Calcium in PDB 2d7f: Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid

The structure of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid, PDB code: 2d7f was solved by P.Delatorre, B.A.M.Rocha, E.P.Souza, B.T.Freitas, F.B.B.M.Moreno, A.H.Sampaio, W.F.Azevedo Jr., B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.99 / 2.31
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	100.915, 115.754, 241.626, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.7

The structure of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid (pdb code 2d7f). 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 A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid, PDB code: 2d7f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


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 A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca240 b:18.3 occ:1.00 O A:TYR12 2.3 17.1 1.0 OD2 A:ASP19 2.3 12.4 1.0 OD2 A:ASP10 2.5 11.5 1.0 OD1 A:ASN14 2.5 15.3 1.0 OD1 A:ASP10 2.6 13.2 1.0 CG A:ASP10 2.9 15.6 1.0 CG A:ASP19 3.5 16.2 1.0 C A:TYR12 3.5 16.7 1.0 CG A:ASN14 3.6 16.6 1.0 OD1 A:ASP19 3.9 11.3 1.0 CB A:ASN14 4.0 16.4 1.0 N A:ASN14 4.0 16.8 1.0 MN A:MN239 4.2 17.6 1.0 CA A:TYR12 4.3 16.5 1.0 CB A:ASP10 4.3 15.9 1.0 N A:TYR12 4.4 16.9 1.0 CB A:TYR12 4.4 16.9 1.0 O A:ASP208 4.4 15.6 1.0 CB A:ARG228 4.4 14.3 1.0 N A:PRO13 4.5 16.4 1.0 CA A:ARG228 4.5 14.3 1.0 CE1 A:HIS24 4.5 12.8 1.0 O A:ARG228 4.6 14.7 1.0 CA A:ASN14 4.6 16.7 1.0 CA A:PRO13 4.6 17.7 1.0 OD2 A:ASP208 4.7 11.8 1.0 CB A:ASP19 4.7 16.0 1.0 NE2 A:HIS24 4.7 13.8 1.0 C A:PRO13 4.7 16.7 1.0 ND2 A:ASN14 4.7 13.3 1.0 CD1 A:TYR12 4.9 16.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


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 A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca240 b:19.2 occ:1.00 O F:TYR12 2.3 19.5 1.0 OD1 F:ASN14 2.3 14.6 1.0 OD2 F:ASP19 2.4 15.1 1.0 OD2 F:ASP10 2.5 10.2 1.0 OD1 F:ASP10 2.5 10.0 1.0 CG F:ASP10 2.9 12.5 1.0 C F:TYR12 3.4 17.9 1.0 CG F:ASN14 3.5 13.8 1.0 CG F:ASP19 3.6 16.3 1.0 N F:ASN14 4.0 16.4 1.0 OD1 F:ASP19 4.0 15.2 1.0 CB F:ASN14 4.2 15.2 1.0 MN F:MN239 4.2 20.8 1.0 CA F:TYR12 4.2 17.7 1.0 CB F:TYR12 4.3 17.6 1.0 N F:TYR12 4.3 18.3 1.0 CB F:ASP10 4.4 14.5 1.0 N F:PRO13 4.4 17.6 1.0 O F:ASP208 4.5 13.9 1.0 CA F:PRO13 4.5 18.0 1.0 ND2 F:ASN14 4.5 11.2 1.0 CB F:ARG228 4.5 16.5 1.0 OD2 F:ASP208 4.5 10.1 1.0 C F:PRO13 4.6 16.0 1.0 CA F:ARG228 4.6 14.8 1.0 CE1 F:HIS24 4.7 16.9 1.0 CB F:ASP19 4.7 16.5 1.0 CA F:ASN14 4.8 15.2 1.0 CD1 F:TYR12 4.8 17.3 1.0 O F:ARG228 4.8 15.7 1.0 NE2 F:HIS24 4.9 18.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


