Calcium in PDB 1w8h: Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide

The structure of Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide, PDB code: 1w8h was solved by S.Perret, C.Sabin, C.Dumon, M.Budova, C.Gautier, O.Galanina, S.Ilia, N.Bovin, M.Nicaise, M.Desmadril, N.Gilboa-Garber, M.Wimmerova, E.P.Mitchell, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.35 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.575, 75.824, 52.746, 90.00, 93.48, 90.00
R / Rfree (%)	12.5 / 16.9

The binding sites of Calcium atom in the Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide (pdb code 1w8h). 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 Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide, PDB code: 1w8h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:7.5 occ:1.00 OD1 A:ASN103 2.3 6.9 1.0 OD1 A:ASP104 2.4 8.1 1.0 O A:ASN21 2.4 7.3 1.0 OD2 A:ASP101 2.4 6.4 1.0 O3 A:FUC331 2.5 6.7 1.0 O4 A:FUC331 2.5 7.3 1.0 O D:GLY114 2.5 8.0 1.0 OD1 A:ASP101 3.0 6.8 1.0 CG A:ASP101 3.1 9.2 1.0 C3 A:FUC331 3.3 6.5 1.0 CG A:ASN103 3.3 6.0 1.0 C4 A:FUC331 3.4 8.5 1.0 C D:GLY114 3.5 9.2 1.0 C A:ASN21 3.6 7.5 1.0 CG A:ASP104 3.6 7.4 1.0 ND2 A:ASN103 3.7 6.3 1.0 OXT D:GLY114 3.7 10.3 1.0 CA A:CA202 3.7 6.8 1.0 C2 A:FUC331 3.7 6.6 1.0 CB A:ASN21 4.2 7.8 1.0 CA A:ASP104 4.2 7.5 1.0 N A:ASP104 4.3 7.6 1.0 OD2 A:ASP104 4.3 7.8 1.0 O2 A:FUC331 4.4 8.0 1.0 CA A:SER22 4.5 7.8 1.0 N A:SER22 4.5 7.9 1.0 C A:ASN103 4.5 7.5 1.0 CB A:ASP104 4.5 7.6 1.0 OD2 A:ASP99 4.5 9.2 1.0 CA A:ASN21 4.6 7.6 1.0 CB A:ASP101 4.6 8.9 1.0 O A:HOH2113 4.6 19.0 1.0 CB A:SER22 4.6 9.3 1.0 CB A:ASN103 4.7 7.5 1.0 C5 A:FUC331 4.8 7.2 1.0 O A:ASN103 4.9 5.5 1.0 CA D:GLY114 4.9 9.2 1.0 N A:ASN103 4.9 7.8 1.0 CA A:ASN103 4.9 7.1 1.0

Calcium binding site 2 out of 8 in the Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:6.8 occ:1.00 OD2 A:ASP104 2.3 7.8 1.0 OD1 A:ASP101 2.4 6.8 1.0 OE2 A:GLU95 2.4 6.0 1.0 OD1 A:ASP99 2.4 7.0 1.0 OE1 A:GLU95 2.5 6.3 1.0 O2 A:FUC331 2.5 8.0 1.0 O3 A:FUC331 2.6 6.7 1.0 OD1 A:ASP104 2.6 8.1 1.0 CD A:GLU95 2.7 7.8 1.0 CG A:ASP104 2.9 7.4 1.0 C2 A:FUC331 3.3 6.6 1.0 C3 A:FUC331 3.4 6.5 1.0 CG A:ASP99 3.4 11.7 1.0 CG A:ASP101 3.5 9.2 1.0 OD2 A:ASP99 3.7 9.2 1.0 CA A:CA201 3.7 7.5 1.0 OD1 A:ASP96 4.0 10.0 1.0 OD2 A:ASP101 4.1 6.4 1.0 N A:ASP101 4.2 10.0 1.0 CG A:GLU95 4.2 9.6 1.0 O A:HOH2108 4.3 11.3 1.0 CB A:ASP104 4.4 7.6 1.0 N A:TYR102 4.4 7.2 1.0 N A:ASP96 4.5 8.1 1.0 N A:ASN100 4.5 11.0 1.0 CB A:ASP101 4.6 8.9 1.0 N A:GLY97 4.6 9.9 1.0 OD1 A:ASN103 4.7 6.9 1.0 CA A:GLU95 4.7 8.8 1.0 C1 A:FUC331 4.7 8.1 1.0 CA A:ASP101 4.7 9.0 1.0 C4 A:FUC331 4.7 8.5 1.0 CB A:ASP99 4.8 11.1 1.0 O4 A:FUC331 4.8 7.3 1.0 N A:ASP99 4.8 11.6 1.0 CB A:GLU95 4.9 8.8 1.0 CG A:ASP96 4.9 10.1 1.0 CA A:GLY97 5.0 10.2 1.0 C A:ASP101 5.0 8.8 1.0 C A:ASP99 5.0 10.9 1.0

