Atomistry » Calcium » PDB 5a3y-5afb » 5a70
Atomistry »
  Calcium »
    PDB 5a3y-5afb »
      5a70 »

Calcium in PDB 5a70: Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide

Protein crystallography data

The structure of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide, PDB code: 5a70 was solved by R.Sommer, S.Wagner, A.Varrot, A.Khaledi, S.Haussler, A.Imberty, A.Titz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.94 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.898, 63.228, 63.889, 90.00, 91.20, 90.00
R / Rfree (%) 13.6 / 17.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide (pdb code 5a70). 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 Lewis X Tetrasaccharide, PDB code: 5a70:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5a70

Go back to Calcium Binding Sites List in 5a70
Calcium binding site 1 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide


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 Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca199

b:11.8
occ:1.00
 OD2 A:ASP104 2.4 10.7 1.0
OD1 A:ASP101 2.4 12.2 1.0
OE2 A:GLU95 2.4 12.9 1.0
OD1 A:ASP99 2.4 14.3 1.0
O3 A:FUC201 2.5 12.1 1.0
OE1 A:GLU95 2.5 11.8 1.0
O2 A:FUC201 2.5 12.1 1.0
OD1 A:ASP104 2.6 10.9 1.0
CD A:GLU95 2.8 12.3 1.0
CG A:ASP104 2.9 10.6 1.0
C2 A:FUC201 3.3 12.8 1.0
CG A:ASP99 3.4 15.1 1.0
C3 A:FUC201 3.4 12.4 1.0
CG A:ASP101 3.5 13.2 1.0
OD2 A:ASP99 3.7 14.7 1.0
CA A:CA200 3.7 11.7 1.0
OD2 A:ASP101 4.0 12.5 1.0
OD1 A:ASP96 4.0 12.5 1.0
N A:ASP101 4.2 12.2 1.0
CG A:GLU95 4.3 12.1 1.0
CB A:ASP104 4.4 10.6 1.0
N A:ASP96 4.5 11.4 1.0
CB A:SER97 4.5 17.1 1.0
N A:ASN100 4.5 15.8 1.0
N A:TYR102 4.6 10.4 1.0
N A:SER97 4.6 13.8 1.0
CB A:ASP101 4.6 12.1 1.0
C4 A:FUC201 4.7 12.2 1.0
CA A:GLU95 4.7 11.0 1.0
OD1 A:ASN103 4.7 9.6 1.0
CB A:ASP99 4.8 15.3 1.0
CG A:ASP96 4.8 11.0 1.0
C1 A:FUC201 4.8 12.8 1.0
O4 A:FUC201 4.8 11.6 1.0
CA A:ASP101 4.8 12.3 1.0
N A:ASP99 4.9 16.4 1.0
CB A:GLU95 5.0 11.7 1.0
O A:HOH2161 5.0 19.4 1.0

Calcium binding site 2 out of 8 in 5a70

Go back to Calcium Binding Sites List in 5a70
Calcium binding site 2 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide


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 Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca200

b:11.7
occ:1.00
 OD1 A:ASN103 2.3 9.6 1.0
OD1 A:ASP104 2.4 10.9 1.0
O A:ASN21 2.4 11.3 1.0
OD2 A:ASP101 2.4 12.5 1.0
O4 A:FUC201 2.5 11.6 1.0
O B:GLY114 2.5 12.5 1.0
O3 A:FUC201 2.5 12.1 1.0
OD1 A:ASP101 3.0 12.2 1.0
CG A:ASP101 3.1 13.2 1.0
CG A:ASN103 3.4 10.1 1.0
C4 A:FUC201 3.4 12.2 1.0
C3 A:FUC201 3.4 12.4 1.0
C B:GLY114 3.4 14.2 1.0
C A:ASN21 3.6 10.0 1.0
CG A:ASP104 3.6 10.6 1.0
CA A:CA199 3.7 11.8 1.0
ND2 A:ASN103 3.7 11.1 1.0
OXT B:GLY114 3.7 14.2 1.0
C2 A:FUC201 3.9 12.8 1.0
CB A:ASN21 4.2 9.6 1.0
CA A:ASP104 4.2 9.9 1.0
N A:ASP104 4.3 9.6 1.0
CA A:SER22 4.4 11.8 1.0
O2 A:FUC201 4.4 12.1 1.0
OD2 A:ASP104 4.4 10.7 1.0
N A:SER22 4.4 10.3 1.0
C A:ASN103 4.5 9.3 1.0
CB A:ASP104 4.5 10.6 1.0
CB A:ASP101 4.5 12.1 1.0
CA A:ASN21 4.5 10.0 1.0
OD2 A:ASP99 4.6 14.7 1.0
O A:HOH2167 4.6 21.9 1.0
CB A:SER22 4.6 12.6 1.0
CB A:ASN103 4.7 10.3 1.0
C5 A:FUC201 4.8 13.2 1.0
CA B:GLY114 4.8 14.6 1.0
O A:ASN103 4.8 10.5 1.0
N A:ASN103 4.9 10.5 1.0
CA A:ASN103 4.9 9.0 1.0

