Calcium in PDB 2wr9: Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide

The structure of Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide, PDB code: 2wr9 was solved by E.Lameignere, T.C.Shiao, R.Roy, M.Wimmerova, F.Dubreuil, A.Varrot, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.38 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.958, 48.974, 76.261, 90.00, 98.89, 90.00
R / Rfree (%)	17.62 / 22.548

The binding sites of Calcium atom in the Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide (pdb code 2wr9). 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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide, PDB code: 2wr9:
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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide


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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1131 b:7.4 occ:1.00 OD1 A:ASN117 2.3 7.0 1.0 O A:ASN28 2.4 9.3 1.0 OXT B:GLY128 2.4 11.3 1.0 OD1 A:ASP118 2.4 9.6 1.0 OD2 A:ASP115 2.4 9.9 1.0 O3 A:MAN1129 2.5 12.8 1.0 O2 A:MAN1129 2.6 11.1 1.0 OD1 A:ASP115 2.9 10.8 1.0 CG A:ASP115 3.1 9.0 1.0 CG A:ASN117 3.3 7.8 1.0 C3 A:MAN1129 3.4 12.4 1.0 C B:GLY128 3.4 13.2 1.0 C2 A:MAN1129 3.4 12.3 1.0 C A:ASN28 3.6 8.8 1.0 O B:GLY128 3.6 14.3 1.0 CG A:ASP118 3.7 9.6 1.0 CA A:CA1132 3.7 5.3 1.0 ND2 A:ASN117 3.8 5.6 1.0 C4 A:MAN1129 3.8 14.4 1.0 CB A:ASN28 4.1 5.8 1.0 CA A:ASP118 4.2 6.8 1.0 N A:ASP118 4.3 7.2 1.0 O4 A:MAN1129 4.3 13.8 1.0 C A:ASN117 4.4 7.3 1.0 N A:ALA29 4.5 9.0 1.0 CA A:ALA29 4.5 8.8 1.0 CB A:ASP118 4.5 7.2 1.0 CA A:ASN28 4.5 6.8 1.0 OD2 A:ASP118 4.5 9.1 1.0 CB A:ASP115 4.6 8.7 1.0 O A:HOH2108 4.6 24.6 1.0 O A:ASN117 4.6 6.7 1.0 OD2 A:ASP113 4.6 13.5 1.0 CB A:ASN117 4.7 7.4 1.0 CA B:GLY128 4.7 13.4 1.0 O B:HOH2101 4.8 16.8 1.0 N A:ASN117 4.8 7.8 1.0 C1 A:MAN1129 4.8 12.4 1.0 OD1 A:ASP113 4.8 8.2 1.0 CA A:ASN117 4.8 7.6 1.0 CB A:ALA29 4.9 9.4 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide


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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1132 b:5.3 occ:1.00 OD1 A:ASP113 2.3 8.2 1.0 OE1 A:GLU109 2.4 5.8 1.0 OD1 A:ASP115 2.4 10.8 1.0 OD2 A:ASP118 2.5 9.1 1.0 O4 A:MAN1129 2.5 13.8 1.0 OE2 A:GLU109 2.5 8.3 1.0 OD1 A:ASP118 2.5 9.6 1.0 O3 A:MAN1129 2.6 12.8 1.0 CD A:GLU109 2.8 8.1 1.0 CG A:ASP118 2.9 9.6 1.0 CG A:ASP113 3.3 11.9 1.0 C4 A:MAN1129 3.4 14.4 1.0 CG A:ASP115 3.5 9.0 1.0 C3 A:MAN1129 3.5 12.4 1.0 OD2 A:ASP113 3.7 13.5 1.0 CA A:CA1131 3.7 7.4 1.0 OD1 A:ASP110 3.9 8.7 1.0 OD2 A:ASP115 4.0 9.9 1.0 N A:ASP113 4.2 9.3 1.0 CG A:GLU109 4.3 10.3 1.0 N A:ASP115 4.3 10.5 1.0 N A:TYR116 4.3 8.2 1.0 CB A:ASP118 4.4 7.2 1.0 N A:ASP110 4.5 9.1 1.0 C A:ASP113 4.5 10.7 1.0 CB A:ASP113 4.5 10.1 1.0 O A:ASP113 4.6 12.0 1.0 CB A:ASP115 4.6 8.7 1.0 CA A:ASP113 4.6 10.8 1.0 CA A:GLU109 4.6 8.0 1.0 CG A:ASP110 4.7 12.2 1.0 OD1 A:ASN117 4.7 7.0 1.0 CA A:ASP115 4.8 9.6 1.0 C2 A:MAN1129 4.8 12.3 1.0 N A:HIS112 4.8 11.4 1.0 C5 A:MAN1129 4.8 13.5 1.0 CB A:GLU109 4.9 9.1 1.0 C A:ASP115 4.9 9.0 1.0 O2 A:MAN1129 4.9 11.1 1.0 C A:HIS112 5.0 10.7 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide


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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1129 b:21.1 occ:1.00 OD1 B:ASP113 2.1 27.7 1.0 O B:HOH2103 2.2 33.2 1.0 OE1 B:GLU109 2.3 23.7 1.0 OD1 B:ASP115 2.3 34.1 1.0 OD2 B:ASP118 2.4 19.8 1.0 OE2 B:GLU109 2.5 24.6 1.0 CD B:GLU109 2.7 22.5 1.0 OD1 B:ASP118 2.8 19.2 1.0 CG B:ASP118 2.9 13.9 1.0 CG B:ASP113 3.0 31.1 1.0 OD2 B:ASP113 3.4 33.3 1.0 CG B:ASP115 3.4 29.3 1.0 CA B:CA1130 3.8 32.8 1.0 OD2 B:ASP115 3.9 35.6 1.0 OD1 B:ASP110 4.0 24.4 1.0 N B:ASP115 4.1 26.5 1.0 N B:ASP113 4.1 30.9 1.0 CG B:GLU109 4.2 18.7 1.0 N B:TYR116 4.3 18.6 1.0 CB B:ASP113 4.3 29.9 1.0 CB B:ASP118 4.4 10.0 1.0 N B:ASP110 4.4 18.5 1.0 C B:ASP113 4.4 30.0 1.0 O B:ASP113 4.5 30.0 1.0 OD1 B:ASN117 4.5 21.1 1.0 CA B:ASP113 4.5 30.3 1.0 O1 B:SO41131 4.5 39.9 1.0 CB B:ASP115 4.6 25.7 1.0 CG B:ASP110 4.6 22.1 1.0 CA B:ASP115 4.7 25.1 1.0 CA B:GLU109 4.7 15.2 1.0 N B:SER114 4.8 29.9 1.0 N B:HIS112 4.9 29.7 1.0 CB B:GLU109 4.9 15.7 1.0 N B:ASP118 4.9 11.1 1.0 C B:ASP115 4.9 22.3 1.0 N B:ASN117 5.0 13.4 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide


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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1130 b:32.8 occ:1.00 OXT A:GLY128 2.5 18.0 0.5 OD1 B:ASN117 2.5 21.1 1.0 OD1 B:ASP118 2.5 19.2 1.0 O B:ASN28 2.6 17.1 1.0 OD1 B:ASP115 3.0 34.1 1.0 OD2 B:ASP115 3.1 35.6 1.0 CG B:ASP115 3.3 29.3 1.0 C A:GLY128 3.4 18.4 0.5 CG B:ASN117 3.5 17.2 1.0 CG B:ASP118 3.7 13.9 1.0 O A:GLY128 3.7 19.4 0.5 C B:ASN28 3.8 14.5 1.0 CA B:CA1129 3.8 21.1 1.0 ND2 B:ASN117 4.0 17.2 1.0 O B:HOH2103 4.1 33.2 1.0 CB B:ASN28 4.2 12.4 1.0 CA B:ASP118 4.3 10.4 1.0 OD2 B:ASP113 4.3 33.3 1.0 N B:ASP118 4.4 11.1 1.0 C B:ASN117 4.4 11.7 1.0 OD2 B:ASP118 4.5 19.8 1.0 CB B:ASP118 4.6 10.0 1.0 O B:ASN117 4.6 12.1 1.0 CA B:ALA29 4.6 15.0 1.0 CB B:ASP115 4.7 25.7 1.0 OD1 B:ASP113 4.7 27.7 1.0 N B:ALA29 4.7 15.9 1.0 CA B:ASN28 4.7 12.0 1.0 O1 B:SO41131 4.7 39.9 1.0 CA A:GLY128 4.8 18.8 0.5 CB B:ASN117 4.8 13.1 1.0 CB B:ALA29 4.9 15.6 1.0 O3 B:SO41131 4.9 34.3 1.0 CG B:ASP113 4.9 31.1 1.0 CA B:ASN117 5.0 12.9 1.0 N B:ASN117 5.0 13.4 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide


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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1130 b:19.1 occ:1.00 O C:ASN28 2.3 14.5 1.0 OD1 C:ASN117 2.4 14.7 1.0 O3 C:MAN1129 2.4 27.4 1.0 OD1 C:ASP118 2.5 14.1 1.0 OXT D:GLY128 2.5 22.7 1.0 O2 C:MAN1129 2.5 25.4 1.0 OD2 C:ASP115 2.6 21.2 1.0 OD1 C:ASP115 3.1 20.5 1.0 CG C:ASP115 3.2 19.1 1.0 C3 C:MAN1129 3.3 26.1 1.0 C2 C:MAN1129 3.4 26.3 1.0 CG C:ASN117 3.4 14.6 1.0 C D:GLY128 3.4 23.5 1.0 C C:ASN28 3.5 11.9 1.0 O D:GLY128 3.6 25.9 1.0 CG C:ASP118 3.7 10.5 1.0 ND2 C:ASN117 3.8 17.3 1.0 CA C:CA1131 3.8 15.5 1.0 C4 C:MAN1129 3.8 27.3 1.0 CB C:ASN28 4.1 9.7 1.0 CA C:ASP118 4.2 10.7 1.0 N C:ALA29 4.3 14.0 1.0 CA C:ALA29 4.4 13.8 1.0 N C:ASP118 4.4 10.8 1.0 C C:ASN117 4.5 11.3 1.0 CA C:ASN28 4.5 9.3 1.0 O4 C:MAN1129 4.5 27.9 1.0 CB C:ASP118 4.5 11.3 1.0 OD2 C:ASP113 4.5 25.8 1.0 OD2 C:ASP118 4.6 14.6 1.0 CB C:ASP115 4.6 18.5 1.0 O C:ASN117 4.7 11.3 1.0 C1 C:MAN1129 4.7 26.7 1.0 CB C:ALA29 4.7 13.2 1.0 CB C:ASN117 4.8 11.6 1.0 O D:HOH2111 4.8 43.6 1.0 OD1 C:ASP113 4.8 18.8 1.0 CA D:GLY128 4.8 22.9 1.0 N C:ASN117 5.0 12.7 1.0 CA C:ASN117 5.0 11.9 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide


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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1131 b:15.5 occ:1.00 OD1 C:ASP113 2.2 18.8 1.0 OE1 C:GLU109 2.3 18.4 1.0 OD2 C:ASP118 2.4 14.6 1.0 OD1 C:ASP115 2.4 20.5 1.0 OE2 C:GLU109 2.5 20.0 1.0 OD1 C:ASP118 2.6 14.1 1.0 CD C:GLU109 2.7 19.0 1.0 O4 C:MAN1129 2.7 27.9 1.0 O3 C:MAN1129 2.7 27.4 1.0 CG C:ASP118 2.8 10.5 1.0 CG C:ASP113 3.3 25.0 1.0 CG C:ASP115 3.4 19.1 1.0 C4 C:MAN1129 3.5 27.3 1.0 C3 C:MAN1129 3.6 26.1 1.0 OD2 C:ASP113 3.7 25.8 1.0 CA C:CA1130 3.8 19.1 1.0 OD1 C:ASP110 3.8 19.4 1.0 OD2 C:ASP115 4.0 21.2 1.0 N C:ASP113 4.1 25.1 1.0 CG C:GLU109 4.2 17.8 1.0 N C:ASP115 4.2 19.3 1.0 CB C:ASP118 4.3 11.3 1.0 N C:TYR116 4.4 15.1 1.0 C C:ASP113 4.4 23.0 1.0 O C:ASP113 4.4 22.7 1.0 N C:ASP110 4.5 19.9 1.0 CB C:ASP113 4.5 23.8 1.0 CA C:ASP113 4.6 24.1 1.0 CB C:ASP115 4.6 18.5 1.0 CG C:ASP110 4.6 21.4 1.0 OD1 C:ASN117 4.7 14.7 1.0 CA C:GLU109 4.7 15.7 1.0 CA C:ASP115 4.7 18.4 1.0 N C:HIS112 4.8 28.7 1.0 N C:SER114 4.9 21.8 1.0 CB C:GLU109 4.9 16.2 1.0 C2 C:MAN1129 4.9 26.3 1.0 C C:ASP115 5.0 17.6 1.0 C5 C:MAN1129 5.0 26.8 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide


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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1131 b:3.9 occ:1.00 OD1 D:ASP113 2.2 10.2 1.0 OD1 D:ASP115 2.3 7.8 1.0 OE1 D:GLU109 2.4 8.1 1.0 OD2 D:ASP118 2.5 12.2 1.0 O3 D:MAN1129 2.5 9.0 1.0 O4 D:MAN1129 2.5 11.5 1.0 OE2 D:GLU109 2.6 6.1 1.0 OD1 D:ASP118 2.6 7.0 1.0 CD D:GLU109 2.8 6.9 1.0 CG D:ASP118 2.9 10.1 1.0 CG D:ASP113 3.3 11.9 1.0 CG D:ASP115 3.4 7.3 1.0 C4 D:MAN1129 3.4 12.2 1.0 C3 D:MAN1129 3.4 11.2 1.0 CA D:CA1132 3.7 7.8 1.0 OD2 D:ASP113 3.7 13.6 1.0 OD2 D:ASP115 3.9 10.0 1.0 OD1 D:ASP110 4.0 9.5 1.0 N D:ASP115 4.2 8.9 1.0 N D:ASP113 4.2 8.1 1.0 CG D:GLU109 4.3 5.7 1.0 N D:TYR116 4.4 6.9 1.0 CB D:ASP118 4.4 6.4 1.0 C D:ASP113 4.5 8.7 1.0 N D:ASP110 4.5 8.1 1.0 CB D:ASP115 4.5 8.2 1.0 CB D:ASP113 4.5 9.1 1.0 O D:ASP113 4.6 9.4 1.0 CA D:ASP113 4.7 9.1 1.0 CA D:GLU109 4.7 6.4 1.0 CA D:ASP115 4.7 8.2 1.0 CG D:ASP110 4.7 10.0 1.0 OD1 D:ASN117 4.7 4.0 1.0 C2 D:MAN1129 4.8 11.2 1.0 N D:HIS112 4.8 9.4 1.0 C5 D:MAN1129 4.8 11.7 1.0 O2 D:MAN1129 4.9 10.9 1.0 N D:SER114 4.9 8.9 1.0 CB D:GLU109 4.9 6.4 1.0 C D:ASP115 4.9 7.9 1.0 C D:HIS112 4.9 9.7 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide


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 Burkholderia Cenocepacia Lectin (Bcla) Complexed with AMAN1-3MAN Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1132 b:7.8 occ:1.00 OD1 D:ASN117 2.3 4.0 1.0 OD2 D:ASP115 2.3 10.0 1.0 OD1 D:ASP118 2.4 7.0 1.0 O3 D:MAN1129 2.4 9.0 1.0 OXT C:GLY128 2.4 10.8 1.0 O D:ASN28 2.5 8.4 1.0 O2 D:MAN1129 2.6 10.9 1.0 OD1 D:ASP115 3.0 7.8 1.0 CG D:ASP115 3.0 7.3 1.0 C3 D:MAN1129 3.3 11.2 1.0 CG D:ASN117 3.3 8.2 1.0 C2 D:MAN1129 3.4 11.2 1.0 C C:GLY128 3.4 14.3 1.0 CG D:ASP118 3.6 10.1 1.0 C D:ASN28 3.6 8.8 1.0 O C:GLY128 3.7 14.0 1.0 CA D:CA1131 3.7 3.9 1.0 ND2 D:ASN117 3.8 8.1 1.0 C4 D:MAN1129 3.8 12.2 1.0 CB D:ASN28 4.1 8.1 1.0 CA D:ASP118 4.2 7.0 1.0 N D:ASP118 4.3 7.4 1.0 C D:ASN117 4.4 7.8 1.0 O4 D:MAN1129 4.4 11.5 1.0 O D:HOH2106 4.4 18.4 1.0 OD2 D:ASP118 4.5 12.2 1.0 CB D:ASP118 4.5 6.4 1.0 CB D:ASP115 4.5 8.2 1.0 N D:ALA29 4.5 7.7 1.0 CA D:ASN28 4.5 7.6 1.0 CA D:ALA29 4.5 8.1 1.0 CB D:ASN117 4.6 8.3 1.0 OD2 D:ASP113 4.7 13.6 1.0 O D:ASN117 4.7 8.8 1.0 N D:ASN117 4.7 6.9 1.0 C1 D:MAN1129 4.8 9.6 1.0 CA D:ASN117 4.8 7.8 1.0 CA C:GLY128 4.8 15.4 1.0 OD1 D:ASP113 4.9 10.2 1.0

E.Lameignere, T.C.Shiao, R.Roy, M.Wimmerova, F.Dubreuil, A.Varrot, A.Imberty. Structural Basis of the Affinity For Oligomannosides and Analogs Displayed By BC2L-A, A Burkholderia Cenocepacia Soluble Lectin. Glycobiology V. 20 87 2010.
ISSN: ISSN 0959-6658
PubMed: 19770128
DOI: 10.1093/GLYCOB/CWP151