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 A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca240 b:19.9 occ:1.00 OD2 L:ASP19 2.3 20.5 1.0 O L:TYR12 2.3 25.2 1.0 OD1 L:ASN14 2.4 20.9 1.0 OD1 L:ASP10 2.4 10.3 1.0 OD2 L:ASP10 2.6 11.9 1.0 CG L:ASP10 2.9 17.8 1.0 CG L:ASP19 3.4 23.2 1.0 C L:TYR12 3.5 23.3 1.0 CG L:ASN14 3.6 21.3 1.0 OD1 L:ASP19 3.9 20.1 1.0 N L:ASN14 3.9 25.2 1.0 MN L:MN239 4.1 22.1 1.0 CB L:ASN14 4.2 24.0 1.0 N L:TYR12 4.3 19.4 1.0 CA L:TYR12 4.3 20.9 1.0 CB L:ASP10 4.4 16.5 1.0 N L:PRO13 4.5 23.6 1.0 CB L:TYR12 4.5 22.4 1.0 CA L:PRO13 4.5 24.5 1.0 O L:ASP208 4.5 19.6 1.0 CA L:ARG228 4.6 24.0 1.0 C L:PRO13 4.6 24.5 1.0 ND2 L:ASN14 4.6 12.1 1.0 CB L:ARG228 4.6 24.0 1.0 CE1 L:HIS24 4.6 14.2 1.0 CA L:ASN14 4.7 24.7 1.0 CB L:ASP19 4.7 21.6 1.0 OD2 L:ASP208 4.7 13.5 1.0 O L:ARG228 4.7 22.5 1.0 NE2 L:HIS24 4.8 13.5 1.0 CD1 L:TYR12 4.9 23.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


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 A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca240 b:20.7 occ:1.00 OD1 S:ASN14 2.3 16.2 1.0 OD2 S:ASP19 2.3 21.6 1.0 O S:TYR12 2.3 19.2 1.0 OD1 S:ASP10 2.5 14.1 1.0 OD2 S:ASP10 2.6 12.8 1.0 CG S:ASP10 2.9 18.4 1.0 CG S:ASP19 3.4 21.6 1.0 CG S:ASN14 3.5 17.8 1.0 C S:TYR12 3.5 18.5 1.0 OD1 S:ASP19 3.8 17.1 1.0 N S:ASN14 4.0 17.9 1.0 CB S:ASN14 4.1 16.1 1.0 MN S:MN239 4.2 21.9 1.0 CA S:TYR12 4.2 19.1 1.0 N S:TYR12 4.3 18.5 1.0 CB S:TYR12 4.3 19.1 1.0 CB S:ASP10 4.4 16.3 1.0 CA S:ARG228 4.5 23.3 1.0 N S:PRO13 4.5 18.9 1.0 ND2 S:ASN14 4.5 15.3 1.0 O S:ASP208 4.5 20.4 1.0 CE1 S:HIS24 4.6 15.6 1.0 CB S:ARG228 4.6 24.3 1.0 CA S:PRO13 4.6 18.8 1.0 OD2 S:ASP208 4.6 19.9 1.0 C S:PRO13 4.6 18.3 1.0 CB S:ASP19 4.7 22.9 1.0 CA S:ASN14 4.7 17.0 1.0 O S:ARG228 4.8 21.6 1.0 NE2 S:HIS24 4.9 17.5 1.0 CD1 S:TYR12 4.9 19.8 1.0

P.Delatorre, B.A.M.Rocha, E.P.Souza, T.M.Oliveira, G.A.Bezerra, F.B.M.B.Moreno, B.T.Freitas, T.Santi-Gadelha, A.H.Sampaio, W.F.Azevedo Jr., B.S.Cavada. Structure of A Lectin From Canavalia Gladiata Seeds: New Structural Insights For Old Molecules Bmc Struct.Biol. V. 7 52 2007.
ISSN: ESSN 1472-6807
PubMed: 17683532
DOI: 10.1186/1472-6807-7-52