:ASN103 4.4 12.1 1.0
CA D:SER22 4.4 12.8 1.0
N D:SER22 4.4 12.0 1.0
CB D:ASP104 4.4 12.3 1.0
OD2 D:ASP104 4.4 15.5 1.0
O D:HOH333 4.5 25.7 1.0
CA D:ASN21 4.5 11.2 1.0
O2 D:FUL202 4.5 13.7 0.7
CB D:ASP101 4.6 22.3 1.0
OD2 D:ASP99 4.6 24.1 1.0
CB D:SER22 4.6 13.7 1.0
O D:ASN103 4.7 11.7 1.0
CB D:ASN103 4.7 12.3 1.0
C5 D:FUL202 4.8 12.2 0.7
CA C:GLY114 4.9 14.8 1.0
N D:ASN103 4.9 12.2 1.0
CA D:ASN103 4.9 11.4 1.0

Calcium binding site 8 out of 8 in 5may

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Calcium binding site 8 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:21.4
occ:1.00
 OD2 D:ASP104 2.3 15.5 1.0
OD1 D:ASP99 2.4 26.3 1.0
OE2 D:GLU95 2.4 20.5 1.0
OD1 D:ASP101 2.4 21.3 1.0
O3 D:FUL202 2.5 12.7 0.7
OE1 D:GLU95 2.5 17.6 1.0
O2 D:FUL202 2.5 13.7 0.7
OD1 D:ASP104 2.6 13.4 1.0
CD D:GLU95 2.8 19.5 1.0
CG D:ASP104 2.8 14.0 1.0
C2 D:FUL202 3.3 13.1 0.7
C3 D:FUL202 3.3 12.9 0.7
CG D:ASP99 3.4 25.5 1.0
CG D:ASP101 3.5 24.3 1.0
OD2 D:ASP99 3.7 24.1 1.0
CA D:CA200 3.8 16.9 1.0
OD1 D:ASP96 3.9 20.8 1.0
OD2 D:ASP101 4.0 21.6 1.0
N D:ASP101 4.2 22.1 1.0
CG D:GLU95 4.3 15.6 1.0
CB D:ASP104 4.3 12.3 1.0
N D:ASP96 4.4 14.6 1.0
N D:ASN100 4.6 23.9 1.0
N D:SER97 4.6 21.9 1.0
N D:TYR102 4.6 15.8 1.0
CA D:GLU95 4.6 13.2 1.0
CB D:ASP101 4.7 22.3 1.0
C4 D:FUL202 4.7 12.2 0.7
OD1 D:ASN103 4.7 14.2 1.0
C1 D:FUL202 4.7 12.3 0.7
CB D:ASP99 4.7 24.8 1.0
CG D:ASP96 4.8 19.0 1.0
CA D:ASP101 4.8 21.8 1.0
O4 D:FUL202 4.8 12.8 0.7
CB D:SER97 4.8 27.6 1.0
N D:ASP99 4.9 26.9 1.0
CB D:GLU95 4.9 14.6 1.0

Reference:

R.Sommer, S.Wagner, K.Rox, A.Varrot, D.Hauck, E.C.Wamhoff, J.Schreiber, T.Ryckmans, T.Brunner, C.Rademacher, R.W.Hartmann, M.Bronstrup, A.Imberty, A.Titz. Glycomimetic, Orally Bioavailable Lecb Inhibitors Block Biofilm Formation of Pseudomonas Aeruginosa. J. Am. Chem. Soc. V. 140 2537 2018.
ISSN: ESSN 1520-5126
PubMed: 29272578
DOI: 10.1021/JACS.7B11133
Page generated: Mon Jul 15 08:00:47 2024

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