Calcium in PDB 2jdp: Mutant (S23A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside

The structure of Mutant (S23A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside, PDB code: 2jdp 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)	87.71 / 1.3
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.062, 45.690, 87.952, 90.00, 94.21, 90.00
R / Rfree (%)	16.9 / 19.7

The binding sites of Calcium atom in the Mutant (S23A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside (pdb code 2jdp). 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 (S23A) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside, PDB code: 2jdp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Mutant (S23A) 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 (S23A) 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:14.1 occ:0.70 O A:ASN21 2.3 13.1 1.0 OD1 A:ASN103 2.3 17.3 1.0 O4 A:MFU1115 2.5 22.2 1.0 OD1 A:ASP104 2.5 12.9 1.0 O B:GLY114 2.5 13.9 0.7 O3 A:MFU1115 2.5 24.9 1.0 OD2 A:ASP101 2.5 17.8 0.7 OD1 A:ASP101 3.1 17.0 0.7 CG A:ASP101 3.2 18.1 0.7 C3 A:MFU1115 3.4 22.6 1.0 CG A:ASN103 3.4 13.3 1.0 C4 A:MFU1115 3.5 23.1 1.0 C B:GLY114 3.5 13.3 0.7 C A:ASN21 3.5 12.6 1.0 OXT B:GLY114 3.6 14.4 0.7 CG A:ASP104 3.7 10.9 1.0 CA A:CA1117 3.7 15.4 0.7 ND2 A:ASN103 3.8 12.2 1.0 C2 A:MFU1115 3.8 21.3 1.0 CA A:ASP104 4.1 9.8 1.0 CB A:ASN21 4.2 10.9 1.0 N A:ASP104 4.2 9.0 1.0 CA A:SER22 4.3 13.5 1.0 N A:SER22 4.3 12.2 1.0 C A:ASN103 4.4 10.2 1.0 O A:HOH2140 4.5 27.4 1.0 OD2 A:ASP99 4.5 28.1 1.0 CA A:ASN21 4.5 11.0 1.0 O2 A:MFU1115 4.5 20.8 1.0 CB A:ASP104 4.5 9.6 1.0 OD2 A:ASP104 4.5 12.4 1.0 O A:ASN103 4.6 9.8 1.0 CB A:SER22 4.6 13.8 1.0 CB A:ASP101 4.7 19.9 1.0 CB A:ASN103 4.7 10.4 1.0 C5 A:MFU1115 4.8 23.4 1.0 CA B:GLY114 4.8 12.7 1.0 CA A:ASN103 4.9 10.1 1.0 N A:ASN103 5.0 9.0 1.0 OD1 A:ASP99 5.0 26.8 1.0 O5 A:MFU1115 5.0 22.1 1.0

Calcium binding site 2 out of 8 in the Mutant (S23A) 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 (S23A) 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:Ca1117 b:15.4 occ:0.70 OD1 A:ASP99 2.4 26.8 1.0 OD2 A:ASP104 2.4 12.4 1.0 O3 A:MFU1115 2.5 24.9 1.0 OD1 A:ASP101 2.5 17.0 0.7 OE2 A:GLU95 2.6 15.8 0.7 OD1 A:ASP104 2.6 12.9 1.0 O2 A:MFU1115 2.6 20.8 1.0 OE1 A:GLU95 2.7 14.0 0.7 CG A:ASP104 2.9 10.9 1.0 CD A:GLU95 2.9 13.7 0.7 C2 A:MFU1115 3.4 21.3 1.0 C3 A:MFU1115 3.4 22.6 1.0 CG A:ASP99 3.4 28.0 1.0 CG A:ASP101 3.5 18.1 0.7 CA A:CA1116 3.7 14.1 0.7 OD2 A:ASP99 3.8 28.1 1.0 OD2 A:ASP101 4.0 17.8 0.7 O A:HOH2148 4.1 34.2 1.0 N A:ASP101 4.2 21.7 1.0 OD1 A:ASP96 4.3 19.0 1.0 CB A:ASP104 4.3 9.6 1.0 CG A:GLU95 4.4 13.2 1.0 N A:ASN100 4.5 26.5 1.0 N A:ASP96 4.6 12.3 1.0 OD1 A:ASN103 4.7 17.3 1.0 N A:GLY97 4.7 19.8 1.0 C4 A:MFU1115 4.8 23.1 1.0 CB A:ASP101 4.8 19.9 1.0 N A:ASP99 4.8 27.6 1.0 CB A:ASP99 4.8 28.1 1.0 N A:TYR102 4.8 14.2 1.0 C1 A:MFU1115 4.8 23.6 1.0 CA A:GLU95 4.8 10.6 1.0 O4 A:MFU1115 4.9 22.2 1.0 CA A:ASP101 4.9 19.5 1.0 N A:ASP104 4.9 9.0 1.0 CG A:ASP96 5.0 18.0 1.0

