Calcium in PDB 2boj: Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside

The structure of Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside, PDB code: 2boj was solved by C.D.Sabin, E.P.Mitchell, M.Wimmerova, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.39 / 1.8
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.636, 80.168, 52.517, 90.00, 109.92, 90.00
R / Rfree (%)	13.6 / 17.2

The binding sites of Calcium atom in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside (pdb code 2boj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside, PDB code: 2boj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1116 b:6.7 occ:1.00 OD1 A:ASN103 2.3 4.7 1.0 O A:ASN21 2.3 6.3 1.0 OD1 A:ASP104 2.4 5.9 1.0 OD2 A:ASP101 2.4 6.7 1.0 O3 A:ARW1115 2.4 7.7 1.0 O C:GLY114 2.5 6.9 1.0 O4 A:ARW1115 2.5 5.7 1.0 OD1 A:ASP101 3.1 3.9 1.0 CG A:ASP101 3.1 7.2 1.0 CG A:ASN103 3.4 5.9 1.0 C3 A:ARW1115 3.4 7.0 1.0 C4 A:ARW1115 3.4 6.3 1.0 C C:GLY114 3.4 8.2 1.0 C A:ASN21 3.5 6.3 1.0 CG A:ASP104 3.6 6.3 1.0 OXT C:GLY114 3.6 7.8 1.0 CA A:CA1117 3.7 6.0 1.0 ND2 A:ASN103 3.8 5.8 1.0 C2 A:ARW1115 3.8 6.6 1.0 CB A:ASN21 4.2 7.0 1.0 CA A:ASP104 4.2 5.8 1.0 N A:ASP104 4.2 4.8 1.0 CA A:SER22 4.3 6.7 1.0 OD2 A:ASP99 4.4 6.2 1.0 N A:SER22 4.4 6.0 1.0 C A:ASN103 4.5 5.0 1.0 OD2 A:ASP104 4.5 5.8 1.0 O2 A:ARW1115 4.5 5.9 1.0 CB A:ASP104 4.5 5.3 1.0 CA A:ASN21 4.5 6.8 1.0 CB A:SER22 4.5 6.7 1.0 O A:HOH2162 4.5 12.7 1.0 CB A:ASP101 4.6 6.7 1.0 CB A:ASN103 4.7 5.6 1.0 C5 A:ARW1115 4.7 6.4 1.0 O A:ASN103 4.8 5.0 1.0 CA C:GLY114 4.8 7.4 1.0 N A:ASN103 4.9 5.1 1.0 CA A:ASN103 4.9 5.1 1.0 OD1 A:ASP99 5.0 5.9 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1117 b:6.0 occ:1.00 OD1 A:ASP99 2.3 5.9 1.0 OD1 A:ASP101 2.3 3.9 1.0 OE1 A:GLU95 2.5 8.5 1.0 OD2 A:ASP104 2.5 5.8 1.0 O2 A:ARW1115 2.5 5.9 1.0 O3 A:ARW1115 2.5 7.7 1.0 OE2 A:GLU95 2.5 6.2 1.0 OD1 A:ASP104 2.7 5.9 1.0 CD A:GLU95 2.8 7.6 1.0 CG A:ASP104 2.9 6.3 1.0 C2 A:ARW1115 3.3 6.6 1.0 CG A:ASP99 3.3 7.9 1.0 C3 A:ARW1115 3.4 7.0 1.0 CG A:ASP101 3.4 7.2 1.0 OD2 A:ASP99 3.6 6.2 1.0 CA A:CA1116 3.7 6.7 1.0 OD2 A:ASP101 4.0 6.7 1.0 N A:ASP101 4.2 8.0 1.0 OD1 A:ASP96 4.2 9.1 1.0 CG A:GLU95 4.3 5.8 1.0 O A:HOH2156 4.4 12.9 1.0 CB A:ASP104 4.4 5.3 1.0 N A:TYR102 4.5 5.2 1.0 N A:ASP96 4.5 6.3 1.0 N A:ASN100 4.5 10.1 1.0 N A:GLY97 4.6 8.2 1.0 