Calcium in PDB 2jdy: Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside

The structure of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside, PDB code: 2jdy 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)	49.45 / 1.7
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.383, 80.085, 52.493, 90.00, 109.55, 90.00
R / Rfree (%)	14.2 / 17.3

The binding sites of Calcium atom in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside (pdb code 2jdy). 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 (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside, PDB code: 2jdy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1116 b:6.2 occ:1.00 OD1 A:ASN103 2.3 3.8 1.0 O A:ASN21 2.3 4.2 1.0 OD1 A:ASP104 2.4 4.5 1.0 O B:GLY114 2.4 5.6 1.0 OD2 A:ASP101 2.5 4.7 1.0 O2 A:MMA1115 2.5 4.5 1.0 O3 A:MMA1115 2.5 4.3 1.0 OD1 A:ASP101 3.1 3.1 1.0 CG A:ASP101 3.2 5.0 1.0 CG A:ASN103 3.4 5.3 1.0 C B:GLY114 3.4 6.9 1.0 C3 A:MMA1115 3.5 8.5 1.0 C2 A:MMA1115 3.5 6.6 1.0 C A:ASN21 3.5 4.5 1.0 CG A:ASP104 3.6 4.6 1.0 OXT B:GLY114 3.7 7.0 1.0 CA A:CA1117 3.7 6.0 1.0 ND2 A:ASN103 3.9 5.5 1.0 C4 A:MMA1115 3.9 8.1 1.0 CA A:ASP104 4.1 4.1 1.0 CB A:ASN21 4.1 4.5 1.0 N A:ASP104 4.1 3.6 1.0 CA A:SER22 4.4 5.1 1.0 N A:SER22 4.4 5.3 1.0 C A:ASN103 4.4 4.4 1.0 CB A:ASP104 4.4 4.1 1.0 OD2 A:ASP104 4.4 5.3 1.0 O A:HOH2100 4.5 11.9 1.0 CA A:ASN21 4.5 4.5 1.0 OD2 A:ASP99 4.5 8.8 1.0 O4 A:MMA1115 4.6 6.5 1.0 CB A:ASP101 4.6 4.5 1.0 CB A:SER22 4.7 6.1 1.0 CB A:ASN103 4.7 4.7 1.0 CA B:GLY114 4.8 5.7 1.0 O A:ASN103 4.8 4.6 1.0 C1 A:MMA1115 4.8 7.9 1.0 N A:ASN103 4.9 4.1 1.0 CA A:ASN103 4.9 4.5 1.0

Calcium binding site 2 out of 8 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1117 b:6.0 occ:1.00 OD1 A:ASP99 2.3 7.2 1.0 OD1 A:ASP101 2.3 3.1 1.0 OE1 A:GLU95 2.4 7.1 1.0 OE2 A:GLU95 2.5 6.5 1.0 O3 A:MMA1115 2.5 4.3 1.0 OD2 A:ASP104 2.5 5.3 1.0 O4 A:MMA1115 2.6 6.5 1.0 OD1 A:ASP104 2.7 4.5 1.0 CD A:GLU95 2.8 7.0 1.0 CG A:ASP104 3.0 4.6 1.0 CG A:ASP99 3.3 8.5 1.0 C4 A:MMA1115 3.4 8.1 1.0 CG A:ASP101 3.4 5.0 1.0 C3 A:MMA1115 3.4 8.5 1.0 OD2 A:ASP99 3.7 8.8 1.0 CA A:CA1116 3.7 6.2 1.0 OD2 A:ASP101 4.0 4.7 1.0 OD1 A:ASP96 4.0 8.5 1.0 N A:ASP101 4.1 6.2 1.0 CG A:GLU95 4.3 5.0 1.0 O A:HOH2107 4.3 13.6 1.0 N A:TYR102 4.4 4.7 1.0 N A:ASN100 4.4 8.1 1.0 CB A:ASP104 4.5 4.1 1.0 N A:ASP96 4.5 5.4 1.0 CB A:ASP101 4.6 4.5 1.0 N A:GLY97 4.6 6.6 1.0 CB A:ASP99 4.7 8.7 1.0 CA A:ASP101 4.7 4.7 1.0 CA A:GLU95 4.7 4.4 1.0 N A:ASP99 4.8 9.4 1.0 OD1 A:ASN103 4.8 3.8 1.0 C2 A:MMA1115 4.8 6.6 1.0 C5 A:MMA1115 4.8 7.0 1.0 O2 A:MMA1115 4.9 4.5 1.0 C A:ASP99 4.9 8.7 1.0 CG A:ASP96 4.9 6.8 1.0 C A:ASP101 4.9 5.3 1.0 CB A:GLU95 4.9 4.2 1.0 CA A:ASP99 5.0 8.8 1.0

