Atomistry » Calcium » PDB 5m2o-5mhp » 5mb1
Atomistry »
  Calcium »
    PDB 5m2o-5mhp »
      5mb1 »

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

Go back to Calcium Binding Sites List in 5mb1
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

Go back to Calcium Binding Sites List in 5mb1
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

Go back to Calcium Binding Sites List in 5mb1
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

Go back to Calcium Binding Sites List in 5mb1
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

Go back to Calcium Binding Sites List in 5mb1
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

Go back to Calcium Binding Sites List in 5mb1
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

Go back to Calcium Binding Sites List in 5mb1
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy