Calcium in PDB 2jdk: Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative

The structure of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative, PDB code: 2jdk was solved by K.Marotte, C.Sabin, C.Preville, M.Pymbock, I.Deguise, M.Wimmerova, E.P.Mitchell, A.Imberty, R.Roy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.31 / 1.1
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.611, 73.078, 54.501, 90.00, 94.35, 90.00
R / Rfree (%)	11.2 / 13.4

The binding sites of Calcium atom in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative (pdb code 2jdk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative, PDB code: 2jdk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1116 b:4.7 occ:1.00 OD1 A:ASN103 2.3 4.8 1.0 O A:ASN21 2.4 5.0 1.0 OD1 A:ASP104 2.4 4.5 1.0 O B:GLY114 2.4 5.5 1.0 OD2 A:ASP101 2.4 6.0 1.0 O4 A:FUC1115 2.5 5.5 1.0 O3 A:FUC1115 2.5 5.6 1.0 OD1 A:ASP101 3.1 5.7 1.0 CG A:ASP101 3.1 5.6 1.0 CG A:ASN103 3.4 4.8 1.0 C3 A:FUC1115 3.4 5.8 1.0 C B:GLY114 3.4 6.3 1.0 C4 A:FUC1115 3.4 6.2 1.0 C A:ASN21 3.6 4.3 1.0 CG A:ASP104 3.6 4.3 1.0 OXT B:GLY114 3.7 7.4 1.0 CA A:CA1117 3.7 5.2 1.0 ND2 A:ASN103 3.8 5.8 1.0 C2 A:FUC1115 3.8 5.7 1.0 CB A:ASN21 4.1 4.8 1.0 CA A:ASP104 4.2 4.6 1.0 N A:ASP104 4.3 4.3 1.0 CA A:SER22 4.4 5.0 1.0 N A:SER22 4.4 4.4 1.0 O A:HOH2161 4.4 15.9 1.0 OD2 A:ASP104 4.4 5.1 1.0 O2 A:FUC1115 4.4 5.9 1.0 C A:ASN103 4.5 4.2 1.0 CB A:ASP104 4.5 4.6 1.0 CA A:ASN21 4.5 4.5 1.0 CB A:ASP101 4.5 6.8 1.0 OD2 A:ASP99 4.5 8.0 1.0 CB A:SER22 4.7 5.1 1.0 CB A:ASN103 4.7 5.0 1.0 C5 A:FUC1115 4.8 6.1 1.0 CA B:GLY114 4.8 6.0 1.0 O A:ASN103 4.8 4.4 1.0 N A:ASN103 4.9 4.5 1.0 CA A:ASN103 4.9 4.6 1.0

Calcium binding site 2 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1117 b:5.2 occ:1.00 OD1 A:ASP101 2.4 5.7 1.0 OD1 A:ASP99 2.4 7.7 1.0 OD2 A:ASP104 2.4 5.1 1.0 OE2 A:GLU95 2.4 6.5 1.0 O3 A:FUC1115 2.5 5.6 1.0 OE1 A:GLU95 2.5 5.9 1.0 O2 A:FUC1115 2.5 5.9 1.0 OD1 A:ASP104 2.6 4.5 1.0 CD A:GLU95 2.8 5.7 1.0 CG A:ASP104 2.9 4.3 1.0 C2 A:FUC1115 3.3 5.7 1.0 C3 A:FUC1115 3.3 5.8 1.0 CG A:ASP99 3.4 7.2 1.0 CG A:ASP101 3.4 5.6 1.0 OD2 A:ASP99 3.7 8.0 1.0 CA A:CA1116 3.7 4.7 1.0 OD2 A:ASP101 4.0 6.0 1.0 N A:ASP101 4.1 7.2 1.0 O A:HOH2148 4.2 12.2 1.0 OD1 A:ASP96 4.2 6.2 1.0 CG A:GLU95 4.3 6.8 1.0 CB A:ASP104 4.4 4.6 1.0 N A:TYR102 4.4 5.9 1.0 N A:ASN100 4.5 8.2 1.0 N A:ASP96 4.5 5.5 1.0 CB A:ASP101 4.6 6.8 1.0 N A:GLY97 4.6 6.8 1.0 C4 A:FUC1115 4.7 6.2 1.0 CA A:ASP101 4.7 7.0 1.0 CA A:GLU95 4.7 5.1 1.0 CB A:ASP99 4.7 9.2 1.0 N A:ASP99 4.7 8.5 1.0 OD1 A:ASN103 4.7 4.8 1.0 C1 A:FUC1115 4.8 6.1 1.0 O4 A:FUC1115 4.8 5.5 1.0 CB A:GLU95 4.9 6.3 1.0 CG A:ASP96 4.9 5.2 1.0 C A:ASP101 5.0 6.2 1.0 C A:ASP99 5.0 8.4 1.0

Calcium binding site 3 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1118 b:4.9 occ:1.00 OD1 B:ASP99 2.3 6.4 1.0 OD1 B:ASP101 2.4 5.1 1.0 OD2 B:ASP104 2.4 5.4 1.0 OE2 B:GLU95 2.4 5.5 1.0 OE1 B:GLU95 2.5 5.0 1.0 O3 B:FUC1115 2.5 5.8 1.0 O2 B:FUC1115 2.5 6.1 1.0 OD1 B:ASP104 2.6 5.2 1.0 CD B:GLU95 2.8 4.7 1.0 CG B:ASP104 2.9 4.5 1.0 C2 B:FUC1115 3.3 6.0 1.0 C3 B:FUC1115 3.4 6.3 1.0 CG B:ASP99 3.4 6.5 1.0 CG B:ASP101 3.4 4.9 1.0 OD2 B:ASP99 3.7 7.1 1.0 CA B:CA1119 3.7 5.0 1.0 OD2 B:ASP101 4.0 6.0 1.0 O B:HOH2146 4.1 8.8 1.0 N B:ASP101 4.1 5.2 1.0 OD1 B:ASP96 4.2 7.4 1.0 CG B:GLU95 4.2 5.1 1.0 CB B:ASP104 4.4 5.1 1.0 N B:TYR102 4.4 4.6 1.0 N B:ASN100 4.5 5.8 1.0 N B:ASP96 4.5 4.9 1.0 CB B:ASP101 4.5 5.8 1.0 N B:GLY97 4.7 6.3 1.0 C4 B:FUC1115 4.7 7.6 1.0 CA B:GLU95 4.7 4.6 1.0 CA B:ASP101 4.7 5.7 1.0 CB B:ASP99 4.7 7.5 1.0 OD1 B:ASN103 4.7 4.9 1.0 N B:ASP99 4.8 6.9 1.0 C1 B:FUC1115 4.8 7.1 1.0 O4 B:FUC1115 4.8 6.6 1.0 CB B:GLU95 4.9 5.0 1.0 C B:ASP101 5.0 5.0 1.0 C B:ASP99 5.0 6.8 1.0 CG B:ASP96 5.0 5.5 1.0

Calcium binding site 4 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1119 b:5.0 occ:1.00 OD1 B:ASN103 2.3 4.9 1.0 OD1 B:ASP104 2.4 5.2 1.0 O B:ASN21 2.4 5.5 1.0 OD2 B:ASP101 2.4 6.0 1.0 O A:GLY114 2.4 5.7 1.0 O4 B:FUC1115 2.5 6.6 1.0 O3 B:FUC1115 2.5 5.8 1.0 OD1 B:ASP101 3.0 5.1 1.0 CG B:ASP101 3.1 4.9 1.0 CG B:ASN103 3.4 4.9 1.0 C3 B:FUC1115 3.4 6.3 1.0 C A:GLY114 3.4 6.4 1.0 C4 B:FUC1115 3.4 7.6 1.0 C B:ASN21 3.6 5.2 1.0 CG B:ASP104 3.6 4.5 1.0 OXT A:GLY114 3.7 7.7 1.0 CA B:CA1118 3.7 4.9 1.0 ND2 B:ASN103 3.8 5.9 1.0 C2 B:FUC1115 3.8 6.0 1.0 CB B:ASN21 4.2 4.9 1.0 CA B:ASP104 4.2 4.5 1.0 N B:ASP104 4.3 4.2 1.0 CA B:SER22 4.4 5.8 1.0 N B:SER22 4.4 5.7 1.0 OD2 B:ASP104 4.4 5.4 1.0 O2 B:FUC1115 4.5 6.1 1.0 C B:ASN103 4.5 4.2 1.0 CB B:ASP104 4.5 5.1 1.0 O B:HOH2154 4.5 16.7 1.0 CB B:ASP101 4.5 5.8 1.0 CA B:ASN21 4.5 5.3 1.0 OD2 B:ASP99 4.6 7.1 1.0 CB B:SER22 4.7 6.5 1.0 CB B:ASN103 4.7 4.8 1.0 CA A:GLY114 4.8 6.2 1.0 C5 B:FUC1115 4.8 8.0 1.0 O B:ASN103 4.8 4.5 1.0 N B:ASN103 4.9 4.4 1.0 CA B:ASN103 4.9 4.3 1.0

