Calcium in PDB 2je9: Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose

The structure of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose, PDB code: 2je9 was solved by C.S.Nagano, L.Sanz, B.S.Cavada, J.J.Calvete, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.71 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.171, 85.153, 175.741, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.9

The structure of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Manganese	(Mn)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose (pdb code 2je9). 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 Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose, PDB code: 2je9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose


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 Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1240 b:12.1 occ:1.00 O A:HOH2131 2.4 9.1 1.0 O A:TYR14 2.4 14.3 1.0 OD1 A:ASN16 2.4 9.2 1.0 OD2 A:ASP21 2.4 13.8 1.0 OD2 A:ASP12 2.4 14.3 1.0 O A:HOH2122 2.5 13.3 1.0 OD1 A:ASP12 2.5 11.6 1.0 CG A:ASP12 2.8 11.5 1.0 CG A:ASP21 3.5 15.8 1.0 CG A:ASN16 3.5 12.6 1.0 C A:TYR14 3.6 14.2 1.0 OD1 A:ASP21 3.9 17.6 1.0 N A:ASN16 3.9 14.5 1.0 CB A:ASN16 4.1 13.5 1.0 MN A:MN1241 4.2 13.4 1.0 CB A:ASP12 4.3 11.1 1.0 CA A:TYR14 4.4 12.8 1.0 N A:PRO15 4.5 15.3 1.0 O A:HOH2139 4.5 17.1 1.0 CA A:PRO15 4.5 15.6 1.0 N A:TYR14 4.6 12.9 1.0 CB A:TYR14 4.6 12.1 1.0 C A:PRO15 4.6 16.0 1.0 ND2 A:ASN16 4.6 8.2 1.0 CE1 A:HIS26 4.7 5.6 1.0 CA A:ASN16 4.7 14.8 1.0 O A:ARG230 4.7 11.6 1.0 CB A:ASP21 4.7 15.9 1.0 OD1 A:ASP210 4.7 11.9 1.0 O A:ASP210 4.7 11.6 1.0 CB A:ARG230 4.8 13.8 1.0 CA A:ARG230 4.9 12.7 1.0 NE2 A:HIS26 4.9 7.5 1.0 CD2 A:TYR14 5.0 12.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose


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 Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1240 b:18.4 occ:1.00 OD1 B:ASN16 2.3 24.5 1.0 O B:TYR14 2.4 19.1 1.0 OD2 B:ASP21 2.4 18.5 1.0 OD2 B:ASP12 2.4 16.9 1.0 O B:HOH2110 2.4 16.6 1.0 O B:HOH2122 2.6 15.3 1.0 OD1 B:ASP12 2.7 19.2 1.0 CG B:ASP12 2.9 17.4 1.0 CG B:ASN16 3.5 22.4 1.0 CG B:ASP21 3.5 23.2 1.0 C B:TYR14 3.6 19.7 1.0 N B:ASN16 3.9 22.5 1.0 OD1 B:ASP21 4.0 25.0 1.0 CB B:ASN16 4.2 22.7 1.0 MN B:MN1241 4.3 16.9 1.0 O B:HOH2131 4.4 16.5 1.0 CA B:TYR14 4.4 18.8 1.0 CB B:ASP12 4.4 15.8 1.0 CB B:TYR14 4.5 18.7 1.0 N B:TYR14 4.5 18.0 1.0 ND2 B:ASN16 4.5 19.3 1.0 CA B:PRO15 4.6 21.1 1.0 N B:PRO15 4.6 20.8 1.0 C B:PRO15 4.6 21.7 1.0 O B:ARG230 4.7 16.5 1.0 O B:ASP210 4.7 14.2 1.0 CA B:ASN16 4.7 23.0 1.0 CB B:ARG230 4.7 16.4 1.0 CB B:ASP21 4.7 23.9 1.0 CE1 B:HIS26 4.8 13.8 1.0 CA B:ARG230 4.8 16.8 1.0 OD1 B:ASP210 4.9 19.9 1.0 CD2 B:TYR14 4.9 16.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose


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 Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1240 b:26.3 occ:1.00 O C:HOH2074 2.2 27.7 1.0 O C:TYR14 2.4 25.5 1.0 OD2 C:ASP21 2.4 21.3 1.0 OD1 C:ASP12 2.5 15.2 1.0 O C:HOH2066 2.5 32.1 1.0 OD1 C:ASN16 2.5 24.6 1.0 OD2 C:ASP12 2.5 25.5 1.0 CG C:ASP12 2.8 21.8 1.0 CG C:ASP21 3.6 26.3 1.0 CG C:ASN16 3.6 27.6 1.0 C C:TYR14 3.6 25.5 1.0 N C:ASN16 3.9 28.4 1.0 OD1 C:ASP21 4.0 25.0 1.0 CB C:ASN16 4.1 28.8 1.0 MN C:MN1241 4.1 21.2 1.0 CB C:ASP12 4.4 20.9 1.0 CA C:TYR14 4.5 25.8 1.0 N C:PRO15 4.5 26.4 1.0 C C:PRO15 4.5 27.4 1.0 CA C:PRO15 4.6 26.4 1.0 N C:TYR14 4.6 25.0 1.0 CA C:ASN16 4.6 28.8 1.0 CE1 C:HIS26 4.6 17.6 1.0 O C:ASP210 4.6 26.1 1.0 CB C:TYR14 4.7 26.3 1.0 O C:ARG230 4.7 28.1 1.0 CB C:ASP21 4.8 27.9 1.0 ND2 C:ASN16 4.8 25.0 1.0 O C:HOH2079 4.8 22.5 1.0 OD1 C:ASP210 4.8 29.3 1.0 CB C:ARG230 4.8 28.9 1.0 CD2 C:TYR14 4.8 26.1 1.0 CA C:ARG230 4.8 29.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose


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 Recombinant Dioclea Grandiflora Lectin Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1240 b:19.7 occ:1.00 O D:HOH2077 2.3 23.7 1.0 O D:TYR14 2.3 21.6 1.0 O D:HOH2005 2.4 18.1 1.0 OD1 D:ASN16 2.4 21.2 1.0 OD2 D:ASP21 2.4 16.3 1.0 OD2 D:ASP12 2.4 19.7 1.0 OD1 D:ASP12 2.7 16.7 1.0 CG D:ASP12 2.9 19.4 1.0 CG D:ASN16 3.5 20.7 1.0 CG D:ASP21 3.5 18.7 1.0 C D:TYR14 3.5 21.6 1.0 N D:ASN16 3.8 21.3 1.0 CB D:ASN16 4.0 20.4 1.0 OD1 D:ASP21 4.0 14.8 1.0 MN D:MN1241 4.2 16.9 1.0 CB D:ASP12 4.4 17.9 1.0 CA D:TYR14 4.4 21.7 1.0 N D:PRO15 4.5 21.7 1.0 O D:HOH2083 4.5 11.3 1.0 N D:TYR14 4.6 21.1 1.0 CA D:PRO15 4.6 22.3 1.0 CB D:TYR14 4.6 21.4 1.0 CA D:ASN16 4.6 20.5 1.0 C D:PRO15 4.6 22.3 1.0 ND2 D:ASN16 4.6 19.6 1.0 CE1 D:HIS26 4.6 12.3 1.0 O D:ARG230 4.6 24.6 1.0 O D:ASP210 4.7 23.5 1.0 OD1 D:ASP210 4.7 24.7 1.0 CB D:ASP21 4.7 18.5 1.0 CB D:ARG230 4.8 24.1 1.0 CA D:ARG230 4.8 24.8 1.0 CD2 D:TYR14 5.0 26.0 1.0

C.S.Nagano, J.J.Calvete, D.Barettino, A.Perez, B.S.Cavada, L.Sanz. Insights Into the Structural Basis of the pH- Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis of Recombinant Diocleinae Lectins. Biochem.J. V. 409 417 2008.
ISSN: ISSN 0264-6021
PubMed: 17937659
DOI: 10.1042/BJ20070942