Calcium in PDB 1ovs: Lecb (Pa-Lii) in Complex with Core Trimannoside

The structure of Lecb (Pa-Lii) in Complex with Core Trimannoside, PDB code: 1ovs was solved by R.Loris, D.Tielker, K.-E.Jaeger, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.800, 72.050, 99.710, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.1

The binding sites of Calcium atom in the Lecb (Pa-Lii) in Complex with Core Trimannoside (pdb code 1ovs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Lecb (Pa-Lii) in Complex with Core Trimannoside, PDB code: 1ovs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Lecb (Pa-Lii) in Complex with Core Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lecb (Pa-Lii) in Complex with Core Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:22.6 occ:1.00 OD1 A:ASP99 2.3 28.0 1.0 OE2 A:GLU95 2.4 23.3 1.0 OD2 A:ASP104 2.4 19.0 1.0 O3 A:MAN201 2.5 25.0 1.0 OD1 A:ASP101 2.5 21.0 1.0 OD1 A:ASP104 2.5 21.3 1.0 O4 A:MAN201 2.5 23.9 1.0 OE1 A:GLU95 2.6 22.6 1.0 CD A:GLU95 2.8 27.2 1.0 CG A:ASP104 2.8 20.7 1.0 CG A:ASP99 3.3 26.3 1.0 C4 A:MAN201 3.3 24.9 1.0 C3 A:MAN201 3.3 25.4 1.0 CG A:ASP101 3.5 23.5 1.0 OD2 A:ASP99 3.5 31.2 1.0 CA A:CA402 3.7 21.0 1.0 OD2 A:ASP101 4.0 21.9 1.0 OD1 A:ASP96 4.1 20.9 1.0 O A:HOH649 4.1 28.9 1.0 N A:ASP101 4.1 23.1 1.0 CG A:GLU95 4.3 23.3 1.0 CB A:ASP104 4.3 20.0 1.0 N A:GLY97 4.5 25.7 1.0 N A:ASP96 4.5 22.2 1.0 N A:ASN100 4.5 23.6 1.0 N A:TYR102 4.5 20.6 1.0 CB A:ASP99 4.6 26.4 1.0 C2 A:MAN201 4.7 24.6 1.0 CA A:GLU95 4.7 20.7 1.0 CB A:ASP101 4.7 23.7 1.0 OD1 A:ASN103 4.7 17.7 1.0 C5 A:MAN201 4.7 25.5 1.0 O2 A:MAN201 4.8 21.9 1.0 CG A:ASP96 4.8 25.0 1.0 N A:ASP99 4.8 24.3 1.0 CA A:ASP101 4.9 22.5 1.0 N A:ASP104 4.9 21.4 1.0 CB A:GLU95 4.9 22.3 1.0 CA A:GLY97 5.0 26.0 1.0 CA A:ASN100 5.0 24.6 1.0

Calcium binding site 2 out of 8 in the Lecb (Pa-Lii) in Complex with Core Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lecb (Pa-Lii) in Complex with Core Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:21.0 occ:1.00 OD1 A:ASN103 2.3 17.7 1.0 O3 A:MAN201 2.4 25.0 1.0 O A:ASN21 2.4 17.8 1.0 OD1 A:ASP104 2.4 21.3 1.0 OD2 A:ASP101 2.4 21.9 1.0 O B:GLY114 2.5 19.7 1.0 O2 A:MAN201 2.6 21.9 1.0 OD1 A:ASP101 3.1 21.0 1.0 CG A:ASP101 3.1 23.5 1.0 C3 A:MAN201 3.3 25.4 1.0 C2 A:MAN201 3.3 24.6 1.0 CG A:ASN103 3.4 22.5 1.0 C B:GLY114 3.4 24.0 1.0 C A:ASN21 3.6 14.9 1.0 CG A:ASP104 3.6 20.7 1.0 OXT B:GLY114 3.6 23.5 1.0 CA A:CA401 3.7 22.6 1.0 ND2 A:ASN103 3.8 20.8 1.0 C4 A:MAN201 3.8 24.9 1.0 N A:ASP104 3.9 21.4 1.0 CA A:ASP104 4.0 20.8 1.0 CB A:ASN21 4.1 18.1 1.0 C A:ASN103 4.4 19.5 1.0 CB A:ASP104 4.4 20.0 1.0 OD2 A:ASP99 4.4 31.2 1.0 CA A:SER22 4.4 19.1 1.0 N A:SER22 4.4 17.1 1.0 OD2 A:ASP104 4.5 19.0 1.0 O A:HOH666 4.5 29.7 1.0 O4 A:MAN201 4.5 23.9 1.0 CA A:ASN21 4.5 17.7 1.0 CB A:SER22 4.6 21.7 1.0 CB A:ASP101 4.6 23.7 1.0 CB A:ASN103 4.7 21.6 1.0 C1 A:MAN201 4.7 24.4 1.0 CA B:GLY114 4.8 23.9 1.0 N A:ASN103 4.8 19.1 1.0 O A:ASN103 4.8 19.3 1.0 CA A:ASN103 4.9 20.5 1.0

