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Calcium in PDB 6r35: Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 in Complex with Lewis X Tetrasaccharide

Protein crystallography data

The structure of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 in Complex with Lewis X Tetrasaccharide, PDB code: 6r35 was solved by M.Lepsik, R.Sommer, S.Kuhaudomlarp, M.Lelimousin, A.Varrot, A.Titz, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.87 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.603, 72.481, 62.061, 90.00, 114.62, 90.00
R / Rfree (%) 13.2 / 17.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 in Complex with Lewis X Tetrasaccharide (pdb code 6r35). 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 PAO1 in Complex with Lewis X Tetrasaccharide, PDB code: 6r35:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6r35

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Calcium binding site 1 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 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 PAO1 in Complex with Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:16.6
occ:1.00
 OD1 D:ASP104 2.3 18.6 1.0
O D:ASN21 2.3 13.8 1.0
OD1 D:ASN103 2.3 12.7 1.0
OD2 D:ASP101 2.4 16.6 1.0
O C:GLY114 2.4 16.3 1.0
O3 D:FUC205 2.5 16.9 1.0
O4 D:FUC205 2.5 17.8 1.0
OD1 D:ASP101 3.1 15.3 1.0
CG D:ASP101 3.1 16.3 1.0
C3 D:FUC205 3.3 19.9 1.0
CG D:ASN103 3.4 18.3 1.0
C C:GLY114 3.4 17.9 1.0
C4 D:FUC205 3.4 17.5 1.0
C D:ASN21 3.5 15.2 1.0
CG D:ASP104 3.5 14.4 1.0
OXT C:GLY114 3.7 18.9 1.0
CA D:CA202 3.7 17.5 1.0
ND2 D:ASN103 3.8 17.3 1.0
C2 D:FUC205 3.8 19.2 1.0
CB D:ASN21 4.1 15.6 1.0
CA D:ASP104 4.2 15.8 1.0
N D:ASP104 4.3 15.8 1.0
OD2 D:ASP104 4.4 14.2 1.0
CA D:SER22 4.4 14.7 1.0
N D:SER22 4.4 15.4 1.0
CB D:ASP104 4.4 16.9 1.0
CA D:ASN21 4.5 14.2 1.0
C D:ASN103 4.5 17.5 1.0
OD2 D:ASP99 4.5 17.6 1.0
O D:HOH344 4.5 29.1 1.0
O2 D:FUC205 4.5 17.1 1.0
CB D:ASP101 4.5 18.0 1.0
CB D:SER22 4.7 18.4 1.0
CB D:ASN103 4.7 12.7 1.0
C5 D:FUC205 4.8 21.8 1.0
O D:ASN103 4.8 14.1 1.0
CA C:GLY114 4.8 21.3 1.0
N D:ASN103 4.9 13.7 1.0
CA D:ASN103 4.9 14.3 1.0
OD1 D:ASP99 5.0 18.6 1.0

Calcium binding site 2 out of 8 in 6r35

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Calcium binding site 2 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 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 PAO1 in Complex with Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:17.5
occ:1.00
 OD1 D:ASP101 2.3 15.3 1.0
OD1 D:ASP99 2.3 18.6 1.0
OD2 D:ASP104 2.4 14.2 1.0
OE2 D:GLU95 2.4 17.0 1.0
O3 D:FUC205 2.5 16.9 1.0
OE1 D:GLU95 2.5 17.1 1.0
O2 D:FUC205 2.6 17.1 1.0
OD1 D:ASP104 2.6 18.6 1.0
CD D:GLU95 2.8 18.2 1.0
CG D:ASP104 2.8 14.4 1.0
C2 D:FUC205 3.3 19.2 1.0
C3 D:FUC205 3.3 19.9 1.0
CG D:ASP99 3.4 19.2 1.0
CG D:ASP101 3.4 16.3 1.0
OD2 D:ASP99 3.7 17.6 1.0
CA D:CA201 3.7 16.6 1.0
OD2 D:ASP101 4.0 16.6 1.0
OD1 D:ASP96 4.1 18.1 1.0
N D:ASP101 4.2 17.6 1.0
CG D:GLU95 4.2 16.9 1.0
O D:HOH381 4.3 25.1 1.0
CB D:ASP104 4.3 16.9 1.0
N D:ASN100 4.5 17.9 1.0
N D:TYR102 4.5 13.6 1.0
N D:ASP96 4.6 15.4 1.0
N D:GLY97 4.6 21.7 1.0
CB D:ASP101 4.6 18.0 1.0
C4 D:FUC205 4.7 17.5 1.0
N D:ASP99 4.7 17.5 1.0
CB D:ASP99 4.7 24.4 1.0
OD1 D:ASN103 4.7 12.7 1.0
CA D:GLU95 4.7 12.8 1.0
C1 D:FUC205 4.7 25.6 1.0
CA D:ASP101 4.8 18.5 1.0
O4 D:FUC205 4.9 17.8 1.0
CG D:ASP96 4.9 16.3 1.0
CB D:GLU95 4.9 13.3 1.0
C D:ASP99 5.0 20.8 1.0