Calcium binding site 3 out of 8 in the Mutant (S23A) 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 (S23A) 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:10.3 occ:0.70 O4 B:MFU1115 2.3 14.4 1.0 OD1 B:ASN103 2.4 13.6 1.0 O B:ASN21 2.4 8.6 1.0 O A:GLY114 2.4 8.2 0.5 OD2 B:ASP101 2.4 14.5 0.7 OD1 B:ASP104 2.5 11.3 1.0 O3 B:MFU1115 2.5 16.6 1.0 OD1 B:ASP101 3.1 14.8 0.7 CG B:ASP101 3.1 15.4 0.7 C4 B:MFU1115 3.3 17.7 1.0 C3 B:MFU1115 3.3 17.9 1.0 C A:GLY114 3.4 8.2 0.5 CG B:ASN103 3.4 11.8 1.0 C B:ASN21 3.6 7.6 1.0 OXT A:GLY114 3.6 8.6 0.5 CG B:ASP104 3.7 8.9 1.0 CA B:CA1117 3.7 12.5 0.7 ND2 B:ASN103 3.8 12.7 1.0 C2 B:MFU1115 3.8 17.9 1.0 CA B:ASP104 4.2 6.5 1.0 N B:ASP104 4.3 6.3 1.0 CB B:ASN21 4.3 7.2 1.0 CA B:SER22 4.3 8.3 1.0 O B:HOH2139 4.4 22.5 1.0 N B:SER22 4.4 7.8 1.0 OD2 B:ASP99 4.4 22.0 1.0 C B:ASN103 4.4 6.9 1.0 O2 B:MFU1115 4.5 17.6 1.0 OD2 B:ASP104 4.5 11.4 1.0 CA A:GLY114 4.5 11.7 0.5 CB B:ASP104 4.6 7.4 1.0 CB B:ASP101 4.6 17.0 1.0 CA B:ASN21 4.6 7.1 1.0 CB B:SER22 4.7 9.0 1.0 C5 B:MFU1115 4.7 18.6 1.0 O B:ASN103 4.7 7.0 1.0 CB B:ASN103 4.7 8.2 1.0 CA A:GLY114 4.8 7.7 0.5 O B:HOH2060 4.9 39.6 1.0 CA B:ASN103 5.0 7.8 1.0 O5 B:MFU1115 5.0 17.1 1.0

Calcium binding site 4 out of 8 in the Mutant (S23A) 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 (S23A) 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:Ca1117 b:12.5 occ:0.70 OD1 B:ASP99 2.3 21.8 1.0 O3 B:MFU1115 2.3 16.6 1.0 OD1 B:ASP101 2.4 14.8 0.7 OE2 B:GLU95 2.5 15.4 1.0 OD2 B:ASP104 2.5 11.4 1.0 O2 B:MFU1115 2.6 17.6 1.0 OE1 B:GLU95 2.6 16.6 1.0 OD1 B:ASP104 2.7 11.3 1.0 CD B:GLU95 2.9 14.5 1.0 CG B:ASP104 3.0 8.9 1.0 C3 B:MFU1115 3.3 17.9 1.0 C2 B:MFU1115 3.3 17.9 1.0 CG B:ASP99 3.3 22.9 1.0 CG B:ASP101 3.4 15.4 0.7 OD2 B:ASP99 3.6 22.0 1.0 CA B:CA1116 3.7 10.3 0.7 OD2 B:ASP101 3.9 14.5 0.7 O B:HOH2137 4.1 23.5 1.0 N B:ASP101 4.1 17.7 1.0 OD1 B:ASP96 4.3 14.6 1.0 CG B:GLU95 4.4 10.9 1.0 N B:ASN100 4.4 22.2 1.0 CB B:ASP104 4.5 7.4 1.0 C4 B:MFU1115 4.6 17.7 1.0 CB B:ASP101 4.6 17.0 1.0 N B:TYR102 4.6 12.0 1.0 OD1 B:ASN103 4.6 13.6 1.0 N B:ASP96 4.6 9.9 1.0 CB B:ASP99 4.7 22.9 1.0 O4 B:MFU1115 4.7 14.4 1.0 N B:GLY97 4.7 15.3 1.0 C1 B:MFU1115 4.7 18.1 1.0 CA B:ASP101 4.8 15.7 1.0 N B:ASP99 4.8 23.4 1.0 CA B:GLU95 4.9 9.3 1.0 C B:ASP99 5.0 23.0 1.0