Calcium binding site 3 out of 8 in the Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:8.5 occ:1.00 O B:ASN21 2.4 7.3 1.0 OD1 B:ASN103 2.4 6.7 1.0 OD1 B:ASP104 2.4 7.3 1.0 O C:GLY114 2.4 10.9 1.0 OD2 B:ASP101 2.4 7.7 1.0 O4 B:FUC331 2.5 7.5 1.0 O3 B:FUC331 2.5 6.7 1.0 OD1 B:ASP101 3.1 7.3 1.0 CG B:ASP101 3.2 7.9 1.0 C3 B:FUC331 3.3 9.2 1.0 C4 B:FUC331 3.4 7.0 1.0 CG B:ASN103 3.4 8.5 1.0 C C:GLY114 3.4 11.9 1.0 C B:ASN21 3.6 8.6 1.0 OXT C:GLY114 3.7 12.4 1.0 CG B:ASP104 3.7 10.1 1.0 ND2 B:ASN103 3.7 8.2 1.0 CA B:CA204 3.7 9.1 1.0 C2 B:FUC331 3.8 9.0 1.0 CB B:ASN21 4.2 7.6 1.0 CA B:ASP104 4.3 8.1 1.0 N B:ASP104 4.4 8.1 1.0 N B:SER22 4.4 9.1 1.0 O2 B:FUC331 4.5 8.3 1.0 CA B:SER22 4.5 9.5 1.0 O B:HOH2093 4.5 23.4 1.0 OD2 B:ASP104 4.5 11.3 1.0 OD2 B:ASP99 4.5 10.6 1.0 CB B:ASP104 4.5 8.4 1.0 C B:ASN103 4.6 8.2 1.0 CA B:ASN21 4.6 7.9 1.0 CB B:ASP101 4.6 9.6 1.0 C5 B:FUC331 4.7 7.1 1.0 CB B:SER22 4.7 10.1 1.0 CB B:ASN103 4.8 8.0 1.0 CA C:GLY114 4.8 11.1 1.0 O B:ASN103 4.9 8.1 1.0 N B:ASN103 4.9 7.6 1.0 O5 B:FUC331 5.0 8.2 1.0

Calcium binding site 4 out of 8 in the Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:9.1 occ:1.00 OD1 B:ASP101 2.4 7.3 1.0 OE2 B:GLU95 2.4 7.8 1.0 OD2 B:ASP104 2.4 11.3 1.0 OD1 B:ASP99 2.4 11.6 1.0 OE1 B:GLU95 2.5 8.6 1.0 O3 B:FUC331 2.5 6.7 1.0 O2 B:FUC331 2.5 8.3 1.0 OD1 B:ASP104 2.6 7.3 1.0 CD B:GLU95 2.8 10.6 1.0 CG B:ASP104 2.9 10.1 1.0 C2 B:FUC331 3.3 9.0 1.0 C3 B:FUC331 3.3 9.2 1.0 CG B:ASP101 3.4 7.9 1.0 CG B:ASP99 3.5 11.4 1.0 OD2 B:ASP99 3.7 10.6 1.0 CA B:CA203 3.7 8.5 1.0 OD2 B:ASP101 4.0 7.7 1.0 OD1 B:ASP96 4.1 10.9 1.0 N B:ASP101 4.1 11.6 1.0 CG B:GLU95 4.2 9.2 1.0 CB B:ASP104 4.4 8.4 1.0 N B:TYR102 4.4 9.0 1.0 N B:GLY97 4.5 10.6 1.0 CB B:ASP101 4.6 9.6 1.0 N B:ASP96 4.6 9.5 1.0 N B:ASN100 4.6 12.1 1.0 CA B:ASP101 4.7 10.0 1.0 C4 B:FUC331 4.7 7.0 1.0 C1 B:FUC331 4.7 7.7 1.0 CA B:GLU95 4.8 8.8 1.0 OD1 B:ASN103 4.8 6.7 1.0 N B:ASP99 4.8 10.9 1.0 O B:HOH2100 4.8 12.1 1.0 CB B:ASP99 4.8 11.6 1.0 O4 B:FUC331 4.8 7.5 1.0 CA B:GLY97 4.9 11.2 1.0 CB B:GLU95 4.9 9.3 1.0 C B:ASP101 5.0 10.0 1.0