Calcium binding site 3 out of 8 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1116 b:9.2 occ:1.00 OD1 B:ASP99 2.3 10.0 1.0 OD1 B:ASP101 2.3 8.2 1.0 O3 B:MMA1115 2.5 7.8 1.0 OE2 B:GLU95 2.5 11.1 1.0 OE1 B:GLU95 2.5 7.9 1.0 OD2 B:ASP104 2.5 10.3 1.0 O4 B:MMA1115 2.6 7.3 1.0 OD1 B:ASP104 2.7 6.3 1.0 CD B:GLU95 2.8 8.6 1.0 CG B:ASP104 3.0 8.3 1.0 CG B:ASP99 3.3 11.6 1.0 C4 B:MMA1115 3.4 10.0 1.0 CG B:ASP101 3.4 7.9 1.0 C3 B:MMA1115 3.4 11.2 1.0 OD2 B:ASP99 3.6 10.8 1.0 CA B:CA1117 3.7 7.3 1.0 OD2 B:ASP101 3.9 6.9 1.0 N B:ASP101 4.0 8.4 1.0 OD1 B:ASP96 4.0 12.1 1.0 O B:HOH2102 4.2 14.7 1.0 CG B:GLU95 4.3 7.9 1.0 N B:TYR102 4.4 6.9 1.0 N B:ASN100 4.4 10.7 1.0 CB B:ASP104 4.5 5.9 1.0 CB B:ASP101 4.5 6.8 1.0 N B:ASP96 4.6 7.6 1.0 CA B:ASP101 4.7 7.9 1.0 CB B:ASP99 4.7 11.6 1.0 N B:GLY97 4.7 10.3 1.0 OD1 B:ASN103 4.7 4.6 1.0 C2 B:MMA1115 4.7 11.0 1.0 CA B:GLU95 4.7 7.2 1.0 N B:ASP99 4.8 12.6 1.0 C5 B:MMA1115 4.8 13.7 1.0 O2 B:MMA1115 4.9 8.3 1.0 C B:ASP99 4.9 11.5 1.0 C B:ASP101 4.9 8.1 1.0 CB B:GLU95 4.9 7.6 1.0 CA B:ASN100 5.0 10.9 1.0

Calcium binding site 4 out of 8 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1117 b:7.3 occ:1.00 OD1 B:ASN103 2.3 4.6 1.0 O B:ASN21 2.3 5.2 1.0 OD1 B:ASP104 2.4 6.3 1.0 O A:GLY114 2.5 7.4 1.0 O3 B:MMA1115 2.5 7.8 1.0 O2 B:MMA1115 2.5 8.3 1.0 OD2 B:ASP101 2.5 6.9 1.0 OD1 B:ASP101 3.1 8.2 1.0 CG B:ASP101 3.2 7.9 1.0 CG B:ASN103 3.3 5.8 1.0 C3 B:MMA1115 3.4 11.2 1.0 C2 B:MMA1115 3.4 11.0 1.0 C A:GLY114 3.5 8.5 1.0 C B:ASN21 3.5 5.7 1.0 CG B:ASP104 3.6 8.3 1.0 OXT A:GLY114 3.7 9.1 1.0 CA B:CA1116 3.7 9.2 1.0 ND2 B:ASN103 3.8 7.2 1.0 C4 B:MMA1115 3.9 10.0 1.0 CA B:ASP104 4.1 6.0 1.0 N B:ASP104 4.1 5.2 1.0 CB B:ASN21 4.2 5.8 1.0 CA B:SER22 4.3 6.6 1.0 N B:SER22 4.4 6.8 1.0 CB B:ASP104 4.4 5.9 1.0 C B:ASN103 4.4 5.2 1.0 OD2 B:ASP104 4.5 10.3 1.0 CA B:ASN21 4.5 6.0 1.0 O B:HOH2095 4.5 14.7 1.0 OD2 B:ASP99 4.5 10.8 1.0 O4 B:MMA1115 4.6 7.3 1.0 CB B:ASP101 4.6 6.8 1.0 CB B:SER22 4.7 6.8 1.0 CB B:ASN103 4.7 5.2 1.0 O B:ASN103 4.8 5.5 1.0 C1 B:MMA1115 4.8 11.3 1.0 CA A:GLY114 4.8 7.3 1.0 N B:ASN103 4.9 6.0 1.0 CA B:ASN103 4.9 4.9 1.0