Calcium binding site 5 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1116 b:5.5 occ:1.00 OD1 C:ASN103 2.3 5.0 1.0 O C:ASN21 2.4 5.3 1.0 OD1 C:ASP104 2.4 5.5 1.0 O D:GLY114 2.4 5.7 1.0 OD2 C:ASP101 2.4 6.8 1.0 O4 C:FUC1118 2.5 7.0 1.0 O3 C:FUC1118 2.5 6.6 1.0 OD1 C:ASP101 3.0 6.2 1.0 CG C:ASP101 3.1 6.7 1.0 CG C:ASN103 3.4 5.1 1.0 C3 C:FUC1118 3.4 6.6 1.0 C D:GLY114 3.4 6.4 1.0 C4 C:FUC1118 3.4 7.0 1.0 C C:ASN21 3.6 5.1 1.0 CG C:ASP104 3.6 5.1 1.0 OXT D:GLY114 3.7 8.3 1.0 ND2 C:ASN103 3.7 5.9 1.0 CA C:CA1117 3.7 6.0 1.0 C2 C:FUC1118 3.8 7.4 1.0 CB C:ASN21 4.2 5.1 1.0 CA C:ASP104 4.2 4.7 1.0 N C:ASP104 4.3 4.6 1.0 CA C:SER22 4.4 6.0 1.0 N C:SER22 4.4 5.7 1.0 OD2 C:ASP104 4.5 5.8 1.0 O2 C:FUC1118 4.5 6.8 1.0 C C:ASN103 4.5 4.2 1.0 CB C:ASP104 4.5 5.1 1.0 O C:HOH2133 4.5 15.8 1.0 CB C:ASP101 4.5 7.7 1.0 CA C:ASN21 4.5 5.2 1.0 OD2 C:ASP99 4.6 8.5 1.0 CB C:SER22 4.7 6.4 1.0 CB C:ASN103 4.7 5.2 1.0 C5 C:FUC1118 4.8 7.1 1.0 CA D:GLY114 4.8 6.7 1.0 O C:ASN103 4.8 4.6 1.0 N C:ASN103 4.9 5.0 1.0 CA C:ASN103 4.9 5.0 1.0 O5 C:FUC1118 5.0 7.1 1.0 OD1 C:ASP99 5.0 8.5 1.0

Calcium binding site 6 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1117 b:6.0 occ:1.00 OD1 C:ASP99 2.4 8.5 1.0 OD1 C:ASP101 2.4 6.2 1.0 OD2 C:ASP104 2.4 5.8 1.0 OE2 C:GLU95 2.4 6.7 1.0 OE1 C:GLU95 2.5 6.6 1.0 O3 C:FUC1118 2.5 6.6 1.0 O2 C:FUC1118 2.5 6.8 1.0 OD1 C:ASP104 2.6 5.5 1.0 CD C:GLU95 2.8 6.7 1.0 CG C:ASP104 2.9 5.1 1.0 C2 C:FUC1118 3.3 7.4 1.0 C3 C:FUC1118 3.4 6.6 1.0 CG C:ASP99 3.4 8.8 1.0 CG C:ASP101 3.4 6.7 1.0 CA C:CA1116 3.7 5.5 1.0 OD2 C:ASP99 3.7 8.5 1.0 OD2 C:ASP101 4.0 6.8 1.0 O C:HOH2129 4.1 9.9 1.0 N C:ASP101 4.1 8.1 1.0 OD1 C:ASP96 4.2 7.3 1.0 CG C:GLU95 4.3 6.5 1.0 N C:TYR102 4.4 6.9 1.0 CB C:ASP104 4.4 5.1 1.0 N C:ASN100 4.5 9.3 1.0 N C:ASP96 4.5 5.9 1.0 CB C:ASP101 4.6 7.7 1.0 N C:GLY97 4.7 7.5 1.0 C4 C:FUC1118 4.7 7.0 1.0 CA C:ASP101 4.7 7.6 1.0 OD1 C:ASN103 4.7 5.0 1.0 CA C:GLU95 4.7 5.6 1.0 CB C:ASP99 4.7 9.9 1.0 N C:ASP99 4.8 9.4 1.0 C1 C:FUC1118 4.8 7.0 1.0 O4 C:FUC1118 4.8 7.0 1.0 CB C:GLU95 4.9 6.6 1.0 C C:ASP101 4.9 6.5 1.0 CG C:ASP96 5.0 6.3 1.0 C C:ASP99 5.0 9.0 1.0