Calcium binding site 5 out of 8 in the Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca205 b:6.7 occ:1.00 OD1 C:ASP101 2.3 6.2 1.0 OD1 C:ASP99 2.4 7.9 1.0 OE2 C:GLU95 2.4 8.6 1.0 OD2 C:ASP104 2.4 8.3 1.0 OE1 C:GLU95 2.4 7.3 1.0 O2 C:FUC331 2.5 6.8 1.0 O3 C:FUC331 2.5 6.3 1.0 OD1 C:ASP104 2.7 8.2 1.0 CD C:GLU95 2.7 9.0 1.0 CG C:ASP104 2.9 7.4 1.0 C2 C:FUC331 3.3 6.6 1.0 C3 C:FUC331 3.4 5.2 1.0 CG C:ASP99 3.4 10.9 1.0 CG C:ASP101 3.4 8.7 1.0 OD2 C:ASP99 3.7 9.5 1.0 CA C:CA206 3.7 6.7 1.0 OD2 C:ASP101 4.0 8.4 1.0 N C:ASP101 4.1 9.9 1.0 OD1 C:ASP96 4.1 10.4 1.0 CG C:GLU95 4.2 8.7 1.0 CB C:ASP104 4.4 6.3 1.0 N C:TYR102 4.4 7.3 1.0 N C:GLY97 4.5 10.4 1.0 O C:HOH2101 4.5 16.9 1.0 N C:ASN100 4.5 10.4 1.0 N C:ASP96 4.5 8.9 1.0 CB C:ASP101 4.6 9.0 1.0 CA C:ASP101 4.7 9.3 1.0 N C:ASP99 4.7 11.7 1.0 C4 C:FUC331 4.7 8.0 1.0 CB C:ASP99 4.7 10.4 1.0 C1 C:FUC331 4.8 8.4 1.0 OD1 C:ASN103 4.8 7.9 1.0 CA C:GLU95 4.8 8.5 1.0 CA C:GLY97 4.8 10.8 1.0 O4 C:FUC331 4.8 6.0 1.0 CB C:GLU95 4.9 8.7 1.0 C C:ASP99 4.9 10.6 1.0 C C:ASP101 4.9 8.0 1.0 CA C:ASP99 5.0 10.8 1.0

Calcium binding site 6 out of 8 in the Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca206 b:6.7 occ:1.00 O C:ASN21 2.4 5.4 1.0 OD2 C:ASP101 2.4 8.4 1.0 OD1 C:ASN103 2.4 7.9 1.0 OD1 C:ASP104 2.4 8.2 1.0 O4 C:FUC331 2.4 6.0 1.0 O B:GLY114 2.4 8.3 1.0 O3 C:FUC331 2.5 6.3 1.0 OD1 C:ASP101 3.0 6.2 1.0 CG C:ASP101 3.1 8.7 1.0 C3 C:FUC331 3.3 5.2 1.0 CG C:ASN103 3.4 8.0 1.0 C4 C:FUC331 3.4 8.0 1.0 C B:GLY114 3.4 10.5 1.0 C C:ASN21 3.6 6.0 1.0 CG C:ASP104 3.7 7.4 1.0 OXT B:GLY114 3.7 9.3 1.0 CA C:CA205 3.7 6.7 1.0 ND2 C:ASN103 3.8 8.8 1.0 C2 C:FUC331 3.8 6.6 1.0 CB C:ASN21 4.1 6.3 1.0 CA C:ASP104 4.3 6.3 1.0 N C:ASP104 4.4 6.0 1.0 OD2 C:ASP104 4.4 8.3 1.0 O2 C:FUC331 4.4 6.8 1.0 N C:SER22 4.4 5.2 1.0 OD2 C:ASP99 4.5 9.5 1.0 CA C:SER22 4.5 6.9 1.0 CA C:ASN21 4.5 6.0 1.0 CB C:ASP104 4.5 6.3 1.0 C C:ASN103 4.5 6.5 1.0 O B:HOH2097 4.5 19.5 1.0 CB C:ASP101 4.5 9.0 1.0 C5 C:FUC331 4.7 9.2 1.0 CB C:ASN103 4.7 6.1 1.0 CB C:SER22 4.8 6.5 1.0 CA B:GLY114 4.8 9.7 1.0 O C:ASN103 4.9 6.6 1.0 N C:ASN103 4.9 7.1 1.0 CA C:ASN103 5.0 6.4 1.0

