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Calcium in PDB 5mb1: Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside

Protein crystallography data

The structure of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside, PDB code: 5mb1 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) 41.83 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.904, 65.251, 108.987, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 15.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside (pdb code 5mb1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside, PDB code: 5mb1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5mb1

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Calcium binding site 1 out of 7 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside


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 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:6.4
occ:1.00
 OD1 A:ASP99 2.4 7.0 1.0
OD1 A:ASP101 2.4 5.9 1.0
OD2 A:ASP104 2.4 5.0 1.0
OE2 A:GLU95 2.4 5.7 1.0
O3 A:FUL203 2.4 6.0 1.0
OE1 A:GLU95 2.5 5.5 1.0
O2 A:FUL203 2.5 7.2 1.0
OD1 A:ASP104 2.6 4.3 1.0
CD A:GLU95 2.8 5.7 1.0
CG A:ASP104 2.9 4.5 1.0
C3 A:FUL203 3.3 6.9 1.0
C2 A:FUL203 3.3 6.9 1.0
CG A:ASP99 3.4 7.3 1.0
CG A:ASP101 3.4 6.0 1.0
OD2 A:ASP99 3.7 7.9 1.0
CA A:CA202 3.7 5.7 1.0
OD2 A:ASP101 4.0 5.2 1.0
OD1 A:ASP96 4.1 6.8 1.0
N A:ASP101 4.2 6.2 1.0
CG A:GLU95 4.3 5.5 1.0
CB A:ASP104 4.4 4.4 1.0
N A:ASN100 4.5 7.7 1.0
N A:TYR102 4.5 5.9 1.0
N A:ASP96 4.5 5.1 1.0
CB A:ASP101 4.6 5.9 1.0
N A:SER97 4.6 6.9 1.0
C4 A:FUL203 4.7 6.9 1.0
OD1 A:ASN103 4.7 4.8 1.0
CB A:ASP99 4.7 7.1 1.0
CA A:GLU95 4.7 5.2 1.0
CA A:ASP101 4.7 6.0 1.0
N A:ASP99 4.7 6.8 1.0
C1 A:FUL203 4.8 8.4 1.0
CB A:SER97 4.8 8.4 1.0
O4 A:FUL203 4.8 6.7 1.0
CG A:ASP96 4.9 6.0 1.0
CB A:GLU95 4.9 5.4 1.0

Calcium binding site 2 out of 7 in 5mb1

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Calcium binding site 2 out of 7 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside


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 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:5.7
occ:1.00
 O A:ASN21 2.3 4.6 1.0
OD1 A:ASN103 2.4 4.8 1.0
OD1 A:ASP104 2.4 4.3 1.0
O B:GLY114 2.4 7.4 1.0
OD2 A:ASP101 2.4 5.2 1.0
O3 A:FUL203 2.5 6.0 1.0
O4 A:FUL203 2.5 6.7 1.0
CG A:ASP101 3.1 6.0 1.0
OD1 A:ASP101 3.1 5.9 1.0
C3 A:FUL203 3.3 6.9 1.0
CG A:ASN103 3.4 4.9 1.0
C4 A:FUL203 3.4 6.9 1.0
C B:GLY114 3.4 7.6 1.0
C A:ASN21 3.5 4.6 1.0
CG A:ASP104 3.6 4.5 1.0
OXT B:GLY114 3.7 9.7 1.0
ND2 A:ASN103 3.7 4.9 1.0
CA A:CA201 3.7 6.4 1.0
C2 A:FUL203 3.8 6.9 1.0
CB A:ASN21 4.1 4.9 1.0
CA A:ASP104 4.2 4.3 1.0
N A:ASP104 4.3 4.8 1.0
O A:HOH309 4.3 19.2 1.0
N A:SER22 4.4 4.8 1.0
CA A:SER22 4.4 5.3 1.0
OD2 A:ASP104 4.4 5.0 1.0
O2 A:FUL203 4.4 7.2 1.0
C A:ASN103 4.5 4.8 1.0
CB A:ASP104 4.5 4.4 1.0
CA A:ASN21 4.5 4.6 1.0
CB A:ASP101 4.5 5.9 1.0
OD2 A:ASP99 4.6 7.9 1.0
CB A:SER22 4.7 5.3 1.0
CB A:ASN103 4.7 5.0 1.0
CA B:GLY114 4.7 7.4 1.0
O A:ASN103 4.8 4.8 1.0
C5 A:FUL203 4.8 7.3 1.0
N A:ASN103 4.9 5.0 1.0
CA A:ASN103 4.9 5.0 1.0