CB A:ASP101 4.6 6.7 1.0 CB A:ASP99 4.7 9.5 1.0 CA A:GLU95 4.7 5.7 1.0 C4 A:ARW1115 4.7 6.3 1.0 CA A:ASP101 4.7 6.7 1.0 C1 A:ARW1115 4.7 6.6 1.0 N A:ASP99 4.7 10.1 1.0 OD1 A:ASN103 4.8 4.7 1.0 O4 A:ARW1115 4.8 5.7 1.0 CG A:ASP96 4.9 7.7 1.0 CB A:GLU95 4.9 5.4 1.0 C A:ASP99 5.0 10.0 1.0 CA A:GLY97 5.0 8.8 1.0 CA A:ASP99 5.0 10.0 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1116 b:8.2 occ:1.00 OD1 B:ASN103 2.3 6.5 1.0 O B:ASN21 2.3 7.3 1.0 OD1 B:ASP104 2.4 7.3 1.0 OD2 B:ASP101 2.5 8.8 1.0 O3 B:ARW1115 2.5 6.3 1.0 O D:GLY114 2.5 10.0 1.0 O4 B:ARW1115 2.5 8.9 1.0 OD1 B:ASP101 3.1 8.4 1.0 CG B:ASP101 3.1 8.8 1.0 CG B:ASN103 3.3 7.3 1.0 C3 B:ARW1115 3.4 8.6 1.0 C D:GLY114 3.4 9.9 1.0 C4 B:ARW1115 3.4 11.4 1.0 C B:ASN21 3.5 7.0 1.0 OXT D:GLY114 3.6 10.2 1.0 CG B:ASP104 3.6 7.7 1.0 ND2 B:ASN103 3.7 7.3 1.0 CA B:CA1117 3.8 9.2 1.0 C2 B:ARW1115 3.9 10.7 1.0 CB B:ASN21 4.1 6.8 1.0 CA B:ASP104 4.2 6.7 1.0 N B:ASP104 4.2 6.6 1.0 N B:SER22 4.4 8.2 1.0 CA B:SER22 4.4 8.9 1.0 C B:ASN103 4.4 6.8 1.0 CA B:ASN21 4.5 7.0 1.0 OD2 B:ASP104 4.5 9.4 1.0 CB B:ASP104 4.5 6.5 1.0 O2 B:ARW1115 4.5 9.4 1.0 OD2 B:ASP99 4.6 12.8 1.0 O B:HOH2122 4.6 23.3 1.0 CB B:ASP101 4.6 9.5 1.0 CB B:ASN103 4.7 7.0 1.0 CB B:SER22 4.7 9.0 1.0 C5 B:ARW1115 4.8 11.1 1.0 O B:ASN103 4.8 6.9 1.0 CA D:GLY114 4.8 9.3 1.0 N B:ASN103 4.8 7.0 1.0 CA B:ASN103 4.9 6.9 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1117 b:9.2 occ:1.00 OD1 B:ASP99 2.4 11.3 1.0 OD1 B:ASP101 2.4 8.4 1.0 OE1 B:GLU95 2.4 9.5 1.0 OD2 B:ASP104 2.5 9.4 1.0 OE2 B:GLU95 2.5 10.9 1.0 O3 B:ARW1115 2.5 6.3 1.0 O2 B:ARW1115 2.5 9.4 1.0 OD1 B:ASP104 2.6 7.3 1.0 CD B:GLU95 2.8 8.7 1.0 CG B:ASP104 2.9 7.7 1.0 C2 B:ARW1115 3.3 10.7 1.0 C3 B:ARW1115 3.4 8.6 1.0 CG B:ASP99 3.4 13.0 1.0 CG B:ASP101 3.5 8.8 1.0 OD2 B:ASP99 3.7 12.8 1.0 CA B:CA1116 3.8 8.2 1.0 OD2 B:ASP101 4.0 8.8 1.0 N B:ASP101 4.1 10.3 1.0 O B:HOH2119 4.2 18.4 1.0 OD1 B:ASP96 4.2 11.3 1.0 CG B:GLU95 4.3 8.5 1.0 N B:TYR102 4.4 7.2 1.0 CB B:ASP104 4.4 6.5 1.0 N B:ASN100 4.5 12.0 1.0 N B:ASP96 4.6 8.8 1.0 CB B:ASP101 4.6 9.5 1.0 N B:GLY97 4.6 12.5 1.0 CA B:ASP101 4.7 9.2 1.0 CA B:GLU95 4.7 7.5 1.0 C4 B:ARW1115 4.7 11.4 1.0 OD1 B:ASN103 4.7 6.5 1.0 N B:ASP99 4.7 13.9 1.0 CB B:ASP99 4.7 12.8 1.0 C1 B:ARW1115 4.8 12.2 1.0 O4 B:ARW1115 4.8 8.9 1.0 CB B:GLU95 4.9 7.7 1.0 CA B:GLY97 4.9 13.4 1.0 C