Calcium binding site 7 out of 8 in the Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca207 b:6.6 occ:1.00 OD1 D:ASN103 2.3 5.1 1.0 OD1 D:ASP104 2.4 5.2 1.0 O D:ASN21 2.4 5.5 1.0 OD2 D:ASP101 2.4 8.3 1.0 O A:GLY114 2.4 8.5 1.0 O4 D:FUC331 2.5 7.7 1.0 O3 D:FUC331 2.5 6.9 1.0 OD1 D:ASP101 3.0 8.6 1.0 CG D:ASP101 3.1 7.5 1.0 C3 D:FUC331 3.3 7.0 1.0 CG D:ASN103 3.4 5.4 1.0 C4 D:FUC331 3.4 9.6 1.0 C A:GLY114 3.4 8.9 1.0 C D:ASN21 3.6 7.1 1.0 CG D:ASP104 3.6 6.5 1.0 OXT A:GLY114 3.7 9.6 1.0 C2 D:FUC331 3.7 6.3 1.0 CA D:CA208 3.8 6.6 1.0 ND2 D:ASN103 3.8 7.8 1.0 CB D:ASN21 4.1 8.1 1.0 CA D:ASP104 4.2 5.9 1.0 N D:ASP104 4.3 5.8 1.0 OD2 D:ASP104 4.4 6.7 1.0 O2 D:FUC331 4.4 8.4 1.0 N D:SER22 4.4 8.2 1.0 CA D:SER22 4.4 8.6 1.0 C D:ASN103 4.5 5.6 1.0 CB D:ASP104 4.5 5.6 1.0 CA D:ASN21 4.5 7.5 1.0 CB D:ASP101 4.6 9.0 1.0 OD2 D:ASP99 4.6 7.6 1.0 O A:HOH2118 4.7 14.8 1.0 CB D:ASN103 4.7 5.0 1.0 CB D:SER22 4.7 9.0 1.0 C5 D:FUC331 4.8 9.7 1.0 CA A:GLY114 4.8 8.7 1.0 O D:ASN103 4.8 5.8 1.0 N D:ASN103 4.9 6.8 1.0 CA D:ASN103 4.9 5.8 1.0

Calcium binding site 8 out of 8 in the Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lewisa Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca208 b:6.6 occ:1.00 OD2 D:ASP104 2.3 6.7 1.0 OD1 D:ASP99 2.4 6.7 1.0 OD1 D:ASP101 2.4 8.6 1.0 O2 D:FUC331 2.4 8.4 1.0 OE2 D:GLU95 2.5 7.6 1.0 OE1 D:GLU95 2.5 7.1 1.0 O3 D:FUC331 2.5 6.9 1.0 OD1 D:ASP104 2.7 5.2 1.0 CD D:GLU95 2.8 9.2 1.0 CG D:ASP104 2.9 6.5 1.0 C2 D:FUC331 3.2 6.3 1.0 C3 D:FUC331 3.3 7.0 1.0 CG D:ASP99 3.4 9.4 1.0 CG D:ASP101 3.5 7.5 1.0 OD2 D:ASP99 3.7 7.6 1.0 CA D:CA207 3.8 6.6 1.0 OD2 D:ASP101 4.0 8.3 1.0 OD1 D:ASP96 4.0 10.3 1.0 N D:ASP101 4.1 10.2 1.0 O D:HOH2079 4.2 13.2 1.0 CG D:GLU95 4.3 6.7 1.0 N D:TYR102 4.4 7.2 1.0 CB D:ASP104 4.4 5.6 1.0 N D:ASN100 4.5 10.7 1.0 N D:ASP96 4.5 8.6 1.0 N D:GLY97 4.5 9.8 1.0 CB D:ASP101 4.6 9.0 1.0 C4 D:FUC331 4.7 9.6 1.0 C1 D:FUC331 4.7 9.4 1.0 CA D:ASP101 4.7 8.4 1.0 N D:ASP99 4.7 11.4 1.0 CA D:GLU95 4.7 7.8 1.0 CB D:ASP99 4.7 11.4 1.0 OD1 D:ASN103 4.8 5.1 1.0 O4 D:FUC331 4.8 7.7 1.0 CA D:GLY97 4.9 10.2 1.0 CB D:GLU95 5.0 8.2 1.0 C D:ASP101 5.0 8.4 1.0 C D:ASP99 5.0 10.7 1.0

S.Perret, C.Sabin, C.Dumon, M.Pokorna, C.Gautier, O.Galanina, S.Ilia, N.Bovin, M.Nicaise, M.Desmadril, N.Gilboa-Garber, M.Wimmerova, E.P.Mitchell, A.Imberty. Structural Basis For the Interaction Between Human Milk Oligosaccharides and the Bacterial Lectin Pa-Iil of Pseudomonas Aeruginosa. Biochem.J. V. 389 325 2005.
ISSN: ISSN 0264-6021
PubMed: 15790314
DOI: 10.1042/BJ20050079