Calcium binding site 3 out of 8 in 5a70

Go back to Calcium Binding Sites List in 5a70
Calcium binding site 3 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide


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 Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca199

b:15.8
occ:1.00
 OE2 B:GLU95 2.3 18.9 1.0
OD1 B:ASP101 2.4 15.9 1.0
OD2 B:ASP104 2.4 15.4 1.0
OD1 B:ASP99 2.4 18.0 1.0
O3 B:FUC201 2.4 19.2 1.0
O2 B:FUC201 2.5 16.2 1.0
OE1 B:GLU95 2.5 14.7 1.0
OD1 B:ASP104 2.6 16.4 1.0
CD B:GLU95 2.8 16.3 1.0
CG B:ASP104 2.9 12.8 1.0
C3 B:FUC201 3.4 18.3 1.0
C2 B:FUC201 3.4 17.3 1.0
CG B:ASP99 3.4 19.3 1.0
CG B:ASP101 3.4 14.9 1.0
OD2 B:ASP99 3.7 18.6 1.0
CA B:CA200 3.7 15.3 1.0
OD2 B:ASP101 4.0 17.1 1.0
OD1 B:ASP96 4.1 18.0 1.0
N B:ASP101 4.2 16.0 1.0
CG B:GLU95 4.3 15.5 1.0
CB B:ASP104 4.4 14.3 1.0
N B:ASP96 4.5 15.8 1.0
CB B:SER97 4.5 23.4 1.0
N B:ASN100 4.5 20.1 1.0
N B:TYR102 4.6 14.0 1.0
N B:SER97 4.6 18.5 1.0
CB B:ASP101 4.6 16.2 1.0
C4 B:FUC201 4.6 18.0 1.0
CA B:GLU95 4.7 14.8 1.0
OD1 B:ASN103 4.7 13.5 1.0
CB B:ASP99 4.8 21.8 1.0
O4 B:FUC201 4.8 16.5 1.0
CA B:ASP101 4.8 15.8 1.0
N B:ASP99 4.8 19.6 1.0
C1 B:FUC201 4.8 17.8 1.0
CG B:ASP96 4.9 16.4 1.0
CB B:GLU95 4.9 15.1 1.0
O B:HOH2120 5.0 23.9 1.0

Calcium binding site 4 out of 8 in 5a70

Go back to Calcium Binding Sites List in 5a70
Calcium binding site 4 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide


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 Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca200

b:15.3
occ:1.00
 OD1 B:ASN103 2.4 13.5 1.0
O B:ASN21 2.4 15.7 1.0
OD1 B:ASP104 2.4 16.4 1.0
OD2 B:ASP101 2.4 17.1 1.0
O A:GLY114 2.4 16.8 1.0
O4 B:FUC201 2.5 16.5 1.0
O3 B:FUC201 2.5 19.2 1.0
OD1 B:ASP101 3.1 15.9 1.0
CG B:ASP101 3.1 14.9 1.0
CG B:ASN103 3.4 12.5 1.0
C4 B:FUC201 3.4 18.0 1.0
C3 B:FUC201 3.4 18.3 1.0
C A:GLY114 3.5 19.0 1.0
C B:ASN21 3.6 16.4 1.0
CG B:ASP104 3.6 12.8 1.0
ND2 B:ASN103 3.7 13.4 1.0
CA B:CA199 3.7 15.8 1.0
OXT A:GLY114 3.8 21.5 1.0
C2 B:FUC201 3.9 17.3 1.0
CB B:ASN21 4.1 15.5 1.0
CA B:ASP104 4.2 12.9 1.0
N B:ASP104 4.3 11.8 1.0
CA B:SER22 4.4 16.2 1.0
N B:SER22 4.4 16.4 1.0
OD2 B:ASP104 4.4 15.4 1.0
O2 B:FUC201 4.4 16.2 1.0
CB B:ASP104 4.5 14.3 1.0
O A:HOH2170 4.5 24.8 1.0
C B:ASN103 4.5 12.1 1.0
CB B:ASP101 4.5 16.2 1.0
CA B:ASN21 4.5 15.1 1.0
CB B:SER22 4.6 17.3 1.0
OD2 B:ASP99 4.6 18.6 1.0
CB B:ASN103 4.7 12.6 1.0
C5 B:FUC201 4.8 18.3 1.0
CA A:GLY114 4.8 18.3 1.0
O B:ASN103 4.8 12.7 1.0
CA B:ASN103 4.9 12.4 1.0
N B:ASN103 4.9 13.6 1.0