Calcium binding site 5 out of 8 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1116 b:6.6 occ:1.00 OD1 C:ASP99 2.3 9.0 1.0 OD1 C:ASP101 2.3 7.1 1.0 OE1 C:GLU95 2.4 7.5 1.0 OE2 C:GLU95 2.5 7.5 1.0 OD2 C:ASP104 2.5 7.6 1.0 O3 C:MMA1115 2.6 4.6 1.0 O4 C:MMA1115 2.7 6.4 1.0 OD1 C:ASP104 2.7 5.2 1.0 CD C:GLU95 2.8 8.0 1.0 CG C:ASP104 3.0 4.7 1.0 CG C:ASP99 3.4 9.3 1.0 CG C:ASP101 3.4 7.8 1.0 C4 C:MMA1115 3.4 8.8 1.0 C3 C:MMA1115 3.5 7.1 1.0 OD2 C:ASP99 3.7 11.6 1.0 CA C:CA1117 3.7 6.5 1.0 OD2 C:ASP101 4.0 5.1 1.0 N C:ASP101 4.0 7.8 1.0 OD1 C:ASP96 4.1 8.7 1.0 O C:HOH2108 4.2 15.9 1.0 CG C:GLU95 4.3 7.1 1.0 N C:TYR102 4.4 5.4 1.0 N C:ASN100 4.4 8.4 1.0 CB C:ASP104 4.5 4.0 1.0 CB C:ASP101 4.5 7.1 1.0 N C:ASP96 4.6 7.0 1.0 N C:GLY97 4.6 8.4 1.0 CA C:ASP101 4.6 7.2 1.0 OD1 C:ASN103 4.7 4.8 1.0 CB C:ASP99 4.7 9.3 1.0 CA C:GLU95 4.8 6.0 1.0 C2 C:MMA1115 4.8 9.6 1.0 N C:ASP99 4.8 10.4 1.0 O2 C:MMA1115 4.9 6.6 1.0 C5 C:MMA1115 4.9 9.8 1.0 CB C:GLU95 4.9 5.8 1.0 C C:ASP101 4.9 7.2 1.0 C C:ASP99 5.0 9.6 1.0 CA C:ASN100 5.0 9.2 1.0 C C:ASN100 5.0 8.7 1.0

Calcium binding site 6 out of 8 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1117 b:6.5 occ:1.00 OD1 C:ASN103 2.3 4.8 1.0 O C:ASN21 2.4 3.8 1.0 OD1 C:ASP104 2.4 5.2 1.0 O3 C:MMA1115 2.5 4.6 1.0 OD2 C:ASP101 2.5 5.1 1.0 O D:GLY114 2.5 7.1 1.0 O2 C:MMA1115 2.5 6.6 1.0 OD1 C:ASP101 3.1 7.1 1.0 CG C:ASP101 3.2 7.8 1.0 CG C:ASN103 3.3 5.5 1.0 C3 C:MMA1115 3.4 7.1 1.0 C2 C:MMA1115 3.5 9.6 1.0 C D:GLY114 3.5 8.0 1.0 C C:ASN21 3.6 4.5 1.0 CG C:ASP104 3.6 4.7 1.0 OXT D:GLY114 3.7 9.7 1.0 ND2 C:ASN103 3.7 5.5 1.0 CA C:CA1116 3.7 6.6 1.0 C4 C:MMA1115 3.9 8.8 1.0 CA C:ASP104 4.1 3.6 1.0 N C:ASP104 4.1 3.1 1.0 CB C:ASN21 4.2 4.8 1.0 CA C:SER22 4.4 6.2 1.0 N C:SER22 4.4 5.8 1.0 OD2 C:ASP104 4.4 7.6 1.0 CB C:ASP104 4.4 4.0 1.0 C C:ASN103 4.4 4.3 1.0 O C:HOH2103 4.4 12.4 1.0 CA C:ASN21 4.5 5.0 1.0 OD2 C:ASP99 4.6 11.6 1.0 O4 C:MMA1115 4.6 6.4 1.0 CB C:ASP101 4.6 7.1 1.0 CB C:SER22 4.7 6.5 1.0 CB C:ASN103 4.7 5.4 1.0 C1 C:MMA1115 4.8 11.3 1.0 O C:ASN103 4.8 4.8 1.0 CA D:GLY114 4.9 7.9 1.0 N C:ASN103 4.9 4.7 1.0 CA C:ASN103 4.9 4.8 1.0

