Calcium in PDB 2jdm: Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside

The structure of Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside, PDB code: 2jdm was solved by J.Adam, M.Pokorna, C.Sabin, E.P.Mitchell, A.Imberty, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.80 / 1.7
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.674, 73.090, 54.917, 90.00, 94.25, 90.00
R / Rfree (%)	17.4 / 22.3

The binding sites of Calcium atom in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside (pdb code 2jdm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside, PDB code: 2jdm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1115 b:8.8 occ:1.00 OD1 A:ASP99 2.3 10.1 1.0 OD1 A:ASP101 2.3 6.5 1.0 OD2 A:ASP104 2.4 8.1 1.0 OE1 A:GLU95 2.4 8.6 1.0 OE2 A:GLU95 2.5 8.4 1.0 O3 A:FUC1118 2.5 5.3 1.0 O2 A:FUC1118 2.6 5.2 1.0 OD1 A:ASP104 2.7 5.4 1.0 CD A:GLU95 2.8 9.1 1.0 CG A:ASP104 2.9 5.3 1.0 C2 A:FUC1118 3.3 7.4 1.0 CG A:ASP99 3.4 10.7 1.0 C3 A:FUC1118 3.4 7.8 1.0 CG A:ASP101 3.4 8.6 1.0 OD2 A:ASP99 3.7 11.4 1.0 CA A:CA1116 3.8 7.7 1.0 OD2 A:ASP101 3.9 8.0 1.0 N A:ASP101 4.1 9.6 1.0 CG A:GLU95 4.3 8.4 1.0 OD1 A:ASP96 4.4 9.9 1.0 O A:HOH2126 4.4 14.6 1.0 N A:TYR102 4.4 6.9 1.0 CB A:ASP104 4.4 4.6 1.0 N A:ASN100 4.5 10.1 1.0 N A:ASP96 4.6 8.1 1.0 CB A:ASP101 4.6 9.1 1.0 CA A:ASP101 4.7 8.0 1.0 N A:GLY97 4.7 8.8 1.0 CB A:ASP99 4.7 10.6 1.0 C4 A:FUC1118 4.7 7.2 1.0 CA A:GLU95 4.8 7.5 1.0 N A:ASP99 4.8 11.1 1.0 OD1 A:ASN103 4.8 6.2 1.0 C1 A:FUC1118 4.8 10.1 1.0 O4 A:FUC1118 4.9 5.8 1.0 CB A:GLU95 5.0 7.5 1.0 C A:ASP101 5.0 7.9 1.0 C A:ASP99 5.0 10.4 1.0

Calcium binding site 2 out of 8 in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1116 b:7.7 occ:1.00 O A:ASN21 2.3 4.8 1.0 OD1 A:ASN103 2.3 6.2 1.0 OD1 A:ASP104 2.4 5.4 1.0 OD2 A:ASP101 2.4 8.0 1.0 O B:GLY114 2.5 7.5 1.0 O4 A:FUC1118 2.5 5.8 1.0 O3 A:FUC1118 2.5 5.3 1.0 OD1 A:ASP101 3.1 6.5 1.0 CG A:ASP101 3.1 8.6 1.0 C4 A:FUC1118 3.4 7.2 1.0 C3 A:FUC1118 3.4 7.8 1.0 CG A:ASN103 3.4 7.0 1.0 C B:GLY114 3.4 8.4 1.0 C A:ASN21 3.5 5.2 1.0 OXT B:GLY114 3.6 9.3 1.0 CG A:ASP104 3.6 5.3 1.0 CA A:CA1115 3.8 8.8 1.0 ND2 A:ASN103 3.8 8.0 1.0 C2 A:FUC1118 3.8 7.4 1.0 CB A:ASN21 4.1 5.6 1.0 CA A:ASP104 4.2 4.9 1.0 N A:ASP104 4.2 5.1 1.0 O A:HOH2133 4.3 14.3 1.0 N A:ALA22 4.4 5.3 1.0 CA A:ALA22 4.4 5.7 1.0 OD2 A:ASP104 4.5 8.1 1.0 C A:ASN103 4.5 5.7 1.0 CB A:ASP104 4.5 4.6 1.0 O2 A:FUC1118 4.5 5.2 1.0 CA A:ASN21 4.5 4.7 1.0 OD2 A:ASP99 4.5 11.4 1.0 CB A:ASP101 4.6 9.1 1.0 CB A:ALA22 4.6 6.4 1.0 CB A:ASN103 4.7 6.6 1.0 C5 A:FUC1118 4.7 7.9 1.0 CA B:GLY114 4.8 8.2 1.0 O A:ASN103 4.8 4.7 1.0 N A:ASN103 4.9 6.0 1.0 CA A:ASN103 5.0 6.3 1.0