Calcium binding site 3 out of 8 in 6r35

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Calcium binding site 3 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 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 PAO1 in Complex with Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca208

b:13.8
occ:1.00
 OD1 C:ASN103 2.3 14.7 1.0
OD1 C:ASP104 2.3 14.1 1.0
O C:ASN21 2.4 13.7 1.0
OD2 C:ASP101 2.4 16.2 1.0
O D:GLY114 2.4 13.2 1.0
O3 D:FUC209 2.5 13.0 1.0
O4 D:FUC209 2.5 14.9 1.0
OD1 C:ASP101 3.0 15.7 1.0
CG C:ASP101 3.1 15.2 1.0
CG C:ASN103 3.3 15.1 1.0
C3 D:FUC209 3.3 14.4 1.0
C4 D:FUC209 3.4 16.9 1.0
C D:GLY114 3.4 17.2 1.0
C C:ASN21 3.5 12.0 1.0
CG C:ASP104 3.6 11.5 1.0
OXT D:GLY114 3.7 17.6 1.0
ND2 C:ASN103 3.7 13.9 1.0
CA C:CA201 3.7 14.3 1.0
C2 D:FUC209 3.8 17.5 1.0
CB C:ASN21 4.1 12.9 1.0
CA C:ASP104 4.2 12.9 1.0
N C:ASP104 4.3 12.1 1.0
N C:SER22 4.4 13.2 1.0
CA C:SER22 4.4 15.3 1.0
OD2 C:ASP104 4.4 12.7 1.0
O C:HOH320 4.4 30.4 1.0
CB C:ASP104 4.4 11.3 1.0
C C:ASN103 4.4 9.6 1.0
O2 D:FUC209 4.5 16.7 1.0
CA C:ASN21 4.5 11.6 1.0
CB C:ASP101 4.5 15.1 1.0
OD2 C:ASP99 4.6 15.6 1.0
CB C:SER22 4.7 14.2 1.0
CB C:ASN103 4.7 12.9 1.0
C5 D:FUC209 4.8 18.5 1.0
O C:ASN103 4.8 12.2 1.0
CA D:GLY114 4.8 16.7 1.0
N C:ASN103 4.9 14.2 1.0
CA C:ASN103 4.9 10.8 1.0

Calcium binding site 4 out of 8 in 6r35

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Calcium binding site 4 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 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 PAO1 in Complex with Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:15.7
occ:1.00
 OD1 A:ASP104 2.3 16.4 1.0
OD1 A:ASN103 2.3 15.0 1.0
O A:ASN21 2.3 16.4 1.0
O B:GLY114 2.4 19.2 1.0
OD2 A:ASP101 2.5 18.7 1.0
O3 A:FUC205 2.5 20.1 1.0
O4 A:FUC205 2.5 15.1 1.0
OD1 A:ASP101 3.0 14.7 1.0
CG A:ASP101 3.1 18.8 1.0
CG A:ASN103 3.3 18.9 1.0
C3 A:FUC205 3.4 20.3 1.0
C B:GLY114 3.4 27.0 1.0
C4 A:FUC205 3.4 20.5 1.0
C A:ASN21 3.5 17.5 1.0
CG A:ASP104 3.6 15.8 1.0
OXT B:GLY114 3.7 23.0 1.0
ND2 A:ASN103 3.7 17.4 1.0
CA A:CA202 3.8 17.3 1.0
C2 A:FUC205 3.8 16.4 1.0
CB A:ASN21 4.1 16.9 1.0
CA A:ASP104 4.2 16.3 1.0
N A:ASP104 4.3 14.6 1.0
N A:SER22 4.4 14.8 1.0
CA A:SER22 4.4 18.3 1.0
CB A:ASP104 4.4 16.8 1.0
OD2 A:ASP104 4.5 15.6 1.0
C A:ASN103 4.5 12.3 1.0
CA A:ASN21 4.5 14.7 1.0
O2 A:FUC205 4.5 15.2 1.0
O A:HOH330 4.5 28.0 1.0
OD2 A:ASP99 4.6 19.0 1.0
CB A:ASP101 4.6 21.6 1.0
CB A:ASN103 4.7 16.4 1.0
CB A:SER22 4.7 22.1 1.0
O A:ASN103 4.8 14.1 1.0
C5 A:FUC205 4.8 25.7 1.0
CA B:GLY114 4.8 22.9 1.0
N A:ASN103 4.9 19.4 1.0
CA A:ASN103 4.9 13.7 1.0

