Calcium in PDB 1w8f: Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv)

The structure of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv), PDB code: 1w8f 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)	14.51 / 1.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.015, 48.352, 52.472, 85.35, 80.05, 65.60
R / Rfree (%)	10.5 / 12.3

The binding sites of Calcium atom in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv) (pdb code 1w8f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv), PDB code: 1w8f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1116 b:4.6 occ:1.00 OD1 A:ASP101 2.3 5.6 1.0 OD1 A:ASP99 2.4 7.4 1.0 OE2 A:GLU95 2.4 5.7 1.0 OD2 A:ASP104 2.4 4.7 1.0 O2 A:FUC1118 2.5 5.3 1.0 OE1 A:GLU95 2.5 5.4 1.0 O3 A:FUC1118 2.5 5.2 1.0 OD1 A:ASP104 2.6 4.1 1.0 CD A:GLU95 2.8 5.3 1.0 CG A:ASP104 2.9 4.0 1.0 C2 A:FUC1118 3.3 4.5 1.0 C3 A:FUC1118 3.4 5.0 1.0 CG A:ASP101 3.4 6.0 1.0 CG A:ASP99 3.4 6.9 1.0 OD2 A:ASP99 3.7 7.3 1.0 CA A:CA1117 3.7 4.0 1.0 OD2 A:ASP101 4.0 6.2 1.0 N A:ASP101 4.2 7.4 1.0 CG A:GLU95 4.2 5.5 1.0 OD1 A:ASP96 4.3 7.7 1.0 CB A:ASP104 4.4 3.8 1.0 N A:TYR102 4.4 5.3 1.0 N A:GLY97 4.5 6.5 1.0 N A:ASN100 4.5 8.1 1.0 CB A:ASP101 4.5 7.2 1.0 N A:ASP96 4.5 5.3 1.0 O A:HOH2157 4.6 13.1 1.0 C4 A:FUC1118 4.7 5.5 1.0 CA A:ASP101 4.7 7.3 1.0 C1 A:FUC1118 4.7 5.5 1.0 CA A:GLU95 4.7 4.8 1.0 OD1 A:ASN103 4.7 4.0 1.0 N A:ASP99 4.7 8.3 1.0 CB A:ASP99 4.7 8.5 1.0 O4 A:FUC1118 4.8 5.1 1.0 CA A:GLY97 4.8 7.3 1.0 CB A:GLU95 4.9 5.2 1.0 C A:ASP101 5.0 5.9 1.0

Calcium binding site 2 out of 8 in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1117 b:4.0 occ:1.00 OD1 A:ASN103 2.3 4.0 1.0 OD1 A:ASP104 2.4 4.1 1.0 O A:ASN21 2.4 3.9 1.0 O C:GLY114 2.4 5.2 1.0 OD2 A:ASP101 2.4 6.2 1.0 O3 A:FUC1118 2.5 5.2 1.0 O4 A:FUC1118 2.5 5.1 1.0 CG A:ASP101 3.1 6.0 1.0 OD1 A:ASP101 3.1 5.6 1.0 CG A:ASN103 3.4 3.8 1.0 C3 A:FUC1118 3.4 5.0 1.0 C C:GLY114 3.4 6.0 1.0 C4 A:FUC1118 3.4 5.5 1.0 C A:ASN21 3.6 3.9 1.0 CG A:ASP104 3.6 4.0 1.0 OXT C:GLY114 3.7 7.5 1.0 ND2 A:ASN103 3.7 5.3 1.0 CA A:CA1116 3.7 4.6 1.0 C2 A:FUC1118 3.8 4.5 1.0 CB A:ASN21 4.1 4.0 1.0 CA A:ASP104 4.2 3.6 1.0 N A:ASP104 4.3 3.5 1.0 O2 A:FUC1118 4.4 5.3 1.0 N A:SER22 4.4 4.2 1.0 CA A:SER22 4.4 4.2 1.0 OD2 A:ASP104 4.4 4.7 1.0 CB A:ASP104 4.5 3.8 1.0 OD2 A:ASP99 4.5 7.3 1.0 C A:ASN103 4.5 3.8 1.0 O A:HOH2144 4.5 13.6 1.0 CB A:ASP101 4.5 7.2 1.0 CA A:ASN21 4.6 3.8 1.0 CB A:SER22 4.7 4.6 1.0 CB A:ASN103 4.7 4.2 1.0 CA C:GLY114 4.8 6.5 1.0 C5 A:FUC1118 4.8 5.5 1.0 O A:ASN103 4.8 3.9 1.0 N A:ASN103 4.9 4.1 1.0 CA A:ASN103 4.9 4.1 1.0 O5 A:FUC1118 5.0 5.2 1.0 OD1 A:ASP99 5.0 7.4 1.0