Calcium binding site 7 out of 8 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1116 b:5.7 occ:1.00 O D:ASN21 2.3 5.3 1.0 OD1 D:ASN103 2.3 3.5 1.0 OD1 D:ASP104 2.4 5.3 1.0 O C:GLY114 2.5 5.0 1.0 OD2 D:ASP101 2.5 4.7 1.0 O3 D:MMA1115 2.5 4.7 1.0 O2 D:MMA1115 2.6 6.2 1.0 OD1 D:ASP101 3.1 4.3 1.0 CG D:ASP101 3.1 5.8 1.0 CG D:ASN103 3.4 5.6 1.0 C3 D:MMA1115 3.4 6.5 1.0 C C:GLY114 3.4 6.5 1.0 C2 D:MMA1115 3.5 5.8 1.0 C D:ASN21 3.5 5.6 1.0 CG D:ASP104 3.6 5.3 1.0 OXT C:GLY114 3.7 6.7 1.0 CA D:CA1117 3.7 6.3 1.0 ND2 D:ASN103 3.8 5.6 1.0 C4 D:MMA1115 3.9 6.8 1.0 CB D:ASN21 4.1 5.7 1.0 CA D:ASP104 4.1 4.2 1.0 N D:ASP104 4.2 4.3 1.0 N D:SER22 4.4 5.8 1.0 CA D:SER22 4.4 5.7 1.0 CB D:ASP104 4.4 5.1 1.0 C D:ASN103 4.4 3.2 1.0 OD2 D:ASP104 4.4 6.2 1.0 CA D:ASN21 4.5 5.6 1.0 O D:HOH2121 4.5 13.9 1.0 OD2 D:ASP99 4.5 8.5 1.0 O4 D:MMA1115 4.5 4.8 1.0 CB D:ASP101 4.6 6.3 1.0 CB D:ASN103 4.7 3.7 1.0 O D:ASN103 4.7 3.7 1.0 CB D:SER22 4.8 6.5 1.0 CA C:GLY114 4.8 5.8 1.0 C1 D:MMA1115 4.8 7.4 1.0 N D:ASN103 4.9 4.0 1.0 CA D:ASN103 4.9 3.8 1.0

Calcium binding site 8 out of 8 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-B-D-Mannoyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1117 b:6.3 occ:1.00 OD1 D:ASP99 2.3 7.2 1.0 OD1 D:ASP101 2.3 4.3 1.0 OE2 D:GLU95 2.4 7.5 1.0 OE1 D:GLU95 2.5 6.2 1.0 O3 D:MMA1115 2.5 4.7 1.0 OD2 D:ASP104 2.5 6.2 1.0 O4 D:MMA1115 2.7 4.8 1.0 OD1 D:ASP104 2.7 5.3 1.0 CD D:GLU95 2.8 7.6 1.0 CG D:ASP104 2.9 5.3 1.0 CG D:ASP99 3.4 7.9 1.0 CG D:ASP101 3.4 5.8 1.0 C4 D:MMA1115 3.4 6.8 1.0 C3 D:MMA1115 3.4 6.5 1.0 OD2 D:ASP99 3.7 8.5 1.0 CA D:CA1116 3.7 5.7 1.0 OD2 D:ASP101 3.9 4.7 1.0 OD1 D:ASP96 4.1 9.8 1.0 O D:HOH2125 4.1 12.0 1.0 N D:ASP101 4.1 7.6 1.0 CG D:GLU95 4.3 5.8 1.0 N D:ASN100 4.5 8.9 1.0 CB D:ASP104 4.5 5.1 1.0 N D:TYR102 4.5 5.9 1.0 N D:ASP96 4.5 5.9 1.0 CB D:ASP101 4.6 6.3 1.0 N D:GLY97 4.6 7.5 1.0 N D:ASP99 4.7 8.9 1.0 CA D:ASP101 4.7 6.7 1.0 OD1 D:ASN103 4.7 3.5 1.0 CB D:ASP99 4.7 8.2 1.0 CA D:GLU95 4.7 5.2 1.0 C2 D:MMA1115 4.8 5.8 1.0 C5 D:MMA1115 4.9 6.2 1.0 O2 D:MMA1115 4.9 6.2 1.0 CA D:GLY97 4.9 7.6 1.0 C D:ASP99 4.9 9.4 1.0 CB D:GLU95 5.0 6.0 1.0 C D:ASP101 5.0 6.3 1.0 CA D:ASP99 5.0 9.2 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