Calcium binding site 5 out of 8 in 6r35

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Calcium binding site 5 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 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 PAO1 in Complex with Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:17.3
occ:1.00
 OD1 A:ASP101 2.3 14.7 1.0
OE2 A:GLU95 2.3 18.4 1.0
OD2 A:ASP104 2.4 15.6 1.0
OE1 A:GLU95 2.4 16.6 1.0
OD1 A:ASP99 2.4 18.4 1.0
O3 A:FUC205 2.5 20.1 1.0
O2 A:FUC205 2.5 15.2 1.0
OD1 A:ASP104 2.6 16.4 1.0
CD A:GLU95 2.7 17.9 1.0
CG A:ASP104 2.9 15.8 1.0
C2 A:FUC205 3.3 16.4 1.0
C3 A:FUC205 3.3 20.3 1.0
CG A:ASP101 3.4 18.8 1.0
CG A:ASP99 3.4 17.4 1.0
CA A:CA201 3.8 15.7 1.0
OD2 A:ASP99 3.8 19.0 1.0
OD2 A:ASP101 4.0 18.7 1.0
OD1 A:ASP96 4.1 18.9 1.0
N A:ASP101 4.2 20.1 1.0
CG A:GLU95 4.2 15.3 1.0
CB A:ASP104 4.4 16.8 1.0
O A:HOH365 4.4 25.2 1.0
N A:TYR102 4.4 15.0 1.0
N A:ASN100 4.5 20.2 1.0
CB A:ASP101 4.5 21.6 1.0
N A:ASP96 4.5 14.1 1.0
N A:GLY97 4.5 18.7 1.0
C4 A:FUC205 4.7 20.5 1.0
C1 A:FUC205 4.7 22.9 1.0
OD1 A:ASN103 4.7 15.0 1.0
CA A:GLU95 4.7 14.5 1.0
CA A:ASP101 4.7 19.9 1.0
N A:ASP99 4.8 21.1 1.0
CB A:ASP99 4.8 26.4 1.0
O4 A:FUC205 4.9 15.1 1.0
CB A:GLU95 4.9 17.1 1.0
CG A:ASP96 4.9 14.4 1.0
C A:ASP101 5.0 16.1 1.0
CA A:GLY97 5.0 23.7 1.0

Calcium binding site 6 out of 8 in 6r35

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Calcium binding site 6 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 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 PAO1 in Complex with Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca208

b:16.0
occ:1.00
 OD1 B:ASP104 2.2 12.2 1.0
O B:ASN21 2.3 14.8 1.0
OD1 B:ASN103 2.4 14.1 1.0
O A:GLY114 2.4 16.2 1.0
OD2 B:ASP101 2.4 14.2 1.0
O3 A:FUC209 2.5 16.9 1.0
O4 A:FUC209 2.5 16.6 1.0
OD1 B:ASP101 3.0 14.6 1.0
CG B:ASP101 3.1 14.5 1.0
C3 A:FUC209 3.3 16.0 1.0
CG B:ASN103 3.4 14.2 1.0
C4 A:FUC209 3.4 21.1 1.0
C A:GLY114 3.4 18.1 1.0
CG B:ASP104 3.5 11.1 1.0
C B:ASN21 3.6 17.2 1.0
OXT A:GLY114 3.7 20.8 1.0
CA B:CA201 3.7 16.3 1.0
ND2 B:ASN103 3.8 14.7 1.0
C2 A:FUC209 3.8 16.4 1.0
CB B:ASN21 4.2 12.4 1.0
CA B:ASP104 4.2 14.0 1.0
N B:ASP104 4.3 15.2 1.0
CA B:SER22 4.4 15.1 1.0
N B:SER22 4.4 14.3 1.0
CB B:ASP104 4.4 12.8 1.0
OD2 B:ASP104 4.4 14.0 1.0
O2 A:FUC209 4.4 16.9 1.0
O B:HOH322 4.5 32.1 1.0
C B:ASN103 4.5 15.4 1.0
CA B:ASN21 4.5 14.5 1.0
OD2 B:ASP99 4.5 20.7 1.0
CB B:ASP101 4.5 17.4 1.0
CB B:SER22 4.6 17.1 1.0
CB B:ASN103 4.7 13.8 1.0
C5 A:FUC209 4.8 20.2 1.0
O B:ASN103 4.8 14.3 1.0
CA A:GLY114 4.8 18.3 1.0
N B:ASN103 4.9 15.0 1.0
CA B:ASN103 5.0 14.4 1.0
OD1 B:ASP99 5.0 18.4 1.0