Calcium binding site 7 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1118 b:4.9 occ:1.00 OD1 D:ASN103 2.4 4.6 1.0 OD1 D:ASP104 2.4 5.3 1.0 O D:ASN21 2.4 5.2 1.0 O C:GLY114 2.4 5.1 1.0 OD2 D:ASP101 2.4 5.8 1.0 O4 D:FUC1115 2.5 5.8 1.0 O3 D:FUC1115 2.5 6.0 1.0 OD1 D:ASP101 3.1 5.7 1.0 CG D:ASP101 3.1 5.2 1.0 C3 D:FUC1115 3.4 6.3 1.0 CG D:ASN103 3.4 4.5 1.0 C C:GLY114 3.4 5.5 1.0 C4 D:FUC1115 3.4 6.4 1.0 C D:ASN21 3.6 5.2 1.0 CG D:ASP104 3.6 5.0 1.0 OXT C:GLY114 3.7 6.8 1.0 ND2 D:ASN103 3.7 5.4 1.0 CA D:CA1119 3.7 5.6 1.0 C2 D:FUC1115 3.8 6.1 1.0 CB D:ASN21 4.1 4.8 1.0 CA D:ASP104 4.2 5.0 1.0 N D:ASP104 4.3 4.7 1.0 OD2 D:ASP104 4.4 5.8 1.0 N D:SER22 4.4 5.6 1.0 CA D:SER22 4.4 5.7 1.0 O2 D:FUC1115 4.4 6.5 1.0 CB D:ASP104 4.5 5.6 1.0 O D:HOH2147 4.5 10.7 1.0 C D:ASN103 4.5 4.3 1.0 CA D:ASN21 4.5 5.0 1.0 CB D:ASP101 4.5 6.8 1.0 OD2 D:ASP99 4.6 7.5 1.0 CB D:SER22 4.7 6.2 1.0 CB D:ASN103 4.7 5.1 1.0 CA C:GLY114 4.7 6.1 1.0 C5 D:FUC1115 4.8 7.0 1.0 O D:ASN103 4.8 4.5 1.0 N D:ASN103 4.9 4.7 1.0 CA D:ASN103 4.9 4.2 1.0 OD1 D:ASP99 5.0 7.2 1.0 O5 D:FUC1115 5.0 7.1 1.0

Calcium binding site 8 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1119 b:5.6 occ:1.00 OD1 D:ASP101 2.3 5.7 1.0 OD1 D:ASP99 2.4 7.2 1.0 OD2 D:ASP104 2.4 5.8 1.0 OE2 D:GLU95 2.4 6.6 1.0 O3 D:FUC1115 2.5 6.0 1.0 OE1 D:GLU95 2.5 6.5 1.0 O2 D:FUC1115 2.5 6.5 1.0 OD1 D:ASP104 2.6 5.3 1.0 CD D:GLU95 2.8 6.3 1.0 CG D:ASP104 2.9 5.0 1.0 C2 D:FUC1115 3.3 6.1 1.0 C3 D:FUC1115 3.4 6.3 1.0 CG D:ASP99 3.4 6.8 1.0 CG D:ASP101 3.4 5.2 1.0 OD2 D:ASP99 3.7 7.5 1.0 CA D:CA1118 3.7 4.9 1.0 OD2 D:ASP101 4.0 5.8 1.0 O D:HOH2142 4.1 9.8 1.0 N D:ASP101 4.1 7.8 1.0 OD1 D:ASP96 4.2 8.2 1.0 CG D:GLU95 4.3 7.0 1.0 CB D:ASP104 4.4 5.6 1.0 N D:TYR102 4.4 5.9 1.0 N D:ASN100 4.5 8.8 1.0 CB D:ASP101 4.5 6.8 1.0 N D:ASP96 4.5 6.2 1.0 N D:GLY97 4.6 7.8 1.0 CA D:ASP101 4.7 6.7 1.0 OD1 D:ASN103 4.7 4.6 1.0 CB D:ASP99 4.7 7.8 1.0 C4 D:FUC1115 4.7 6.4 1.0 CA D:GLU95 4.7 5.7 1.0 N D:ASP99 4.8 8.8 1.0 C1 D:FUC1115 4.8 6.8 1.0 O4 D:FUC1115 4.8 5.8 1.0 CB D:GLU95 4.9 7.0 1.0 C D:ASP101 5.0 6.3 1.0 C D:ASP99 5.0 8.3 1.0 CG D:ASP96 5.0 7.0 1.0

K.Marotte, C.Sabin, C.Preville, M.Pymbock, M.Wimmerova, E.P.Mitchell, A.Imberty, R.Roy. X-Ray Structures and Thermodynamics of the Interaction of Pa-Iil From Pseudomonas Aeruginosa with Disaccharide Derivatives. Chemmedchem V. 2 1328 2007.
ISSN: ISSN 1860-7179
PubMed: 17623286
DOI: 10.1002/CMDC.200700100