B:ASP99 5.0 12.6 1.0 C B:ASP101 5.0 8.9 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1116 b:9.3 occ:1.00 OD1 C:ASP99 2.3 11.2 1.0 OD1 C:ASP101 2.3 9.7 1.0 OE2 C:GLU95 2.4 11.7 1.0 O3 C:ARW1115 2.4 9.6 1.0 OD2 C:ASP104 2.4 10.6 1.0 OE1 C:GLU95 2.5 9.4 1.0 O2 C:ARW1115 2.6 9.2 1.0 OD1 C:ASP104 2.6 6.9 1.0 CD C:GLU95 2.8 10.0 1.0 CG C:ASP104 2.9 7.0 1.0 C2 C:ARW1115 3.3 10.0 1.0 C3 C:ARW1115 3.3 10.8 1.0 CG C:ASP99 3.3 11.8 1.0 CG C:ASP101 3.4 9.8 1.0 OD2 C:ASP99 3.7 11.9 1.0 CA C:CA1117 3.7 8.4 1.0 OD2 C:ASP101 3.9 8.5 1.0 N C:ASP101 4.1 11.4 1.0 O C:HOH2128 4.2 17.7 1.0 CG C:GLU95 4.3 8.0 1.0 OD1 C:ASP96 4.3 13.0 1.0 CB C:ASP104 4.4 7.4 1.0 N C:TYR102 4.4 7.9 1.0 N C:ASN100 4.4 12.9 1.0 N C:ASP96 4.5 10.1 1.0 CB C:ASP101 4.6 10.0 1.0 C4 C:ARW1115 4.7 11.2 1.0 CB C:ASP99 4.7 12.7 1.0 CA C:ASP101 4.7 10.0 1.0 OD1 C:ASN103 4.7 6.6 1.0 N C:GLY97 4.7 12.1 1.0 CA C:GLU95 4.8 8.2 1.0 C1 C:ARW1115 4.8 11.7 1.0 N C:ASP99 4.8 13.5 1.0 O4 C:ARW1115 4.8 8.8 1.0 CB C:GLU95 4.9 8.7 1.0 C C:ASP99 4.9 12.6 1.0 CA C:ASP99 5.0 13.0 1.0 C C:ASP101 5.0 9.2 1.0 CG C:ASP96 5.0 11.5 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1117 b:8.4 occ:1.00 OD1 C:ASN103 2.3 6.6 1.0 OD1 C:ASP104 2.4 6.9 1.0 O C:ASN21 2.4 7.5 1.0 OD2 C:ASP101 2.4 8.5 1.0 O A:GLY114 2.5 10.1 1.0 O3 C:ARW1115 2.5 9.6 1.0 O4 C:ARW1115 2.5 8.8 1.0 OD1 C:ASP101 3.0 9.7 1.0 CG C:ASP101 3.1 9.8 1.0 C3 C:ARW1115 3.4 10.8 1.0 CG C:ASN103 3.4 6.4 1.0 C4 C:ARW1115 3.4 11.2 1.0 C A:GLY114 3.5 10.2 1.0 C C:ASN21 3.6 8.0 1.0 CG C:ASP104 3.6 7.0 1.0 OXT A:GLY114 3.6 10.8 1.0 CA C:CA1116 3.7 9.3 1.0 ND2 C:ASN103 3.8 7.1 1.0 C2 C:ARW1115 3.8 10.0 1.0 CA C:ASP104 4.1 7.1 1.0 CB C:ASN21 4.2 7.2 1.0 N C:ASP104 4.2 6.8 1.0 CA C:SER22 4.4 9.3 1.0 N C:SER22 4.4 8.6 1.0 C C:ASN103 4.4 6.2 1.0 OD2 C:ASP104 4.4 10.6 1.0 CB C:ASP104 4.5 7.4 1.0 O2 C:ARW1115 4.5 9.2 1.0 OD2 C:ASP99 4.5 11.9 1.0 CA C:ASN21 4.5 7.8 1.0 O A:HOH2166 4.5 20.3 1.0 CB C:ASP101 4.5 10.0 1.0 CB C:SER22 4.6 9.7 1.0 CB C:ASN103 4.7 5.7 1.0 C5 C:ARW1115 4.7 9.5 1.0 O C:ASN103 4.8 5.9 1.0 N C:ASN103 4.8 6.5 1.0 CA A:GLY114 4.9 10.1 1.0 CA C:ASN103 4.9 6.3 1.0 OD1 C:ASP99 4.9 11.2 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1116 b:6.8 occ:1.00 OD1 D:ASP99 2.4 7.7 1.0 OD1 D:ASP101 2.4 5.0 1.0 OE1 D:GLU95 2.4 5.6 1.0 OE2 D:GLU95 2.5 8.0 1.0 OD2 D:ASP104 2.5 7.2 