Calcium binding site 7 out of 8 in 6r35

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Calcium binding site 7 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 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 PAO1 in Complex with Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:16.3
occ:1.00
 OD1 B:ASP101 2.4 14.6 1.0
OD2 B:ASP104 2.4 14.0 1.0
OD1 B:ASP99 2.4 18.4 1.0
OE2 B:GLU95 2.4 17.9 1.0
OE1 B:GLU95 2.5 16.8 1.0
O2 A:FUC209 2.5 16.9 1.0
O3 A:FUC209 2.5 16.9 1.0
OD1 B:ASP104 2.6 12.2 1.0
CD B:GLU95 2.8 19.2 1.0
CG B:ASP104 2.8 11.1 1.0
C2 A:FUC209 3.2 16.4 1.0
C3 A:FUC209 3.3 16.0 1.0
CG B:ASP99 3.4 19.9 1.0
CG B:ASP101 3.4 14.5 1.0
CA A:CA208 3.7 16.0 1.0
OD2 B:ASP99 3.8 20.7 1.0
OD2 B:ASP101 4.0 14.2 1.0
OD1 B:ASP96 4.1 17.3 1.0
N B:ASP101 4.2 18.2 1.0
CG B:GLU95 4.2 15.3 1.0
O A:HOH360 4.3 24.3 1.0
CB B:ASP104 4.3 12.8 1.0
N B:TYR102 4.4 13.9 1.0
N B:ASN100 4.5 17.2 1.0
N B:ASP96 4.5 15.4 1.0
N B:GLY97 4.6 18.9 1.0
CB B:ASP101 4.6 17.4 1.0
C4 A:FUC209 4.7 21.1 1.0
C1 A:FUC209 4.7 18.9 1.0
CA B:GLU95 4.7 14.1 1.0
CA B:ASP101 4.8 18.1 1.0
CB B:ASP99 4.8 21.4 1.0
OD1 B:ASN103 4.8 14.1 1.0
N B:ASP99 4.8 20.1 1.0
O4 A:FUC209 4.9 16.6 1.0
CG B:ASP96 4.9 16.7 1.0
CB B:GLU95 4.9 16.2 1.0
CA B:GLY97 5.0 25.6 1.0

Calcium binding site 8 out of 8 in 6r35

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Calcium binding site 8 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PAO1 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 PAO1 in Complex with Lewis X Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:14.3
occ:1.00
 OD2 C:ASP104 2.3 12.7 1.0
OD1 C:ASP101 2.3 15.7 1.0
OD1 C:ASP99 2.4 17.1 1.0
OE2 C:GLU95 2.4 14.5 1.0
O3 D:FUC209 2.5 13.0 1.0
OE1 C:GLU95 2.5 17.2 1.0
O2 D:FUC209 2.5 16.7 1.0
OD1 C:ASP104 2.6 14.1 1.0
CD C:GLU95 2.8 16.0 1.0
CG C:ASP104 2.8 11.5 1.0
C2 D:FUC209 3.3 17.5 1.0
C3 D:FUC209 3.3 14.4 1.0
CG C:ASP101 3.4 15.2 1.0
CG C:ASP99 3.4 18.5 1.0
OD2 C:ASP99 3.7 15.6 1.0
CA D:CA208 3.7 13.8 1.0
OD2 C:ASP101 4.0 16.2 1.0
OD1 C:ASP96 4.1 13.4 1.0
O C:HOH377 4.2 17.9 1.0
N C:ASP101 4.2 14.3 1.0
CG C:GLU95 4.3 12.6 1.0
CB C:ASP104 4.3 11.3 1.0
N C:TYR102 4.5 13.3 1.0
N C:ASN100 4.5 13.5 1.0
N C:ASP96 4.5 13.8 1.0
CB C:ASP101 4.5 15.1 1.0
N C:GLY97 4.6 12.8 1.0
C4 D:FUC209 4.7 16.9 1.0
OD1 C:ASN103 4.7 14.7 1.0
C1 D:FUC209 4.7 18.5 1.0
CA C:GLU95 4.7 10.0 1.0
CB C:ASP99 4.8 19.3 1.0
CA C:ASP101 4.8 14.2 1.0
O4 D:FUC209 4.8 14.9 1.0
N C:ASP99 4.8 17.0 1.0
CG C:ASP96 4.9 12.5 1.0
CB C:GLU95 4.9 11.6 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: Tue Jul 16 14:14:26 2024

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