Calcium binding site 3 out of 8 in the Lecb (Pa-Lii) in Complex with Core Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lecb (Pa-Lii) in Complex with Core Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:18.4 occ:1.00 OD1 B:ASP99 2.3 17.9 1.0 OD1 B:ASP101 2.3 17.5 1.0 OE2 B:GLU95 2.4 21.5 1.0 OD2 B:ASP104 2.5 15.4 1.0 O3 B:MAN203 2.5 17.8 1.0 OE1 B:GLU95 2.5 22.7 1.0 OD1 B:ASP104 2.6 14.3 1.0 O4 B:MAN203 2.6 19.5 1.0 CD B:GLU95 2.8 20.1 1.0 CG B:ASP104 2.9 17.7 1.0 CG B:ASP99 3.3 24.2 1.0 C4 B:MAN203 3.3 16.9 1.0 C3 B:MAN203 3.4 16.8 1.0 CG B:ASP101 3.4 18.9 1.0 OD2 B:ASP99 3.6 24.4 1.0 CA B:CA404 3.7 16.3 1.0 OD2 B:ASP101 3.9 19.8 1.0 N B:ASP101 4.1 20.1 1.0 OD1 B:ASP96 4.1 19.2 1.0 O B:HOH617 4.2 26.4 1.0 CG B:GLU95 4.3 20.2 1.0 CB B:ASP104 4.4 15.8 1.0 N B:TYR102 4.4 17.5 1.0 N B:ASP96 4.5 18.2 1.0 CB B:ASP101 4.6 20.4 1.0 N B:GLY97 4.6 19.7 1.0 N B:ASN100 4.6 21.8 1.0 CB B:ASP99 4.7 21.4 1.0 CA B:GLU95 4.7 18.1 1.0 C2 B:MAN203 4.7 19.1 1.0 OD1 B:ASN103 4.7 16.2 1.0 CA B:ASP101 4.8 17.6 1.0 C5 B:MAN203 4.8 19.5 1.0 CG B:ASP96 4.8 21.7 1.0 N B:ASP99 4.9 21.8 1.0 O2 B:MAN203 4.9 20.8 1.0 CB B:GLU95 4.9 19.0 1.0 N B:ASP104 4.9 16.4 1.0 C B:ASP99 4.9 22.5 1.0 CA B:ASN100 5.0 24.3 1.0 C B:ASP101 5.0 18.7 1.0

Calcium binding site 4 out of 8 in the Lecb (Pa-Lii) in Complex with Core Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lecb (Pa-Lii) in Complex with Core Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:16.3 occ:1.00 OD1 B:ASN103 2.3 16.2 1.0 OD2 B:ASP101 2.3 19.8 1.0 O B:ASN21 2.4 15.8 1.0 OD1 B:ASP104 2.4 14.3 1.0 O3 B:MAN203 2.4 17.8 1.0 O2 B:MAN203 2.5 20.8 1.0 O A:GLY114 2.5 20.0 1.0 CG B:ASP101 3.1 18.9 1.0 OD1 B:ASP101 3.1 17.5 1.0 C3 B:MAN203 3.3 16.8 1.0 C2 B:MAN203 3.3 19.1 1.0 CG B:ASN103 3.4 17.8 1.0 C A:GLY114 3.5 21.4 1.0 C B:ASN21 3.6 13.0 1.0 CG B:ASP104 3.6 17.7 1.0 CA B:CA403 3.7 18.4 1.0 OXT A:GLY114 3.7 20.5 1.0 ND2 B:ASN103 3.8 17.2 1.0 C4 B:MAN203 3.8 16.9 1.0 N B:ASP104 4.0 16.4 1.0 CA B:ASP104 4.1 15.8 1.0 CB B:ASN21 4.2 13.5 1.0 C B:ASN103 4.3 13.3 1.0 CA B:SER22 4.4 16.4 1.0 N B:SER22 4.4 15.2 1.0 CB B:ASP104 4.4 15.8 1.0 O B:HOH546 4.4 20.1 1.0 OD2 B:ASP104 4.5 15.4 1.0 O4 B:MAN203 4.5 19.5 1.0 CB B:ASP101 4.5 20.4 1.0 OD2 B:ASP99 4.5 24.4 1.0 CA B:ASN21 4.5 14.7 1.0 CB B:SER22 4.5 14.6 1.0 O B:ASN103 4.7 15.2 1.0 CB B:ASN103 4.7 17.8 1.0 C1 B:MAN203 4.7 20.8 1.0 N B:ASN103 4.8 16.5 1.0 CA A:GLY114 4.9 19.9 1.0 CA B:ASN103 4.9 16.9 1.0