Calcium binding site 3 out of 7 in 5mb1

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Calcium binding site 3 out of 7 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside


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 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:6.6
occ:1.00
 OD2 B:ASP104 2.4 5.4 1.0
OE2 B:GLU95 2.4 7.5 1.0
O3 B:FUL203 2.4 6.8 1.0
OD1 B:ASP101 2.4 5.2 1.0
OD1 B:ASP99 2.4 9.2 1.0
OE1 B:GLU95 2.5 7.8 1.0
O2 B:FUL203 2.5 7.7 1.0
OD1 B:ASP104 2.7 5.1 1.0
CD B:GLU95 2.7 6.3 1.0
CG B:ASP104 2.9 5.4 1.0
C3 B:FUL203 3.3 7.2 1.0
C2 B:FUL203 3.4 7.8 1.0
CG B:ASP99 3.4 8.4 1.0
CG B:ASP101 3.5 5.8 1.0
OD2 B:ASP99 3.7 9.3 1.0
CA B:CA202 3.8 5.9 1.0
OD2 B:ASP101 4.0 5.7 1.0
OD1 B:ASP96 4.1 6.4 1.0
N B:ASP101 4.2 6.9 1.0
CG B:GLU95 4.2 5.7 1.0
CB B:ASP104 4.4 5.4 1.0
N B:ASP96 4.5 5.5 1.0
N B:ASN100 4.5 7.7 1.0
N B:TYR102 4.5 5.8 1.0
CB B:ASP101 4.6 6.0 1.0
CA B:GLU95 4.6 5.3 1.0
N B:SER97 4.6 7.9 1.0
C4 B:FUL203 4.7 7.1 1.0
CB B:SER97 4.7 11.1 1.0
OD1 B:ASN103 4.7 5.9 1.0
CB B:ASP99 4.7 8.5 1.0
CA B:ASP101 4.8 6.3 1.0
C1 B:FUL203 4.8 8.1 1.0
N B:ASP99 4.8 8.5 1.0
O4 B:FUL203 4.8 6.7 1.0
CB B:GLU95 4.8 5.6 1.0
CG B:ASP96 4.9 7.1 1.0

Calcium binding site 4 out of 7 in 5mb1

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Calcium binding site 4 out of 7 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside


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 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:5.9
occ:1.00
 OD1 B:ASN103 2.3 5.9 1.0
OD1 B:ASP104 2.3 5.1 1.0
O B:ASN21 2.4 5.4 1.0
OD2 B:ASP101 2.4 5.7 1.0
O A:GLY114 2.5 6.3 1.0
O4 B:FUL203 2.5 6.7 1.0
O3 B:FUL203 2.5 6.8 1.0
OD1 B:ASP101 3.1 5.2 1.0
CG B:ASP101 3.1 5.8 1.0
CG B:ASN103 3.4 5.8 1.0
C3 B:FUL203 3.4 7.2 1.0
C A:GLY114 3.4 7.6 1.0
C4 B:FUL203 3.4 7.1 1.0
CG B:ASP104 3.6 5.4 1.0
C B:ASN21 3.6 5.3 1.0
OXT A:GLY114 3.7 8.3 1.0
ND2 B:ASN103 3.7 5.6 1.0
CA B:CA201 3.8 6.6 1.0
C2 B:FUL203 3.9 7.8 1.0
CA B:ASP104 4.2 5.0 1.0
CB B:ASN21 4.2 5.0 1.0
N B:ASP104 4.2 5.0 1.0
OD2 B:ASP104 4.4 5.4 1.0
O B:HOH310 4.4 19.8 1.0
CA B:SER22 4.4 5.8 1.0
C B:ASN103 4.4 5.3 1.0
N B:SER22 4.4 5.4 1.0
CB B:ASP104 4.4 5.4 1.0
O2 B:FUL203 4.5 7.7 1.0
CB B:ASP101 4.5 6.0 1.0
CA B:ASN21 4.5 5.0 1.0
OD2 B:ASP99 4.6 9.3 1.0
CB B:SER22 4.7 5.9 1.0
CB B:ASN103 4.7 6.0 1.0
O B:ASN103 4.7 5.6 1.0
C5 B:FUL203 4.8 7.4 1.0
CA A:GLY114 4.8 7.1 1.0
N B:ASN103 4.9 5.4 1.0
CA B:ASN103 4.9 5.6 1.0