Calcium binding site 3 out of 8 in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1115 b:6.4 occ:1.00 OD1 B:ASN103 2.3 4.3 1.0 O3 B:MFU1117 2.4 4.8 1.0 OD2 B:ASP101 2.4 9.3 1.0 O B:ASN21 2.4 8.4 1.0 OD1 B:ASP104 2.5 5.7 1.0 O A:GLY114 2.5 6.7 1.0 O4 B:MFU1117 2.5 8.7 1.0 OD1 B:ASP101 3.0 7.1 1.0 CG B:ASP101 3.0 6.8 1.0 C3 B:MFU1117 3.3 9.5 1.0 CG B:ASN103 3.4 6.3 1.0 C4 B:MFU1117 3.4 9.6 1.0 C A:GLY114 3.4 8.5 1.0 OXT A:GLY114 3.6 9.9 1.0 C B:ASN21 3.6 8.0 1.0 CG B:ASP104 3.7 5.0 1.0 CA B:CA1116 3.7 7.2 1.0 ND2 B:ASN103 3.8 6.2 1.0 C2 B:MFU1117 3.9 9.2 1.0 N B:ASP104 4.2 5.0 1.0 CA B:ASP104 4.3 5.2 1.0 CB B:ASN21 4.3 7.3 1.0 CA B:ALA22 4.4 8.2 1.0 O B:HOH2127 4.4 27.7 1.0 O B:HOH2129 4.4 13.3 1.0 N B:ALA22 4.5 8.5 1.0 C B:ASN103 4.5 5.2 1.0 CB B:ASP101 4.5 6.0 1.0 OD2 B:ASP104 4.5 8.2 1.0 O2 B:MFU1117 4.5 5.6 1.0 CB B:ASP104 4.6 5.7 1.0 CB B:ALA22 4.6 8.6 1.0 OD2 B:ASP99 4.6 9.1 1.0 CA B:ASN21 4.6 7.3 1.0 CB B:ASN103 4.7 5.2 1.0 C5 B:MFU1117 4.8 9.4 1.0 O B:ASN103 4.8 4.9 1.0 CA A:GLY114 4.8 7.7 1.0 N B:ASN103 4.9 5.3 1.0 CA B:ASN103 4.9 5.5 1.0

Calcium binding site 4 out of 8 in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1116 b:7.2 occ:1.00 OD1 B:ASP101 2.4 7.1 1.0 OD1 B:ASP99 2.4 6.3 1.0 OD2 B:ASP104 2.5 8.2 1.0 O3 B:MFU1117 2.5 4.8 1.0 OE1 B:GLU95 2.5 6.5 1.0 O2 B:MFU1117 2.5 5.6 1.0 OE2 B:GLU95 2.5 6.1 1.0 OD1 B:ASP104 2.6 5.7 1.0 CD B:GLU95 2.8 6.1 1.0 CG B:ASP104 2.9 5.0 1.0 C2 B:MFU1117 3.3 9.2 1.0 C3 B:MFU1117 3.3 9.5 1.0 CG B:ASP99 3.4 7.8 1.0 CG B:ASP101 3.4 6.8 1.0 CA B:CA1115 3.7 6.4 1.0 OD2 B:ASP99 3.7 9.1 1.0 OD2 B:ASP101 4.0 9.3 1.0 N B:ASP101 4.1 5.9 1.0 O B:HOH2133 4.2 10.8 1.0 OD1 B:ASP96 4.3 8.2 1.0 CG B:GLU95 4.3 5.4 1.0 N B:TYR102 4.4 5.3 1.0 CB B:ASP104 4.4 5.7 1.0 N B:ASN100 4.5 7.1 1.0 N B:ASP96 4.5 6.5 1.0 CB B:ASP101 4.6 6.0 1.0 C4 B:MFU1117 4.6 9.6 1.0 CA B:ASP101 4.7 5.8 1.0 OD1 B:ASN103 4.7 4.3 1.0 CA B:GLU95 4.7 5.1 1.0 C1 B:MFU1117 4.7 10.8 1.0 N B:GLY97 4.7 7.8 1.0 CB B:ASP99 4.8 8.9 1.0 O4 B:MFU1117 4.8 8.7 1.0 N B:ASP99 4.9 9.7 1.0 CG B:ASP96 4.9 8.8 1.0 CB B:GLU95 4.9 5.5 1.0 C B:ASP101 5.0 5.9 1.0 N B:ASP104 5.0 5.0 1.0