Calcium binding site 3 out of 8 in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1116 b:4.7 occ:1.00 OD1 B:ASP101 2.3 5.8 1.0 OD1 B:ASP99 2.4 8.0 1.0 OE2 B:GLU95 2.4 5.9 1.0 OD2 B:ASP104 2.4 5.3 1.0 O2 B:FUC1118 2.4 5.2 1.0 O3 B:FUC1118 2.5 5.2 1.0 OE1 B:GLU95 2.5 5.8 1.0 OD1 B:ASP104 2.6 4.4 1.0 CD B:GLU95 2.8 4.9 1.0 CG B:ASP104 2.9 4.2 1.0 C2 B:FUC1118 3.3 5.1 1.0 C3 B:FUC1118 3.3 5.1 1.0 CG B:ASP101 3.4 5.3 1.0 CG B:ASP99 3.4 7.0 1.0 CA B:CA1117 3.7 4.1 1.0 OD2 B:ASP99 3.7 7.0 1.0 OD2 B:ASP101 4.0 5.7 1.0 N B:ASP101 4.1 6.9 1.0 CG B:GLU95 4.2 5.8 1.0 OD1 B:ASP96 4.3 8.4 1.0 CB B:ASP104 4.4 4.1 1.0 N B:GLY97 4.4 6.2 1.0 N B:TYR102 4.4 4.9 1.0 N B:ASP96 4.5 4.9 1.0 N B:ASN100 4.5 8.4 1.0 CB B:ASP101 4.5 6.6 1.0 C4 B:FUC1118 4.7 5.3 1.0 CA B:ASP101 4.7 6.8 1.0 CA B:GLY97 4.7 7.5 1.0 CA B:GLU95 4.7 4.6 1.0 C1 B:FUC1118 4.7 5.1 1.0 OD1 B:ASN103 4.7 4.2 1.0 N B:ASP99 4.7 8.0 1.0 O B:HOH2186 4.7 11.3 1.0 CB B:ASP99 4.8 8.5 1.0 O4 B:FUC1118 4.8 5.1 1.0 CB B:GLU95 4.9 5.7 1.0 C B:ASP101 5.0 5.9 1.0 C B:GLY97 5.0 7.4 1.0 C B:ASP99 5.0 7.9 1.0

Calcium binding site 4 out of 8 in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1117 b:4.1 occ:1.00 OD1 B:ASP104 2.3 4.4 1.0 OD1 B:ASN103 2.4 4.2 1.0 O B:ASN21 2.4 4.5 1.0 O D:GLY114 2.4 5.1 1.0 OD2 B:ASP101 2.4 5.7 1.0 O3 B:FUC1118 2.5 5.2 1.0 O4 B:FUC1118 2.5 5.1 1.0 OD1 B:ASP101 3.1 5.8 1.0 CG B:ASP101 3.1 5.3 1.0 C3 B:FUC1118 3.4 5.1 1.0 C D:GLY114 3.4 5.9 1.0 CG B:ASN103 3.4 4.2 1.0 C4 B:FUC1118 3.4 5.3 1.0 C B:ASN21 3.6 4.5 1.0 CG B:ASP104 3.6 4.2 1.0 OXT D:GLY114 3.7 7.2 1.0 CA B:CA1116 3.7 4.7 1.0 C2 B:FUC1118 3.7 5.1 1.0 ND2 B:ASN103 3.7 5.6 1.0 CB B:ASN21 4.1 4.3 1.0 CA B:ASP104 4.3 3.9 1.0 N B:ASP104 4.3 4.0 1.0 O2 B:FUC1118 4.4 5.2 1.0 OD2 B:ASP104 4.4 5.3 1.0 N B:SER22 4.4 4.1 1.0 OD2 B:ASP99 4.5 7.0 1.0 CA B:SER22 4.5 4.3 1.0 C B:ASN103 4.5 4.1 1.0 CB B:ASP104 4.5 4.1 1.0 CA B:ASN21 4.5 4.2 1.0 O B:HOH2167 4.5 11.1 1.0 CB B:ASP101 4.5 6.6 1.0 CB B:ASN103 4.7 4.4 1.0 CA D:GLY114 4.7 6.2 1.0 CB B:SER22 4.8 5.0 1.0 C5 B:FUC1118 4.8 5.4 1.0 O B:ASN103 4.8 4.2 1.0 N B:ASN103 4.9 4.2 1.0 CA B:ASN103 4.9 4.2 1.0 OD1 B:ASP99 5.0 8.0 1.0 C1 B:FUC1118 5.0 5.1 1.0 O5 B:FUC1118 5.0 5.3 1.0

