Calcium in PDB 4yw6: Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca

The structure of Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca, PDB code: 4yw6 was solved by R.Visini, X.Jin, G.Michaud, M.Bergmann, E.Gillon, A.Imberty, A.Stocker, T.Darbre, R.Pieters, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.93 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.870, 72.980, 79.020, 117.52, 104.99, 90.00
R / Rfree (%)	18.6 / 20.6

The binding sites of Calcium atom in the Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca (pdb code 4yw6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca, PDB code: 4yw6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:9.7 occ:1.00 H431 A:G0P902 1.8 13.8 1.0 H411 A:G0P902 2.0 11.6 1.0 O A:THR104 2.3 11.1 1.0 O A:TYR36 2.3 10.0 1.0 OD1 A:ASN108 2.4 9.6 1.0 OD1 A:ASN107 2.5 10.6 1.0 O43 A:G0P902 2.5 11.5 1.0 O41 A:G0P902 2.5 9.6 1.0 OD2 A:ASP100 2.5 9.3 1.0 C A:TYR36 3.3 9.9 1.0 C40 A:G0P902 3.4 11.2 1.0 C42 A:G0P902 3.4 13.2 1.0 CG A:ASN108 3.4 8.2 1.0 C A:THR104 3.5 9.2 1.0 H441 A:G0P902 3.5 14.4 1.0 CG A:ASP100 3.5 7.8 1.0 CG A:ASN107 3.5 10.3 1.0 H401 A:G0P902 3.6 13.4 1.0 OG1 A:THR104 3.7 12.4 1.0 OD1 A:ASP100 3.8 9.0 1.0 ND2 A:ASN108 3.9 9.7 1.0 CA A:TYR36 3.9 9.1 1.0 ND2 A:ASN107 3.9 11.2 1.0 CB A:THR104 4.0 11.6 1.0 C44 A:G0P902 4.0 12.0 1.0 CB A:TYR36 4.1 11.3 1.0 H421 A:G0P902 4.2 15.8 1.0 CA A:THR104 4.3 10.5 1.0 N A:TYR105 4.4 10.1 1.0 CA A:TYR105 4.4 10.2 1.0 N A:GLY37 4.4 9.9 1.0 N A:ASN108 4.6 9.0 1.0 O A:HOH1060 4.7 19.0 1.0 O45 A:G0P902 4.7 13.9 1.0 CA A:GLY37 4.7 10.4 1.0 C A:TYR105 4.7 10.2 1.0 CB A:ASN108 4.8 9.7 1.0 C37 A:G0P902 4.8 10.6 1.0 C A:ASN107 4.8 9.6 1.0 CB A:ASP100 4.8 9.1 1.0 N A:ASN107 4.8 10.7 1.0 CB A:ASN107 4.9 11.3 1.0 CA A:ASN108 4.9 9.3 1.0 H381 A:G0P902 5.0 15.8 1.0

Calcium binding site 2 out of 4 in the Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:9.7 occ:1.00 H411 B:G0P902 2.0 11.5 1.0 OD1 B:ASN108 2.3 10.7 1.0 O B:TYR36 2.3 10.8 1.0 O B:THR104 2.3 11.2 1.0 O43 B:G0P902 2.4 12.6 1.0 O41 B:G0P902 2.5 9.6 1.0 OD1 B:ASN107 2.5 11.0 1.0 OD2 B:ASP100 2.5 8.8 1.0 H431 B:G0P902 3.0 15.1 1.0 C B:TYR36 3.3 10.6 1.0 C42 B:G0P902 3.4 13.8 1.0 C40 B:G0P902 3.4 10.6 1.0 CG B:ASN108 3.4 9.6 1.0 H441 B:G0P902 3.5 15.7 1.0 C B:THR104 3.5 9.7 1.0 CG B:ASN107 3.5 9.5 1.0 CG B:ASP100 3.5 8.8 1.0 H401 B:G0P902 3.6 12.7 1.0 OG1 B:THR104 3.7 13.4 1.0 OD1 B:ASP100 3.9 9.0 1.0 ND2 B:ASN108 3.9 9.8 1.0 CA B:TYR36 3.9 8.7 1.0 C44 B:G0P902 3.9 13.1 1.0 ND2 B:ASN107 4.0 11.4 1.0 CB B:THR104 4.0 12.1 1.0 CB B:TYR36 4.1 12.0 1.0 H421 B:G0P902 4.2 16.5 1.0 CA B:THR104 4.4 10.9 1.0 N B:TYR105 4.4 10.2 1.0 CA B:TYR105 4.4 10.3 1.0 N B:GLY37 4.4 10.7 1.0 N B:ASN108 4.6 10.4 1.0 O B:HOH1053 4.6 19.8 1.0 O45 B:G0P902 4.6 13.6 1.0 CA B:GLY37 4.7 10.2 1.0 C B:TYR105 4.7 10.8 1.0 C37 B:G0P902 4.7 12.4 1.0 CB B:ASN108 4.7 10.8 1.0 C B:ASN107 4.7 11.7 1.0 N B:ASN107 4.8 11.1 1.0 CB B:ASP100 4.8 9.4 1.0 CB B:ASN107 4.9 11.0 1.0 CA B:ASN108 4.9 9.6 1.0 H381 B:G0P902 5.0 14.3 1.0

Calcium binding site 3 out of 4 in the Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca901 b:9.8 occ:1.00 H411 C:G0P902 2.0 12.8 1.0 O C:THR104 2.3 10.2 1.0 O C:TYR36 2.3 10.8 1.0 OD1 C:ASN108 2.4 10.7 1.0 O43 C:G0P902 2.4 11.7 1.0 OD1 C:ASN107 2.4 9.8 1.0 O41 C:G0P902 2.5 10.6 1.0 OD2 C:ASP100 2.5 9.3 1.0 H431 C:G0P902 3.0 14.0 1.0 C C:TYR36 3.3 10.3 1.0 C42 C:G0P902 3.4 12.9 1.0 C40 C:G0P902 3.4 10.1 1.0 C C:THR104 3.5 9.1 1.0 CG C:ASN108 3.5 9.5 1.0 H441 C:G0P902 3.5 14.6 1.0 CG C:ASN107 3.5 10.2 1.0 CG C:ASP100 3.5 9.9 1.0 H401 C:G0P902 3.6 12.1 1.0 OG1 C:THR104 3.7 13.1 1.0 OD1 C:ASP100 3.9 9.3 1.0 CA C:TYR36 3.9 9.7 1.0 ND2 C:ASN107 3.9 12.9 1.0 ND2 C:ASN108 4.0 9.2 1.0 C44 C:G0P902 4.0 12.2 1.0 CB C:THR104 4.0 10.7 1.0 CB C:TYR36 4.1 10.9 1.0 H421 C:G0P902 4.2 15.5 1.0 N C:TYR105 4.4 10.6 1.0 CA C:THR104 4.4 10.6 1.0 CA C:TYR105 4.4 10.8 1.0 N C:GLY37 4.4 11.4 1.0 N C:ASN108 4.6 9.3 1.0 O C:HOH1071 4.7 17.6 1.0 O45 C:G0P902 4.7 13.1 1.0 CA C:GLY37 4.7 10.6 1.0 C C:TYR105 4.7 10.6 1.0 C37 C:G0P902 4.8 10.5 1.0 C C:ASN107 4.8 9.8 1.0 CB C:ASN108 4.8 10.2 1.0 N C:ASN107 4.8 11.0 1.0 CB C:ASP100 4.8 9.8 1.0 CB C:ASN107 4.8 11.1 1.0 CA C:ASN108 4.9 9.4 1.0 H381 C:G0P902 5.0 13.9 1.0

Calcium binding site 4 out of 4 in the Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Insight Into Divalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca901 b:9.8 occ:1.00 H411 D:G0P902 2.0 12.7 1.0 O D:THR104 2.3 10.5 1.0 O D:TYR36 2.3 10.4 1.0 OD1 D:ASN108 2.4 10.4 1.0 O43 D:G0P902 2.4 10.8 1.0 OD1 D:ASN107 2.4 9.4 1.0 OD2 D:ASP100 2.5 9.0 1.0 O41 D:G0P902 2.5 10.6 1.0 H431 D:G0P902 3.0 13.0 1.0 C D:TYR36 3.3 8.8 1.0 C42 D:G0P902 3.4 12.4 1.0 C40 D:G0P902 3.4 9.1 1.0 C D:THR104 3.5 9.3 1.0 CG D:ASN108 3.5 8.2 1.0 CG D:ASP100 3.5 8.1 1.0 H441 D:G0P902 3.5 14.3 1.0 CG D:ASN107 3.5 10.4 1.0 H401 D:G0P902 3.7 10.9 1.0 OG1 D:THR104 3.7 12.5 1.0 OD1 D:ASP100 3.9 9.0 1.0 CA D:TYR36 3.9 9.2 1.0 ND2 D:ASN108 3.9 9.5 1.0 ND2 D:ASN107 4.0 11.2 1.0 C44 D:G0P902 4.0 11.9 1.0 CB D:THR104 4.0 12.0 1.0 CB D:TYR36 4.1 11.4 1.0 H421 D:G0P902 4.2 14.9 1.0 N D:TYR105 4.3 9.9 1.0 CA D:TYR105 4.4 9.9 1.0 CA D:THR104 4.4 9.7 1.0 N D:GLY37 4.4 10.0 1.0 N D:ASN108 4.6 9.7 1.0 O D:HOH1061 4.7 19.1 1.0 O45 D:G0P902 4.7 13.5 1.0 CA D:GLY37 4.7 9.8 1.0 C D:TYR105 4.7 9.9 1.0 C D:ASN107 4.7 9.8 1.0 CB D:ASN108 4.8 9.5 1.0 C37 D:G0P902 4.8 10.0 1.0 CB D:ASP100 4.8 9.8 1.0 N D:ASN107 4.8 11.4 1.0 CB D:ASN107 4.9 10.8 1.0 CA D:ASN108 4.9 10.1 1.0

R.Visini, X.Jin, M.Bergmann, G.Michaud, F.Pertici, O.Fu, A.Pukin, T.R.Branson, D.M.Thies-Weesie, J.Kemmink, E.Gillon, A.Imberty, A.Stocker, T.Darbre, R.J.Pieters, J.L.Reymond. Structural Insight Into Multivalent Galactoside Binding to Pseudomonas Aeruginosa Lectin Leca. Acs Chem.Biol. V. 10 2455 2015.
ISSN: ESSN 1554-8937
PubMed: 26295304
DOI: 10.1021/ACSCHEMBIO.5B00302