Calcium binding site 5 out of 8 in the Lecb (Pa-Lii) in Complex with Core Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Lecb (Pa-Lii) in Complex with Core Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca405 b:19.3 occ:1.00 OD1 C:ASP101 2.3 16.7 1.0 OD1 C:ASP99 2.4 23.1 1.0 OD2 C:ASP104 2.4 16.3 1.0 OE2 C:GLU95 2.4 25.6 1.0 OE1 C:GLU95 2.4 23.7 1.0 O3 C:MAN205 2.6 18.8 1.0 OD1 C:ASP104 2.7 17.2 1.0 O4 C:MAN205 2.7 24.2 1.0 CD C:GLU95 2.7 23.0 1.0 CG C:ASP104 2.9 17.4 1.0 CG C:ASP101 3.3 22.0 1.0 C4 C:MAN205 3.4 24.4 1.0 CG C:ASP99 3.4 24.5 1.0 C3 C:MAN205 3.5 25.3 1.0 CA C:CA406 3.7 18.4 1.0 OD2 C:ASP99 3.7 22.2 1.0 OD2 C:ASP101 3.8 25.2 1.0 O C:HOH675 4.0 30.3 1.0 N C:ASP101 4.0 20.3 1.0 CG C:GLU95 4.2 21.3 1.0 OD1 C:ASP96 4.3 22.3 1.0 CB C:ASP104 4.4 14.9 1.0 N C:TYR102 4.4 16.4 1.0 N C:ASN100 4.5 21.6 1.0 N C:GLY97 4.5 23.0 1.0 N C:ASP96 4.5 19.7 1.0 CB C:ASP101 4.5 20.8 1.0 CA C:GLU95 4.6 18.3 1.0 CA C:ASP101 4.7 18.0 1.0 OD1 C:ASN103 4.8 15.9 1.0 CB C:ASP99 4.8 24.6 1.0 C2 C:MAN205 4.8 23.9 1.0 CB C:GLU95 4.8 18.3 1.0 C5 C:MAN205 4.9 26.3 1.0 N C:ASP104 4.9 16.4 1.0 N C:ASP99 4.9 23.6 1.0 CA C:ASN100 5.0 22.6 1.0 CA C:GLY97 5.0 24.9 1.0 C C:ASP101 5.0 19.6 1.0 O2 C:MAN205 5.0 23.0 1.0 C C:ASP99 5.0 23.8 1.0 C C:ASN100 5.0 20.6 1.0

Calcium binding site 6 out of 8 in the Lecb (Pa-Lii) in Complex with Core Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Lecb (Pa-Lii) in Complex with Core Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca406 b:18.4 occ:1.00 OD1 C:ASN103 2.3 15.9 1.0 OD2 C:ASP101 2.4 25.2 1.0 O3 C:MAN205 2.4 18.8 1.0 O C:ASN21 2.4 19.2 1.0 OD1 C:ASP104 2.5 17.2 1.0 O D:GLY114 2.5 17.7 1.0 O2 C:MAN205 2.5 23.0 1.0 CG C:ASP101 3.1 22.0 1.0 OD1 C:ASP101 3.1 16.7 1.0 C3 C:MAN205 3.3 25.3 1.0 C2 C:MAN205 3.3 23.9 1.0 CG C:ASN103 3.4 22.2 1.0 C D:GLY114 3.4 17.7 1.0 CG C:ASP104 3.6 17.4 1.0 C C:ASN21 3.6 17.6 1.0 OXT D:GLY114 3.7 22.4 1.0 CA C:CA405 3.7 19.3 1.0 ND2 C:ASN103 3.8 20.9 1.0 C4 C:MAN205 3.8 24.4 1.0 N C:ASP104 4.0 16.4 1.0 CA C:ASP104 4.1 14.4 1.0 CB C:ASN21 4.2 16.6 1.0 O C:HOH680 4.2 30.9 1.0 C C:ASN103 4.3 15.2 1.0 OD2 C:ASP104 4.4 16.3 1.0 CB C:ASP104 4.4 14.9 1.0 O4 C:MAN205 4.5 24.2 1.0 OD2 C:ASP99 4.5 22.2 1.0 CB C:ASP101 4.5 20.8 1.0 CA C:SER22 4.5 20.7 1.0 N C:SER22 4.5 18.2 1.0 CA C:ASN21 4.6 18.0 1.0 CB C:SER22 4.7 20.6 1.0 CB C:ASN103 4.7 18.7 1.0 O C:ASN103 4.7 15.4 1.0 C1 C:MAN205 4.7 30.4 1.0 N C:ASN103 4.8 17.3 1.0 CA D:GLY114 4.8 20.0 1.0 CA C:ASN103 4.9 17.1 1.0 OD1 C:ASP99 5.0 23.1 1.0

Calcium binding site 7 out of 8 in the Lecb (Pa-Lii) in Complex with Core Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Lecb (Pa-Lii) in Complex with Core Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca407 b:30.2 occ:0.50 OD1 D:ASP99 2.2 58.5 1.0 O D:HOH785 2.5 39.5 1.0 OE2 D:GLU95 2.6 28.3 1.0 O D:HOH817 2.6 45.0 1.0 OD2 D:ASP104 2.7 28.9 1.0 OD1 D:ASP104 2.8 26.8 1.0 OE1 D:GLU95 2.8 30.9 1.0 CG D:ASP99 2.9 54.3 1.0 OD2 D:ASP99 3.0 58.2 1.0 CD D:GLU95 3.0 25.3 1.0 CG D:ASP104 3.1 25.5 1.0 CA D:CA408 3.6 25.1 0.5 OD1 D:ASP96 4.3 30.2 1.0 CB D:ASP99 4.3 52.5 1.0 OD1 D:ASN103 4.4 30.9 1.0 N D:ASP101 4.5 36.1 1.0 CG D:GLU95 4.5 25.0 1.0 CB D:ASP104 4.5 18.0 1.0 N D:ASP99 4.6 49.4 1.0 N D:GLY97 4.7 34.3 1.0 CB D:ASP101 4.7 33.9 1.0 C D:ASP99 4.7 48.9 1.0 N D:TYR102 4.7 26.2 1.0 CA D:ASP99 4.8 49.7 1.0 N D:ASP96 4.8 23.1 1.0 N D:ASN100 4.8 46.5 1.0 N D:ASP104 4.9 16.5 1.0 CG D:ASP96 5.0 33.0 1.0

Calcium binding site 8 out of 8 in the Lecb (Pa-Lii) in Complex with Core Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Lecb (Pa-Lii) in Complex with Core Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca408 b:25.1 occ:0.50 O D:ASN21 2.4 21.1 1.0 O D:HOH817 2.5 45.0 1.0 OD1 D:ASP104 2.6 26.8 1.0 OD1 D:ASN103 2.8 30.9 1.0 CG D:ASN103 3.5 27.0 1.0 C D:ASN21 3.6 20.2 1.0 CA D:CA407 3.6 30.2 0.5 ND2 D:ASN103 3.7 27.1 1.0 CG D:ASP104 3.7 25.5 1.0 N D:ASP104 4.1 16.5 1.0 CA D:ASP104 4.1 15.8 1.0 CA D:SER22 4.2 22.9 1.0 N D:SER22 4.4 21.4 1.0 C D:ASN103 4.4 15.6 1.0 CA C:GLY114 4.4 26.6 1.0 CB D:ASN21 4.5 18.5 1.0 CB D:SER22 4.5 20.9 1.0 CB D:ASP104 4.5 18.0 1.0 OD2 D:ASP104 4.5 28.9 1.0 O D:HOH785 4.6 39.5 1.0 OD1 D:ASP99 4.6 58.5 1.0 O D:HOH704 4.6 32.8 1.0 CA D:ASN21 4.7 19.2 1.0 O D:ASN103 4.7 16.8 1.0 OD2 D:ASP99 4.8 58.2 1.0 CB D:ASN103 4.8 18.3 1.0 OG D:SER22 5.0 23.8 1.0

R.Loris, D.Tielker, K.-E.Jaeger, L.Wyns. Structural Basis of Carbohydrate Recognition By the Lectin Lecb From Pseudomonas Aeruginosa J.Mol.Biol. V. 331 861 2003.
ISSN: ISSN 0022-2836
PubMed: 12909014
DOI: 10.1016/S0022-2836(03)00754-X