Calcium binding site 5 out of 8 in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1115 b:7.9 occ:1.00 O3 C:MFU1117 2.4 7.7 1.0 OD1 C:ASN103 2.4 3.8 1.0 O C:ASN21 2.4 6.0 1.0 O4 C:MFU1117 2.4 8.2 1.0 OD2 C:ASP101 2.4 9.2 1.0 OD1 C:ASP104 2.5 7.0 1.0 O D:GLY114 2.6 7.3 1.0 OD1 C:ASP101 3.1 9.9 1.0 CG C:ASP101 3.1 9.6 1.0 C3 C:MFU1117 3.2 9.7 1.0 C4 C:MFU1117 3.3 9.2 1.0 CG C:ASN103 3.4 5.5 1.0 C D:GLY114 3.5 8.0 1.0 C C:ASN21 3.6 6.6 1.0 OXT D:GLY114 3.6 9.6 1.0 CA C:CA1116 3.7 9.4 1.0 CG C:ASP104 3.7 6.6 1.0 C2 C:MFU1117 3.8 9.9 1.0 ND2 C:ASN103 3.8 6.7 1.0 CA C:ASP104 4.2 6.4 1.0 CB C:ASN21 4.2 7.1 1.0 N C:ASP104 4.3 6.0 1.0 CA C:ALA22 4.3 7.7 1.0 N C:ALA22 4.4 7.5 1.0 C C:ASN103 4.5 6.2 1.0 O2 C:MFU1117 4.5 8.1 1.0 OD2 C:ASP99 4.5 11.1 1.0 CB C:ALA22 4.5 8.4 1.0 CB C:ASP104 4.5 6.2 1.0 O C:HOH2112 4.5 14.8 1.0 OD2 C:ASP104 4.6 7.6 1.0 O C:HOH2110 4.6 26.5 1.0 CA C:ASN21 4.6 6.5 1.0 CB C:ASP101 4.6 8.3 1.0 C5 C:MFU1117 4.7 9.6 1.0 O C:ASN103 4.7 5.8 1.0 CB C:ASN103 4.8 5.9 1.0 CA D:GLY114 4.9 8.8 1.0 N C:ASN103 4.9 6.3 1.0 CA C:ASN103 5.0 5.8 1.0 O5 C:MFU1117 5.0 10.2 1.0 OD1 C:ASP99 5.0 12.2 1.0

Calcium binding site 6 out of 8 in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1116 b:9.4 occ:1.00 OD1 C:ASP101 2.4 9.9 1.0 O3 C:MFU1117 2.4 7.7 1.0 OD1 C:ASP99 2.4 12.2 1.0 OE2 C:GLU95 2.5 7.6 1.0 OD2 C:ASP104 2.5 7.6 1.0 O2 C:MFU1117 2.5 8.1 1.0 OD1 C:ASP104 2.6 7.0 1.0 OE1 C:GLU95 2.6 7.6 1.0 CD C:GLU95 2.9 7.6 1.0 CG C:ASP104 2.9 6.6 1.0 C3 C:MFU1117 3.3 9.7 1.0 C2 C:MFU1117 3.3 9.9 1.0 CG C:ASP99 3.4 11.9 1.0 CG C:ASP101 3.4 9.6 1.0 CA C:CA1115 3.7 7.9 1.0 OD2 C:ASP99 3.7 11.1 1.0 OD2 C:ASP101 4.0 9.2 1.0 O C:HOH2107 4.2 18.0 1.0 N C:ASP101 4.2 9.2 1.0 OD1 C:ASP96 4.2 9.6 1.0 CG C:GLU95 4.4 8.6 1.0 CB C:ASP104 4.4 6.2 1.0 N C:TYR102 4.4 6.1 1.0 N C:ASN100 4.6 10.8 1.0 N C:ASP96 4.6 6.9 1.0 CB C:ASP101 4.6 8.3 1.0 C4 C:MFU1117 4.6 9.2 1.0 N C:GLY97 4.7 9.6 1.0 CA C:ASP101 4.7 8.3 1.0 CB C:ASP99 4.7 11.5 1.0 C1 C:MFU1117 4.8 10.7 1.0 OD1 C:ASN103 4.8 3.8 1.0 O4 C:MFU1117 4.8 8.2 1.0 CA C:GLU95 4.8 7.3 1.0 N C:ASP99 4.8 12.6 1.0 C C:ASP101 4.9 7.8 1.0 CG C:ASP96 5.0 9.3 1.0