1.0 O2 D:ARW1115 2.5 7.3 1.0 O3 D:ARW1115 2.5 5.3 1.0 OD1 D:ASP104 2.6 4.8 1.0 CD D:GLU95 2.8 6.1 1.0 CG D:ASP104 2.9 5.3 1.0 C2 D:ARW1115 3.3 7.1 1.0 C3 D:ARW1115 3.4 8.0 1.0 CG D:ASP99 3.4 10.0 1.0 CG D:ASP101 3.4 7.5 1.0 OD2 D:ASP99 3.7 6.6 1.0 CA D:CA1117 3.7 6.9 1.0 OD2 D:ASP101 3.9 7.0 1.0 N D:ASP101 4.2 8.3 1.0 OD1 D:ASP96 4.2 8.7 1.0 O D:HOH2171 4.2 14.4 1.0 CG D:GLU95 4.3 6.5 1.0 CB D:ASP104 4.4 5.3 1.0 N D:ASP96 4.5 6.9 1.0 N D:TYR102 4.5 6.1 1.0 N D:ASN100 4.5 9.0 1.0 N D:GLY97 4.6 8.0 1.0 CB D:ASP101 4.6 8.0 1.0 N D:ASP99 4.7 10.5 1.0 OD1 D:ASN103 4.7 5.2 1.0 CA D:GLU95 4.7 6.3 1.0 C4 D:ARW1115 4.7 6.7 1.0 CB D:ASP99 4.7 10.0 1.0 C1 D:ARW1115 4.7 7.4 1.0 CA D:ASP101 4.8 7.9 1.0 O4 D:ARW1115 4.8 5.7 1.0 CA D:GLY97 4.9 8.9 1.0 CB D:GLU95 4.9 5.5 1.0 C D:ASP99 5.0 10.0 1.0 CG D:ASP96 5.0 8.3 1.0 CA D:ASP99 5.0 10.1 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Pseudomonas Aeruginosa Lectin (Pa-Iil) Complexed with Methyl-B-D-Arabinopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1117 b:6.9 occ:1.00 OD1 D:ASN103 2.3 5.2 1.0 O D:ASN21 2.4 5.5 1.0 OD1 D:ASP104 2.4 4.8 1.0 O B:GLY114 2.4 6.7 1.0 OD2 D:ASP101 2.4 7.0 1.0 O3 D:ARW1115 2.5 5.3 1.0 O4 D:ARW1115 2.5 5.7 1.0 OD1 D:ASP101 3.0 5.0 1.0 CG D:ASP101 3.1 7.5 1.0 CG D:ASN103 3.4 5.9 1.0 C3 D:ARW1115 3.4 8.0 1.0 C B:GLY114 3.4 8.4 1.0 C4 D:ARW1115 3.5 6.7 1.0 C D:ASN21 3.5 5.8 1.0 OXT B:GLY114 3.6 8.8 1.0 CG D:ASP104 3.6 5.3 1.0 CA D:CA1116 3.7 6.8 1.0 ND2 D:ASN103 3.8 6.1 1.0 C2 D:ARW1115 3.8 7.1 1.0 CB D:ASN21 4.1 4.9 1.0 CA D:ASP104 4.2 5.1 1.0 N D:ASP104 4.3 5.0 1.0 N D:SER22 4.4 5.8 1.0 O D:HOH2176 4.4 18.3 1.0 CA D:SER22 4.4 6.1 1.0 OD2 D:ASP104 4.5 7.2 1.0 C D:ASN103 4.5 5.2 1.0 OD2 D:ASP99 4.5 6.6 1.0 CB D:ASP104 4.5 5.3 1.0 O2 D:ARW1115 4.5 7.3 1.0 CA D:ASN21 4.5 5.2 1.0 CB D:ASP101 4.6 8.0 1.0 CB D:ASN103 4.7 5.2 1.0 CB D:SER22 4.7 6.1 1.0 CA B:GLY114 4.8 7.4 1.0 C5 D:ARW1115 4.8 6.6 1.0 O D:ASN103 4.8 5.1 1.0 N D:ASN103 4.9 5.5 1.0 CA D:ASN103 4.9 5.5 1.0 OD1 D:ASP99 5.0 7.7 1.0

C.D.Sabin, E.P.Mitchell, M.Pokarna, C.Gautier, J.-P.Utille, M.Wimmerova, A.Imberty. Binding of Different Monosaccharides By Lectin Pa-Iil From Pseudoman Aeruginosa: Thermodynamics Data Correlated with X-Ray Structures. Febs Lett. V. 580 982 2006.
ISSN: ISSN 0014-5793
PubMed: 16438968
DOI: 10.1016/J.FEBSLET.2006.01.030