Calcium binding site 5 out of 8 in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1116 b:3.9 occ:1.00 OD1 C:ASP101 2.4 4.7 1.0 OD1 C:ASP99 2.4 6.0 1.0 OE2 C:GLU95 2.4 4.7 1.0 OD2 C:ASP104 2.4 4.3 1.0 OE1 C:GLU95 2.5 4.7 1.0 O2 C:FUC1118 2.5 4.8 1.0 O3 C:FUC1118 2.5 4.3 1.0 OD1 C:ASP104 2.6 3.8 1.0 CD C:GLU95 2.8 4.5 1.0 CG C:ASP104 2.9 3.8 1.0 C2 C:FUC1118 3.3 4.4 1.0 C3 C:FUC1118 3.4 4.8 1.0 CG C:ASP99 3.4 5.1 1.0 CG C:ASP101 3.4 4.8 1.0 OD2 C:ASP99 3.7 5.5 1.0 CA C:CA1117 3.7 3.7 1.0 OD2 C:ASP101 4.0 5.1 1.0 N C:ASP101 4.2 5.5 1.0 CG C:GLU95 4.2 5.0 1.0 OD1 C:ASP96 4.4 6.8 1.0 CB C:ASP104 4.4 3.5 1.0 N C:TYR102 4.4 4.7 1.0 N C:ASP96 4.5 4.7 1.0 N C:GLY97 4.5 5.6 1.0 CB C:ASP101 4.5 6.1 1.0 N C:ASN100 4.6 5.7 1.0 O C:HOH2182 4.7 10.7 1.0 CA C:GLU95 4.7 4.2 1.0 C4 C:FUC1118 4.7 5.1 1.0 CA C:ASP101 4.7 5.7 1.0 CB C:ASP99 4.7 5.9 1.0 C1 C:FUC1118 4.7 5.4 1.0 N C:ASP99 4.7 6.5 1.0 OD1 C:ASN103 4.7 3.9 1.0 O4 C:FUC1118 4.8 5.0 1.0 CA C:GLY97 4.8 5.8 1.0 CB C:GLU95 4.9 4.6 1.0 C C:ASP101 5.0 4.8 1.0 C C:ASP99 5.0 5.9 1.0

Calcium binding site 6 out of 8 in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1117 b:3.7 occ:1.00 OD1 C:ASN103 2.3 3.9 1.0 OD1 C:ASP104 2.4 3.8 1.0 O C:ASN21 2.4 4.0 1.0 O A:GLY114 2.4 5.4 1.0 OD2 C:ASP101 2.4 5.1 1.0 O3 C:FUC1118 2.5 4.3 1.0 O4 C:FUC1118 2.5 5.0 1.0 OD1 C:ASP101 3.1 4.7 1.0 CG C:ASP101 3.1 4.8 1.0 C3 C:FUC1118 3.4 4.8 1.0 C A:GLY114 3.4 6.2 1.0 CG C:ASN103 3.4 3.9 1.0 C4 C:FUC1118 3.4 5.1 1.0 C C:ASN21 3.6 3.9 1.0 CG C:ASP104 3.6 3.8 1.0 OXT A:GLY114 3.7 8.1 1.0 CA C:CA1116 3.7 3.9 1.0 ND2 C:ASN103 3.7 5.6 1.0 C2 C:FUC1118 3.8 4.4 1.0 CB C:ASN21 4.1 4.2 1.0 CA C:ASP104 4.2 4.0 1.0 N C:ASP104 4.3 3.5 1.0 O2 C:FUC1118 4.4 4.8 1.0 O C:HOH2166 4.4 16.1 1.0 OD2 C:ASP104 4.4 4.3 1.0 N C:SER22 4.4 4.6 1.0 CA C:SER22 4.5 4.6 1.0 C C:ASN103 4.5 4.0 1.0 CB C:ASP104 4.5 3.5 1.0 OD2 C:ASP99 4.5 5.5 1.0 CA C:ASN21 4.5 3.9 1.0 CB C:ASP101 4.5 6.1 1.0 CB C:ASN103 4.7 4.2 1.0 CB C:SER22 4.8 5.1 1.0 CA A:GLY114 4.8 6.8 1.0 C5 C:FUC1118 4.8 5.7 1.0 O C:ASN103 4.8 4.0 1.0 N C:ASN103 4.9 4.1 1.0 CA C:ASN103 4.9 3.8 1.0 O5 C:FUC1118 5.0 5.5 1.0