Calcium binding site 5 out of 8 in the Mutant (S23A) 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 (S23A) 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:12.5 occ:0.70 O3 C:MFU1115 2.3 18.3 1.0 OD1 C:ASN103 2.4 17.7 1.0 O C:ASN21 2.4 11.9 1.0 O4 C:MFU1115 2.4 21.2 1.0 OD1 C:ASP104 2.5 14.1 1.0 O D:GLY114 2.5 10.0 0.5 OD2 C:ASP101 2.5 20.5 0.7 C3 C:MFU1115 3.3 19.4 1.0 CG C:ASP101 3.3 19.6 0.7 OD1 C:ASP101 3.3 19.9 0.7 C4 C:MFU1115 3.3 20.3 1.0 CG C:ASN103 3.4 13.2 1.0 C D:GLY114 3.4 10.5 0.5 OXT D:GLY114 3.6 10.4 0.5 C C:ASN21 3.6 9.9 1.0 ND2 C:ASN103 3.7 11.5 1.0 CG C:ASP104 3.7 10.8 1.0 CA C:CA1117 3.7 14.9 0.7 C2 C:MFU1115 3.8 22.1 1.0 CA C:ASP104 4.3 7.3 1.0 N C:ASP104 4.3 7.8 1.0 CB C:ASN21 4.3 9.7 1.0 CA C:SER22 4.3 11.6 1.0 N C:SER22 4.4 11.1 1.0 C C:ASN103 4.4 7.8 1.0 O C:HOH2147 4.4 30.3 1.0 OD2 C:ASP104 4.5 12.4 1.0 O2 C:MFU1115 4.5 21.3 1.0 CA D:GLY114 4.5 10.9 0.5 OD2 C:ASP99 4.6 25.8 0.7 CB C:ASP104 4.6 8.2 1.0 CA C:ASN21 4.7 8.1 1.0 O C:ASN103 4.7 7.6 1.0 C5 C:MFU1115 4.7 19.1 1.0 CB C:ASP101 4.7 19.6 1.0 CB C:SER22 4.7 11.9 1.0 CB C:ASN103 4.7 9.6 1.0 CA D:GLY114 4.8 10.1 0.5 O5 C:MFU1115 4.9 18.6 1.0 OD1 C:ASP99 4.9 22.0 0.7 CA C:ASN103 5.0 9.2 1.0

Calcium binding site 6 out of 8 in the Mutant (S23A) 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 (S23A) 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:Ca1117 b:14.9 occ:0.70 OD1 C:ASP99 2.3 22.0 0.7 O3 C:MFU1115 2.3 18.3 1.0 OD1 C:ASP101 2.4 19.9 0.7 OE2 C:GLU95 2.5 18.9 1.0 OD2 C:ASP104 2.5 12.4 1.0 O2 C:MFU1115 2.6 21.3 1.0 OD1 C:ASP104 2.7 14.1 1.0 OE1 C:GLU95 2.7 19.2 1.0 CD C:GLU95 3.0 18.4 1.0 CG C:ASP104 3.0 10.8 1.0 C3 C:MFU1115 3.2 19.4 1.0 C2 C:MFU1115 3.3 22.1 1.0 CG C:ASP99 3.4 25.3 0.7 CG C:ASP101 3.4 19.6 0.7 CA C:CA1116 3.7 12.5 0.7 OD2 C:ASP99 3.7 25.8 0.7 OD2 C:ASP101 3.8 20.5 0.7 OD1 C:ASP96 4.3 17.9 1.0 N C:ASP101 4.3 20.8 1.0 N C:ASN100 4.4 24.7 1.0 CG C:GLU95 4.5 14.6 1.0 CB C:ASP104 4.5 8.2 1.0 OD1 C:ASN103 4.5 17.7 1.0 C4 C:MFU1115 4.6 20.3 1.0 N C:GLY97 4.6 19.4 1.0 N C:ASP99 4.7 25.7 1.0 CB C:ASP99 4.7 25.7 1.0 C1 C:MFU1115 4.7 21.0 1.0 CB C:ASP101 4.7 19.6 1.0 N C:TYR102 4.7 14.1 1.0 N C:ASP96 4.8 13.0 1.0 O4 C:MFU1115 4.8 21.2 1.0 CA C:GLY97 4.9 21.1 1.0 CA C:ASP101 4.9 18.7 1.0 C C:ASP99 5.0 25.4 1.0 CA C:ASP99 5.0 25.7 1.0 CA C:GLU95 5.0 11.1 1.0

