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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

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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 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

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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 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

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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 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

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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 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

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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 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

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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 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

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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 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

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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 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

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