Calcium binding site 7 out of 8 in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1116 b:4.8 occ:1.00 OD1 D:ASP101 2.3 5.9 1.0 OD1 D:ASP99 2.4 7.5 1.0 OE2 D:GLU95 2.4 5.8 1.0 OD2 D:ASP104 2.4 4.7 1.0 O2 D:FUC1118 2.5 5.1 1.0 OE1 D:GLU95 2.5 5.9 1.0 O3 D:FUC1118 2.5 5.3 1.0 OD1 D:ASP104 2.6 4.1 1.0 CD D:GLU95 2.7 5.5 1.0 CG D:ASP104 2.9 3.9 1.0 C2 D:FUC1118 3.3 4.7 1.0 C3 D:FUC1118 3.3 5.1 1.0 CG D:ASP101 3.4 6.0 1.0 CG D:ASP99 3.4 7.3 1.0 OD2 D:ASP99 3.7 7.3 1.0 CA D:CA1117 3.7 3.9 1.0 OD2 D:ASP101 4.0 5.7 1.0 N D:ASP101 4.1 8.2 1.0 CG D:GLU95 4.2 6.0 1.0 OD1 D:ASP96 4.3 7.8 1.0 CB D:ASP104 4.4 3.7 1.0 N D:TYR102 4.4 6.0 1.0 N D:GLY97 4.5 6.4 1.0 CB D:ASP101 4.5 7.9 1.0 N D:ASP96 4.5 5.2 1.0 N D:ASN100 4.6 8.8 1.0 O D:HOH2157 4.7 11.3 1.0 CA D:ASP101 4.7 7.5 1.0 C4 D:FUC1118 4.7 5.2 1.0 CA D:GLU95 4.7 4.4 1.0 C1 D:FUC1118 4.7 5.1 1.0 OD1 D:ASN103 4.7 3.7 1.0 N D:ASP99 4.7 8.5 1.0 CB D:ASP99 4.7 9.0 1.0 CA D:GLY97 4.8 7.2 1.0 O4 D:FUC1118 4.8 4.9 1.0 CB D:GLU95 4.9 5.7 1.0 C D:ASP101 5.0 6.9 1.0 C D:ASP99 5.0 8.8 1.0

Calcium binding site 8 out of 8 in the Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Lacto-N-Neo-Fucopentaose V(Lnpfv) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1117 b:3.9 occ:1.00 OD1 D:ASN103 2.3 3.7 1.0 OD1 D:ASP104 2.3 4.1 1.0 O D:ASN21 2.4 3.7 1.0 O B:GLY114 2.4 5.0 1.0 OD2 D:ASP101 2.4 5.7 1.0 O3 D:FUC1118 2.5 5.3 1.0 O4 D:FUC1118 2.5 4.9 1.0 OD1 D:ASP101 3.1 5.9 1.0 CG D:ASP101 3.1 6.0 1.0 C3 D:FUC1118 3.4 5.1 1.0 CG D:ASN103 3.4 4.1 1.0 C B:GLY114 3.4 5.6 1.0 C4 D:FUC1118 3.5 5.2 1.0 C D:ASN21 3.6 3.8 1.0 CG D:ASP104 3.6 3.9 1.0 OXT B:GLY114 3.7 6.9 1.0 CA D:CA1116 3.7 4.8 1.0 ND2 D:ASN103 3.7 5.2 1.0 C2 D:FUC1118 3.8 4.7 1.0 CB D:ASN21 4.1 4.2 1.0 CA D:ASP104 4.2 3.8 1.0 N D:ASP104 4.3 3.8 1.0 O2 D:FUC1118 4.4 5.1 1.0 N D:SER22 4.4 4.1 1.0 CA D:SER22 4.4 4.1 1.0 OD2 D:ASP104 4.4 4.7 1.0 CB D:ASP104 4.5 3.7 1.0 C D:ASN103 4.5 3.7 1.0 O D:HOH2139 4.5 11.1 1.0 OD2 D:ASP99 4.5 7.3 1.0 CB D:ASP101 4.5 7.9 1.0 CA D:ASN21 4.5 3.6 1.0 CB D:ASN103 4.7 3.9 1.0 CB D:SER22 4.7 4.1 1.0 CA B:GLY114 4.8 6.2 1.0 O D:ASN103 4.8 3.8 1.0 C5 D:FUC1118 4.8 5.0 1.0 N D:ASN103 4.9 4.3 1.0 CA D:ASN103 4.9 3.9 1.0 O5 D:FUC1118 5.0 5.0 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