Calcium binding site 7 out of 8 in the Mutant (S23A) 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 (S23A) 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:12.2 occ:0.70 OD1 D:ASN103 2.3 18.9 1.0 O D:ASN21 2.3 11.0 1.0 O4 D:MFU1115 2.4 18.6 1.0 O C:GLY114 2.5 12.7 0.7 OD1 D:ASP104 2.5 13.1 1.0 OD2 D:ASP101 2.5 14.5 0.7 O3 D:MFU1115 2.5 17.9 1.0 OD1 D:ASP101 3.2 14.6 0.7 CG D:ASP101 3.2 16.5 0.7 CG D:ASN103 3.2 16.4 1.0 C3 D:MFU1115 3.4 17.1 1.0 C C:GLY114 3.4 12.3 0.7 C4 D:MFU1115 3.4 18.4 1.0 C D:ASN21 3.5 8.6 1.0 ND2 D:ASN103 3.6 16.8 1.0 OXT C:GLY114 3.6 13.5 0.7 CG D:ASP104 3.7 10.0 1.0 CA D:CA1117 3.7 13.2 0.7 C2 D:MFU1115 3.8 17.7 1.0 N D:ASP104 4.1 8.2 1.0 CB D:ASN21 4.1 7.4 1.0 CA D:ASP104 4.1 7.3 1.0 O D:HOH2144 4.3 28.8 1.0 C D:ASN103 4.3 9.0 1.0 N D:SER22 4.4 9.0 1.0 CA D:SER22 4.4 10.7 1.0 O2 D:MFU1115 4.5 18.5 1.0 CB D:ASP104 4.5 7.9 1.0 CA D:ASN21 4.5 7.9 1.0 OD2 D:ASP104 4.5 14.3 1.0 OD2 D:ASP99 4.5 25.1 1.0 CB D:ASN103 4.5 11.0 1.0 CB D:SER22 4.7 11.3 1.0 CB D:ASP101 4.7 17.2 1.0 C5 D:MFU1115 4.7 18.3 1.0 O D:ASN103 4.7 10.4 1.0 CA C:GLY114 4.8 11.4 1.0 CA D:ASN103 4.8 9.5 1.0 N D:ASN103 4.9 9.0 1.0

Calcium binding site 8 out of 8 in the Mutant (S23A) 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 (S23A) 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:Ca1117 b:13.2 occ:0.70 OD1 D:ASP101 2.3 14.6 0.7 O3 D:MFU1115 2.3 17.9 1.0 OD1 D:ASP99 2.4 23.5 1.0 OE2 D:GLU95 2.4 15.0 1.0 OD2 D:ASP104 2.4 14.3 1.0 O2 D:MFU1115 2.5 18.5 1.0 OD1 D:ASP104 2.6 13.1 1.0 OE1 D:GLU95 2.6 15.6 1.0 CG D:ASP104 2.9 10.0 1.0 CD D:GLU95 2.9 14.4 1.0 C3 D:MFU1115 3.3 17.1 1.0 C2 D:MFU1115 3.3 17.7 1.0 CG D:ASP99 3.4 23.4 1.0 CG D:ASP101 3.4 16.5 0.7 CA D:CA1116 3.7 12.2 0.7 OD2 D:ASP99 3.7 25.1 1.0 OD2 D:ASP101 3.9 14.5 0.7 OD1 D:ASP96 4.2 19.9 1.0 N D:ASP101 4.3 18.9 1.0 OD1 D:ASN103 4.3 18.9 1.0 CB D:ASP104 4.3 7.9 1.0 CG D:GLU95 4.4 11.6 1.0 N D:ASN100 4.6 22.6 1.0 N D:ASP96 4.6 12.7 1.0 N D:TYR102 4.6 12.4 1.0 N D:GLY97 4.6 18.5 1.0 C4 D:MFU1115 4.6 18.4 1.0 CB D:ASP101 4.7 17.2 1.0 CB D:ASP99 4.7 23.9 1.0 O4 D:MFU1115 4.8 18.6 1.0 C1 D:MFU1115 4.8 17.3 1.0 CA D:GLU95 4.8 9.5 1.0 N D:ASP99 4.8 24.5 1.0 CA D:ASP101 4.8 17.3 1.0 N D:ASP104 4.8 8.2 1.0 CA D:GLY97 5.0 20.5 1.0 CG D:ASP96 5.0 17.6 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