Calcium binding site 5 out of 8 in 5a70

Go back to Calcium Binding Sites List in 5a70
Calcium binding site 5 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide


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 Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca199

b:9.6
occ:1.00
 OD1 C:ASP101 2.4 10.2 1.0
OE2 C:GLU95 2.4 9.9 1.0
OD2 C:ASP104 2.4 8.7 1.0
OD1 C:ASP99 2.4 11.7 1.0
OE1 C:GLU95 2.5 10.1 1.0
O3 C:FUC201 2.5 9.4 1.0
O2 C:FUC201 2.5 10.5 1.0
OD1 C:ASP104 2.6 8.0 1.0
CD C:GLU95 2.8 8.8 1.0
CG C:ASP104 2.9 8.7 1.0
C2 C:FUC201 3.4 10.4 1.0
C3 C:FUC201 3.4 10.2 1.0
CG C:ASP101 3.4 10.8 1.0
CG C:ASP99 3.4 12.3 1.0
OD2 C:ASP99 3.7 11.6 1.0
CA C:CA200 3.7 9.4 1.0
OD2 C:ASP101 4.0 11.7 1.0
OD1 C:ASP96 4.1 9.8 1.0
N C:ASP101 4.2 9.8 1.0
CG C:GLU95 4.3 8.5 1.0
CB C:ASP104 4.4 7.9 1.0
N C:ASP96 4.5 8.8 1.0
CB C:SER97 4.5 11.6 1.0
N C:TYR102 4.5 8.9 1.0
N C:ASN100 4.6 10.8 1.0
CB C:ASP101 4.6 10.3 1.0
N C:SER97 4.6 9.6 1.0
C4 C:FUC201 4.7 10.0 1.0
CA C:GLU95 4.7 8.1 1.0
OD1 C:ASN103 4.7 9.6 1.0
CB C:ASP99 4.8 12.1 1.0
CA C:ASP101 4.8 9.8 1.0
C1 C:FUC201 4.8 11.7 1.0
CG C:ASP96 4.8 9.4 1.0
N C:ASP99 4.9 12.9 1.0
O4 C:FUC201 4.9 9.2 1.0
CB C:GLU95 4.9 8.4 1.0

Calcium binding site 6 out of 8 in 5a70

Go back to Calcium Binding Sites List in 5a70
Calcium binding site 6 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide


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 Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca200

b:9.4
occ:1.00
 OD1 C:ASN103 2.4 9.6 1.0
O C:ASN21 2.4 9.1 1.0
OD1 C:ASP104 2.4 8.0 1.0
OD2 C:ASP101 2.4 11.7 1.0
O D:GLY114 2.4 9.1 1.0
O3 C:FUC201 2.5 9.4 1.0
O4 C:FUC201 2.5 9.2 1.0
OD1 C:ASP101 3.0 10.2 1.0
CG C:ASP101 3.1 10.8 1.0
C3 C:FUC201 3.4 10.2 1.0
CG C:ASN103 3.4 9.2 1.0
C D:GLY114 3.4 10.8 1.0
C4 C:FUC201 3.4 10.0 1.0
C C:ASN21 3.6 8.9 1.0
CG C:ASP104 3.6 8.7 1.0
CA C:CA199 3.7 9.6 1.0
OXT D:GLY114 3.7 11.1 1.0
ND2 C:ASN103 3.7 9.3 1.0
C2 C:FUC201 3.8 10.4 1.0
CB C:ASN21 4.1 8.1 1.0
CA C:ASP104 4.2 7.7 1.0
N C:ASP104 4.3 7.8 1.0
O C:HOH2145 4.4 19.5 1.0
N C:SER22 4.4 8.8 1.0
CA C:SER22 4.4 9.6 1.0
O2 C:FUC201 4.4 10.5 1.0
OD2 C:ASP104 4.4 8.7 1.0
CB C:ASP104 4.5 7.9 1.0
C C:ASN103 4.5 8.4 1.0
CA C:ASN21 4.5 8.4 1.0
CB C:ASP101 4.5 10.3 1.0
OD2 C:ASP99 4.6 11.6 1.0
CB C:SER22 4.6 9.7 1.0
CB C:ASN103 4.7 9.4 1.0
C5 C:FUC201 4.8 11.0 1.0
CA D:GLY114 4.8 11.2 1.0
O C:ASN103 4.8 8.0 1.0
N C:ASN103 4.9 9.2 1.0
CA C:ASN103 4.9 9.1 1.0

Calcium binding site 7 out of 8 in 5a70

Go back to Calcium Binding Sites List in 5a70
Calcium binding site 7 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide


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 Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca199

b:11.4
occ:1.00
 OD1 D:ASP99 2.4 12.5 1.0
OE2 D:GLU95 2.4 10.5 1.0
OD1 D:ASP101 2.4 11.5 1.0
OD2 D:ASP104 2.4 11.1 1.0
OE1 D:GLU95 2.5 11.2 1.0
O2 D:FUC201 2.5 12.1 1.0
O3 D:FUC201 2.5 10.1 1.0
OD1 D:ASP104 2.7 9.8 1.0
CD D:GLU95 2.8 10.6 1.0
CG D:ASP104 2.9 10.1 1.0
CG D:ASP99 3.3 12.9 1.0
C2 D:FUC201 3.4 11.1 1.0
C3 D:FUC201 3.4 11.5 1.0
CG D:ASP101 3.5 11.6 1.0
OD2 D:ASP99 3.6 13.1 1.0
CA D:CA200 3.8 10.7 1.0
OD2 D:ASP101 4.0 10.7 1.0
OD1 D:ASP96 4.1 11.2 1.0
N D:ASP101 4.2 13.8 1.0
CG D:GLU95 4.3 10.9 1.0
CB D:ASP104 4.4 9.8 1.0
N D:ASP96 4.5 10.8 1.0
CB D:SER97 4.5 16.0 1.0
N D:ASN100 4.5 14.7 1.0
N D:TYR102 4.6 11.1 1.0
CB D:ASP101 4.6 11.9 1.0
N D:SER97 4.7 11.6 1.0
CB D:ASP99 4.7 13.7 1.0
CA D:GLU95 4.7 11.0 1.0
C4 D:FUC201 4.7 12.3 1.0
C1 D:FUC201 4.8 12.8 1.0
OD1 D:ASN103 4.8 9.6 1.0
CA D:ASP101 4.8 11.8 1.0
N D:ASP99 4.8 14.0 1.0
CG D:ASP96 4.8 10.9 1.0
O4 D:FUC201 4.8 11.8 1.0
O D:HOH2120 4.9 21.1 1.0
CB D:GLU95 4.9 10.8 1.0
C D:ASP99 5.0 15.9 1.0

Calcium binding site 8 out of 8 in 5a70

Go back to Calcium Binding Sites List in 5a70
Calcium binding site 8 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Lewis X Tetrasaccharide


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 Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca200

b:10.7
occ:1.00
 OD1 D:ASN103 2.3 9.6 1.0
OD1 D:ASP104 2.4 9.8 1.0
O D:ASN21 2.4 11.3 1.0
OD2 D:ASP101 2.4 10.7 1.0
O C:GLY114 2.5 11.4 1.0
O3 D:FUC201 2.5 10.1 1.0
O4 D:FUC201 2.6 11.8 1.0
OD1 D:ASP101 3.0 11.5 1.0
CG D:ASP101 3.1 11.6 1.0
CG D:ASN103 3.4 10.6 1.0
C3 D:FUC201 3.4 11.5 1.0
C C:GLY114 3.4 12.4 1.0
C4 D:FUC201 3.5 12.3 1.0
C D:ASN21 3.6 10.4 1.0
CG D:ASP104 3.6 10.1 1.0
OXT C:GLY114 3.7 13.2 1.0
ND2 D:ASN103 3.7 11.1 1.0
CA D:CA199 3.8 11.4 1.0
C2 D:FUC201 3.8 11.1 1.0
CB D:ASN21 4.1 9.7 1.0
CA D:ASP104 4.2 9.1 1.0
N D:ASP104 4.3 8.9 1.0
OD2 D:ASP104 4.4 11.1 1.0
O2 D:FUC201 4.4 12.1 1.0
CA D:SER22 4.4 10.9 1.0
N D:SER22 4.4 11.2 1.0
CB D:ASP104 4.5 9.8 1.0
CB D:ASP101 4.5 11.9 1.0
C D:ASN103 4.5 8.7 1.0
CA D:ASN21 4.5 9.7 1.0
OD2 D:ASP99 4.6 13.1 1.0
O C:HOH2147 4.6 22.1 1.0
CB D:SER22 4.7 11.7 1.0
CB D:ASN103 4.7 10.3 1.0
CA C:GLY114 4.8 11.0 1.0
C5 D:FUC201 4.8 12.6 1.0
O D:ASN103 4.8 8.7 1.0
N D:ASN103 4.9 9.4 1.0
CA D:ASN103 4.9 9.1 1.0

Reference:

M.Lepsik, R.Sommer, S.Kuhaudomlarp, M.Lelimousin, E.Paci, A.Varrot, A.Titz, A.Imberty. Induction of Rare Conformation of Oligosaccharide By Binding to Calcium-Dependent Bacterial Lectin: X-Ray Crystallography and Modelling Study. Eur.J.Med.Chem. V. 177 212 2019.
ISSN: ISSN 0223-5234
PubMed: 31146126
DOI: 10.1016/J.EJMECH.2019.05.049
Page generated: Sun Jul 14 16:22:10 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy