Calcium in PDB 3zyf: Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution

The structure of Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution, PDB code: 3zyf was solved by R.U.Kadam, M.Bergmann, M.Hurley, D.Garg, M.Cacciarini, M.A.Swiderska, C.Nativi, M.Sattler, A.R.Smyth, P.Williams, M.Camara, A.Stocker, T.Darbre, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.284 / 1.94
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.562, 84.562, 163.709, 90.00, 90.00, 90.00
R / Rfree (%)	18.55 / 21

The binding sites of Calcium atom in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution (pdb code 3zyf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution, PDB code: 3zyf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution


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 Pa-Il Lectin Complexed with Npg at 1.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:31.4 occ:1.00 OD2 A:ASP100 2.5 20.4 1.0 O A:TYR36 2.6 28.6 1.0 OD1 A:ASN108 2.6 30.9 1.0 O3 A:1471001 2.6 22.2 1.0 O A:THR104 2.6 32.4 1.0 O4 A:1471001 2.6 30.7 1.0 OD1 A:ASN107 2.7 39.7 1.0 C A:TYR36 3.4 25.6 1.0 CG A:ASP100 3.5 24.1 1.0 C3 A:1471001 3.5 27.3 1.0 OG1 A:THR104 3.5 32.8 1.0 C4 A:1471001 3.6 28.1 1.0 C A:THR104 3.6 31.7 1.0 CG A:ASN108 3.7 29.4 1.0 CG A:ASN107 3.7 38.7 1.0 OD1 A:ASP100 3.7 24.8 1.0 CB A:THR104 3.9 36.1 1.0 CA A:TYR36 3.9 23.4 1.0 C2 A:1471001 4.0 31.4 1.0 ND2 A:ASN107 4.1 35.9 1.0 CB A:TYR36 4.1 22.6 1.0 ND2 A:ASN108 4.1 24.5 1.0 CA A:THR104 4.4 35.3 1.0 N A:TYR105 4.4 31.4 1.0 N A:GLY37 4.4 32.5 1.0 CA A:TYR105 4.5 31.2 1.0 O A:HOH2119 4.6 38.0 1.0 O2 A:1471001 4.7 33.5 1.0 N A:ASN108 4.7 35.8 1.0 CA A:GLY37 4.8 34.7 1.0 C A:TYR105 4.8 33.4 1.0 CB A:ASP100 4.9 21.1 1.0 C5 A:1471001 4.9 28.3 1.0 O A:HOH2116 4.9 40.6 1.0 C A:ASN107 4.9 36.7 1.0 N A:ASN107 5.0 37.2 1.0 CB A:ASN108 5.0 28.7 1.0 CD2 A:TYR36 5.0 23.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution


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 Pa-Il Lectin Complexed with Npg at 1.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:26.1 occ:1.00 OD1 B:ASN108 2.5 20.6 1.0 O B:THR104 2.5 27.2 1.0 O3 B:1471002 2.6 22.5 1.0 O B:TYR36 2.6 24.3 1.0 O4 B:1471002 2.6 24.5 1.0 OD2 B:ASP100 2.6 23.6 1.0 OD1 B:ASN107 2.6 27.7 1.0 C B:TYR36 3.4 20.1 1.0 C4 B:1471002 3.5 24.6 1.0 C3 B:1471002 3.5 24.7 1.0 CG B:ASN108 3.6 26.3 1.0 C B:THR104 3.6 26.9 1.0 CG B:ASP100 3.6 23.5 1.0 CG B:ASN107 3.7 29.6 1.0 OG1 B:THR104 3.7 22.6 1.0 CA B:TYR36 3.9 21.1 1.0 OD1 B:ASP100 3.9 22.9 1.0 CB B:THR104 4.0 26.7 1.0 CB B:TYR36 4.0 19.4 1.0 C2 B:1471002 4.0 27.3 1.0 ND2 B:ASN108 4.1 26.3 1.0 ND2 B:ASN107 4.2 27.9 1.0 N B:GLY37 4.4 32.9 1.0 CA B:THR104 4.4 27.2 1.0 N B:TYR105 4.5 26.1 1.0 CA B:TYR105 4.5 25.9 1.0 N B:ASN108 4.6 30.2 1.0 O B:HOH2090 4.6 38.3 1.0 O2 B:1471002 4.7 26.1 1.0 C B:ASN107 4.8 31.1 1.0 CA B:GLY37 4.8 35.3 1.0 C B:TYR105 4.8 26.9 1.0 CB B:ASN108 4.8 26.8 1.0 C5 B:1471002 4.8 22.4 1.0 N B:ASN107 4.8 31.4 1.0 CA B:ASN108 4.9 26.7 1.0 CB B:ASP100 4.9 17.6 1.0 CB B:ASN107 5.0 31.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution


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 Pa-Il Lectin Complexed with Npg at 1.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca903 b:28.3 occ:1.00 O C:TYR36 2.5 30.8 1.0 O C:THR104 2.5 34.4 1.0 OD2 C:ASP100 2.6 24.5 1.0 OD1 C:ASN108 2.6 28.5 1.0 O3 C:1471003 2.6 25.9 1.0 OD1 C:ASN107 2.6 35.0 1.0 O4 C:1471003 2.6 30.9 1.0 C C:TYR36 3.4 30.4 1.0 C3 C:1471003 3.5 30.8 1.0 C4 C:1471003 3.5 32.7 1.0 CG C:ASP100 3.6 27.9 1.0 C C:THR104 3.7 34.1 1.0 CG C:ASN108 3.7 27.7 1.0 CG C:ASN107 3.7 33.0 1.0 OG1 C:THR104 3.7 28.8 1.0 OD1 C:ASP100 3.8 26.4 1.0 CA C:TYR36 3.9 27.1 1.0 C2 C:1471003 4.0 30.9 1.0 CB C:TYR36 4.1 25.3 1.0 ND2 C:ASN107 4.1 31.9 1.0 CB C:THR104 4.1 32.0 1.0 ND2 C:ASN108 4.1 26.1 1.0 N C:GLY37 4.4 27.2 1.0 CA C:TYR105 4.5 34.2 1.0 N C:TYR105 4.5 34.0 1.0 CA C:THR104 4.5 34.5 1.0 O2 C:1471003 4.7 29.9 1.0 N C:ASN108 4.7 28.6 1.0 CA C:GLY37 4.8 29.0 1.0 C C:ASN107 4.8 30.6 1.0 C C:TYR105 4.8 32.3 1.0 C5 C:1471003 4.9 31.9 1.0 O C:HOH2096 4.9 37.8 1.0 N C:ASN107 4.9 34.0 1.0 CB C:ASP100 4.9 24.8 1.0 CD1 C:TYR36 5.0 28.5 1.0 CB C:ASN108 5.0 26.8 1.0 CB C:ASN107 5.0 34.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution


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 Pa-Il Lectin Complexed with Npg at 1.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca904 b:36.0 occ:1.00 OD1 D:ASN108 2.5 34.4 1.0 OD2 D:ASP100 2.5 30.2 1.0 O3 D:1471004 2.6 32.6 1.0 O D:THR104 2.6 42.4 1.0 O D:TYR36 2.6 43.4 1.0 O4 D:1471004 2.7 35.5 1.0 OD1 D:ASN107 2.7 44.2 1.0 C D:TYR36 3.4 41.5 1.0 CG D:ASP100 3.5 33.8 1.0 C3 D:1471004 3.5 34.9 1.0 C D:THR104 3.5 43.5 1.0 OG1 D:THR104 3.6 34.2 1.0 CG D:ASN108 3.6 35.2 1.0 C4 D:1471004 3.6 37.1 1.0 CG D:ASN107 3.8 45.0 1.0 OD1 D:ASP100 3.8 31.6 1.0 CA D:TYR36 3.9 35.4 1.0 C2 D:1471004 3.9 37.5 1.0 CB D:THR104 4.0 39.9 1.0 ND2 D:ASN108 4.1 33.9 1.0 CB D:TYR36 4.1 32.1 1.0 ND2 D:ASN107 4.2 46.2 1.0 N D:TYR105 4.4 44.7 1.0 CA D:THR104 4.4 41.2 1.0 CA D:TYR105 4.4 43.1 1.0 N D:GLY37 4.4 42.6 1.0 O2 D:1471004 4.5 40.3 1.0 N D:ASN108 4.7 38.8 1.0 C D:TYR105 4.8 44.6 1.0 CA D:GLY37 4.8 43.5 1.0 N D:ASN107 4.8 44.4 1.0 C D:ASN107 4.8 39.4 1.0 CB D:ASP100 4.9 29.4 1.0 C5 D:1471004 4.9 37.1 1.0 CB D:ASN108 4.9 36.4 1.0 O D:HOH2086 4.9 35.1 1.0

R.U.Kadam, M.Bergmann, M.Hurley, D.Garg, M.Cacciarini, M.A.Swiderska, C.Nativi, M.Sattler, A.R.Smyth, P.Williams, M.Camara, A.Stocker, T.Darbre, J.-L.Reymond. A Glycopeptide Dendrimer Inhibitor of the Galactose- Specific Lectin Leca and of Pseudomonas Aeruginosa Biofilms. Angew.Chem.Int.Ed.Engl. V. 50 10631 2011.
ISSN: ISSN 1433-7851
PubMed: 21919164
DOI: 10.1002/ANIE.201104342