Calcium binding site 7 out of 8 in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1115 b:8.1 occ:1.00 O D:ASN21 2.4 8.4 1.0 OD1 D:ASN103 2.4 6.2 1.0 O C:GLY114 2.4 8.0 1.0 OD1 D:ASP104 2.5 6.2 1.0 O3 D:MFU1117 2.5 7.3 1.0 OD2 D:ASP101 2.5 6.5 1.0 O4 D:MFU1117 2.5 8.1 1.0 OD1 D:ASP101 3.1 7.5 1.0 CG D:ASP101 3.2 8.3 1.0 C3 D:MFU1117 3.3 9.8 1.0 C4 D:MFU1117 3.4 10.4 1.0 CG D:ASN103 3.4 4.8 1.0 C C:GLY114 3.4 9.5 1.0 C D:ASN21 3.6 8.5 1.0 OXT C:GLY114 3.6 10.2 1.0 CG D:ASP104 3.7 7.0 1.0 CA D:CA1116 3.8 9.1 1.0 ND2 D:ASN103 3.8 8.0 1.0 C2 D:MFU1117 3.8 11.2 1.0 CB D:ASN21 4.2 8.4 1.0 CA D:ASP104 4.2 6.2 1.0 N D:ASP104 4.2 5.4 1.0 CA D:ALA22 4.4 9.3 1.0 N D:ALA22 4.5 8.4 1.0 C D:ASN103 4.5 5.7 1.0 O2 D:MFU1117 4.5 9.3 1.0 OD2 D:ASP104 4.5 7.2 1.0 CB D:ASP104 4.5 5.9 1.0 CA D:ASN21 4.5 8.0 1.0 CB D:ALA22 4.5 9.1 1.0 OD2 D:ASP99 4.6 11.7 1.0 CB D:ASP101 4.6 8.1 1.0 O D:HOH2122 4.7 11.7 1.0 CB D:ASN103 4.7 5.3 1.0 C5 D:MFU1117 4.8 10.5 1.0 CA C:GLY114 4.8 8.7 1.0 O D:ASN103 4.8 5.7 1.0 N D:ASN103 4.9 6.0 1.0 CA D:ASN103 5.0 5.0 1.0

Calcium binding site 8 out of 8 in the Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mutant (S22A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1116 b:9.1 occ:1.00 OD1 D:ASP101 2.3 7.5 1.0 OD1 D:ASP99 2.3 11.4 1.0 OE2 D:GLU95 2.4 10.4 1.0 O3 D:MFU1117 2.5 7.3 1.0 OE1 D:GLU95 2.5 9.0 1.0 OD2 D:ASP104 2.5 7.2 1.0 O2 D:MFU1117 2.6 9.3 1.0 OD1 D:ASP104 2.7 6.2 1.0 CD D:GLU95 2.8 10.2 1.0 CG D:ASP104 3.0 7.0 1.0 C2 D:MFU1117 3.4 11.2 1.0 CG D:ASP99 3.4 12.7 1.0 C3 D:MFU1117 3.4 9.8 1.0 CG D:ASP101 3.4 8.3 1.0 OD2 D:ASP99 3.7 11.7 1.0 CA D:CA1115 3.8 8.1 1.0 OD2 D:ASP101 4.0 6.5 1.0 N D:ASP101 4.1 9.4 1.0 OD1 D:ASP96 4.2 11.1 1.0 O D:HOH2119 4.2 16.1 1.0 CG D:GLU95 4.3 8.3 1.0 N D:TYR102 4.4 8.0 1.0 CB D:ASP104 4.5 5.9 1.0 N D:ASN100 4.5 11.1 1.0 N D:ASP96 4.5 7.4 1.0 CB D:ASP101 4.6 8.1 1.0 N D:GLY97 4.6 11.0 1.0 CA D:ASP101 4.7 8.5 1.0 CB D:ASP99 4.7 12.2 1.0 C4 D:MFU1117 4.7 10.4 1.0 CA D:GLU95 4.8 7.0 1.0 OD1 D:ASN103 4.8 6.2 1.0 N D:ASP99 4.8 12.5 1.0 C1 D:MFU1117 4.8 11.4 1.0 O4 D:MFU1117 4.9 8.1 1.0 CA D:GLY97 4.9 11.2 1.0 C D:ASP99 4.9 11.9 1.0 CB D:GLU95 4.9 7.6 1.0 CG D:ASP96 4.9 10.9 1.0 C D:ASP101 5.0 8.1 1.0 CA D:ASP99 5.0 12.0 1.0

J.Adam, M.Pokorna, C.Sabin, E.P.Mitchell, A.Imberty, M.Wimmerova. Engineering of Pa-Iil Lectin From Pseudomonas Aeruginosa - Unravelling the Role of the Specificity Loop For Sugar Preference. Bmc Struct.Biol. V. 7 36 2007.
ISSN: ISSN 1472-6807
PubMed: 17540045
DOI: 10.1186/1472-6807-7-36