Calcium binding site 5 out of 7 in 5mb1

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Calcium binding site 5 out of 7 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside


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 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:20.5
occ:1.00
 O C:ASN21 2.3 9.4 1.0
OD1 C:ASN103 2.3 10.1 1.0
OD2 C:ASP99 2.3 27.2 0.5
OD1 C:ASP104 2.4 10.0 1.0
O D:GLY114 2.5 13.9 1.0
O D:HOH306 2.6 21.6 1.0
CG C:ASN103 3.3 9.9 1.0
CG C:ASP99 3.4 26.2 0.5
C D:GLY114 3.4 14.5 1.0
C C:ASN21 3.5 9.1 1.0
OXT D:GLY114 3.6 17.4 1.0
CG C:ASP104 3.6 10.2 1.0
ND2 C:ASN103 3.7 9.8 1.0
CB C:ASP99 3.7 24.7 0.5
CA C:ASP104 4.0 9.5 1.0
CB C:ASN21 4.0 8.8 1.0
N C:ASP104 4.1 9.4 1.0
CB C:ASP101 4.2 23.9 1.0
C C:ASN103 4.3 9.8 1.0
N C:SER22 4.4 9.3 1.0
CA C:SER22 4.4 10.1 1.0
CB C:ASP104 4.4 9.0 1.0
CA C:ASN21 4.4 8.6 1.0
OD1 C:ASP99 4.5 24.1 0.5
OD2 C:ASP104 4.5 11.8 1.0
O C:ASN103 4.6 9.0 1.0
CB C:ASN103 4.7 9.4 1.0
CB C:SER22 4.7 10.4 1.0
CA D:GLY114 4.8 10.8 1.0
O C:ASP101 4.8 22.8 1.0
CG C:ASP101 4.8 31.9 1.0
CA C:ASN103 4.9 9.4 1.0
O C:HOH304 5.0 19.5 1.0
N C:ASN103 5.0 9.8 1.0

Calcium binding site 6 out of 7 in 5mb1

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Calcium binding site 6 out of 7 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside


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 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:10.1
occ:0.50
 O D:ASP99 1.6 15.1 0.4
C D:ASP99 2.1 16.4 0.4
OD1 D:ASP99 2.4 16.3 0.6
OD2 D:ASP104 2.4 7.2 1.0
OD1 D:ASP101 2.4 13.1 0.6
OE1 D:GLU95 2.4 13.1 0.6
O2 D:FUL203 2.5 13.1 0.6
O3 D:FUL203 2.5 13.4 0.6
OD1 D:ASP104 2.6 7.5 1.0
OE2 D:GLU95 2.6 10.7 0.6
N D:ASP101 2.6 14.1 0.4
CB D:ASP99 2.7 15.6 0.4
CA D:ASP99 2.8 16.1 0.4
CG D:ASP104 2.8 7.3 1.0
CG D:ASP99 2.8 16.6 0.4
CD D:GLU95 2.8 10.6 0.6
O D:ASP101 2.9 9.5 0.4
N D:ASN100 2.9 17.2 0.4
OD2 D:ASP99 3.1 15.2 0.4
CG D:ASP99 3.3 18.4 0.6
C2 D:FUL203 3.3 12.4 0.6
CA D:ASP101 3.3 12.5 0.4
CB D:ASP101 3.4 12.9 0.4
C3 D:FUL203 3.4 12.6 0.6
CG D:ASP101 3.5 15.6 0.6
C D:ASN100 3.5 16.3 0.4
C D:ASP101 3.5 10.9 0.4
N D:ASP99 3.5 15.4 0.4
CA D:ASN100 3.6 17.7 0.4
OD2 D:ASP99 3.6 17.4 0.6
OD1 D:ASP99 3.6 16.5 0.4
CA D:CA202 3.8 3.3 0.6
OD2 D:ASP101 4.0 14.6 0.6
N D:ASP101 4.2 17.3 0.6
OD1 D:ASP96 4.3 11.1 0.6
OD1 D:ASP96 4.3 12.4 0.4
CB D:ASP104 4.3 6.4 1.0
CG D:GLU95 4.3 9.7 0.6
CG D:GLU95 4.4 11.1 0.4
O D:ASP96 4.5 12.5 0.4
N D:ASN100 4.5 20.2 0.6
N D:SER97 4.6 13.8 0.6
O D:ASN100 4.6 16.5 0.4
N D:TYR102 4.6 10.0 0.6
N D:ASP96 4.6 8.8 0.6
N D:ASP96 4.6 10.2 0.4
OD1 D:ASN103 4.6 8.4 1.0
CB D:SER97 4.7 17.9 0.6
CB D:ASP101 4.7 15.2 0.6
CB D:ASP99 4.7 19.9 0.6
C4 D:FUL203 4.8 11.3 0.6
C1 D:FUL203 4.8 13.3 0.6
N D:TYR102 4.8 9.4 0.4
O4 D:FUL203 4.8 9.6 0.6
CG D:ASP101 4.8 13.7 0.4
CA D:GLU95 4.8 7.7 0.6
CA D:ASP101 4.8 14.9 0.6
C D:THR98 4.8 15.6 0.4
N D:ASP99 4.8 20.5 0.6
CA D:GLU95 4.9 8.8 0.4
O C:HOH301 4.9 7.7 0.4
C D:ASP99 5.0 20.6 0.6

Calcium binding site 7 out of 7 in 5mb1

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Calcium binding site 7 out of 7 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside


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 2,4,6-Trimethylphenylsulfonamide-N-Methyl-L- Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:3.3
occ:0.60
 OD2 D:ASP99 2.3 15.2 0.4
O D:ASN21 2.3 5.9 1.0
OD1 D:ASN103 2.3 8.4 1.0
OD1 D:ASP104 2.3 7.5 1.0
O4 D:FUL203 2.5 9.6 0.6
O C:GLY114 2.5 8.9 1.0
OD2 D:ASP101 2.6 14.6 0.6
O C:HOH301 2.6 7.7 0.4
O3 D:FUL203 2.6 13.4 0.6
OD1 D:ASP101 3.2 13.1 0.6
CG D:ASP101 3.2 15.6 0.6
CG D:ASP99 3.3 16.6 0.4
CG D:ASN103 3.4 8.3 1.0
C4 D:FUL203 3.4 11.3 0.6
C3 D:FUL203 3.5 12.6 0.6
C C:GLY114 3.5 9.7 1.0
C D:ASN21 3.6 5.6 1.0
CG D:ASP104 3.6 7.3 1.0
OXT C:GLY114 3.7 11.1 1.0
CB D:ASP99 3.7 15.6 0.4
ND2 D:ASN103 3.7 8.1 1.0
CA D:CA201 3.8 10.1 0.5
C2 D:FUL203 3.9 12.4 0.6
CA D:ASP104 4.1 5.7 1.0
N D:ASP104 4.1 6.2 1.0
CB D:ASN21 4.2 6.0 1.0
CB D:ASP101 4.2 12.9 0.4
C D:ASN103 4.3 5.9 1.0
CA D:SER22 4.4 5.9 1.0
CB D:ASP104 4.4 6.4 1.0
N D:SER22 4.4 5.6 1.0
OD2 D:ASP104 4.4 7.2 1.0
OD1 D:ASP99 4.4 16.5 0.4
CA D:ASN21 4.5 5.7 1.0
O2 D:FUL203 4.5 13.1 0.6
OD2 D:ASP99 4.6 17.4 0.6
CB D:SER22 4.6 5.6 1.0
O D:HOH387 4.6 29.9 1.0
CB D:ASP101 4.7 15.2 0.6
O D:ASN103 4.7 5.1 1.0
CB D:ASN103 4.7 7.5 1.0
C5 D:FUL203 4.8 12.3 0.6
CG D:ASP101 4.8 13.7 0.4
CA C:GLY114 4.9 8.8 1.0
CA D:ASN103 4.9 6.9 1.0
O D:HOH313 4.9 12.3 0.4
N D:ASN103 4.9 7.5 1.0
O D:ASP101 5.0 9.5 0.4
O5 D:FUL203 5.0 10.8 0.6

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 08:01:24 2024

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