Calcium in PDB 4k1y: Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome

The structure of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome, PDB code: 4k1y was solved by G.A.Bezerra, R.Viertlmayr, T.R.Moura, P.Delatorre, B.A.M.Rocha, B.S.Cavada, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.94 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.880, 95.660, 94.610, 90.00, 132.29, 90.00
R / Rfree (%)	20.4 / 22.8

The structure of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome also contains other interesting chemical elements:

Cadmium	(Cd)	9 atoms
Manganese	(Mn)	4 atoms

The binding sites of Calcium atom in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome (pdb code 4k1y). 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 Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome, PDB code: 4k1y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


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 Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:29.6 occ:1.00 O A:TYR12 2.5 31.2 1.0 O A:HOH422 2.7 23.6 1.0 OD1 A:ASN14 2.7 19.4 1.0 OD1 A:ASP10 2.7 20.0 1.0 OD2 A:ASP19 2.8 28.7 1.0 OD2 A:ASP10 2.8 26.7 1.0 CG A:ASP10 3.1 22.7 1.0 CG A:ASN14 3.6 25.6 1.0 C A:TYR12 3.7 28.7 1.0 N A:ASN14 3.9 30.1 1.0 CG A:ASP19 3.9 30.5 1.0 CB A:ASN14 4.0 32.2 1.0 O A:ARG228 4.3 32.2 1.0 O A:ASP208 4.5 22.8 1.0 CA A:ARG228 4.5 28.5 1.0 CB A:ARG228 4.6 28.0 1.0 OD1 A:ASP208 4.6 31.2 1.0 CA A:TYR12 4.6 22.0 1.0 CA A:ASN14 4.6 28.8 1.0 CB A:TYR12 4.6 26.5 1.0 CB A:ASP10 4.6 23.3 1.0 OD1 A:ASP19 4.6 31.5 1.0 N A:PRO13 4.6 29.9 1.0 O A:HOH417 4.7 27.3 1.0 MN A:MN301 4.7 23.0 1.0 N A:TYR12 4.8 30.9 1.0 C A:PRO13 4.8 29.5 1.0 ND2 A:ASN14 4.8 30.9 1.0 CA A:PRO13 4.8 28.2 1.0 CD1 A:TYR12 4.8 29.2 1.0 CB A:ASP19 4.9 27.2 1.0 C A:ARG228 4.9 31.6 1.0 CB A:ASP208 5.0 28.5 1.0 CE1 A:HIS24 5.0 26.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


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 Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:30.6 occ:1.00 O B:TYR12 2.6 35.9 1.0 OD2 B:ASP10 2.7 29.2 1.0 O B:HOH402 2.8 26.4 1.0 OD2 B:ASP19 2.8 38.0 1.0 OD1 B:ASN14 2.8 32.9 1.0 OD1 B:ASP10 2.9 33.2 1.0 CG B:ASP10 3.2 32.8 1.0 N B:ASN14 3.8 33.5 1.0 CG B:ASN14 3.8 40.2 1.0 C B:TYR12 3.9 34.0 1.0 CG B:ASP19 3.9 30.7 1.0 CB B:ASN14 4.0 36.4 1.0 OD1 B:ASP208 4.4 28.6 1.0 O B:ARG228 4.4 30.2 1.0 MN B:MN301 4.4 23.0 1.0 CA B:ASN14 4.5 32.7 1.0 OD1 B:ASP19 4.6 33.7 1.0 CB B:ARG228 4.6 33.4 1.0 CA B:ARG228 4.6 27.8 1.0 CB B:ASP10 4.7 31.4 1.0 N B:PRO13 4.7 32.8 1.0 C B:PRO13 4.7 30.9 1.0 CA B:PRO13 4.7 30.0 1.0 CD1 B:ILE17 4.7 33.7 1.0 O B:HOH408 4.7 27.2 1.0 O B:ASP208 4.7 27.6 1.0 CB B:ASP19 4.9 36.0 1.0 CA B:TYR12 4.9 26.6 1.0 CE1 B:HIS24 4.9 32.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


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 Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:32.9 occ:1.00 O C:HOH411 2.6 24.2 1.0 O C:TYR12 2.7 29.5 1.0 OD2 C:ASP19 2.7 28.9 1.0 O C:HOH455 2.7 38.9 1.0 OD2 C:ASP10 2.7 27.3 1.0 OD1 C:ASP10 2.8 27.7 1.0 OD1 C:ASN14 2.9 29.1 1.0 CG C:ASP10 3.1 29.1 1.0 CG C:ASN14 3.7 35.0 1.0 CG C:ASP19 3.8 29.1 1.0 N C:ASN14 3.8 34.0 1.0 C C:TYR12 3.9 29.9 1.0 CB C:ASN14 3.9 31.4 1.0 O C:HOH405 4.1 25.8 1.0 MN C:MN301 4.2 24.8 1.0 OD1 C:ASP19 4.2 35.0 1.0 O C:ARG228 4.4 31.2 1.0 CA C:ASN14 4.5 36.3 1.0 CB C:ARG228 4.5 32.2 1.0 CA C:ARG228 4.5 32.3 1.0 OD1 C:ASP208 4.6 28.6 1.0 CB C:ASP10 4.6 26.7 1.0 CD1 C:ILE17 4.7 39.2 1.0 C C:PRO13 4.8 34.5 1.0 CA C:TYR12 4.8 27.9 1.0 N C:PRO13 4.8 30.4 1.0 CB C:TYR12 4.8 31.0 1.0 CA C:PRO13 4.8 30.6 1.0 O C:ASP208 4.9 20.8 1.0 CB C:ASP19 4.9 25.0 1.0 ND2 C:ASN14 4.9 36.7 1.0 C C:ARG228 5.0 30.4 1.0 N C:TYR12 5.0 29.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome


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 Canavalia Boliviana Lectin in Complex with MAN1- 3MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:37.0 occ:1.00 O D:TYR12 2.5 38.4 1.0 O D:HOH402 2.6 35.5 1.0 OD1 D:ASP10 2.8 28.0 1.0 OD2 D:ASP19 2.8 40.7 1.0 OD2 D:ASP10 2.9 33.1 1.0 OD1 D:ASN14 3.0 33.5 1.0 CG D:ASP10 3.2 32.1 1.0 C D:TYR12 3.7 36.0 1.0 N D:ASN14 3.8 37.8 1.0 CG D:ASN14 3.8 36.3 1.0 CG D:ASP19 3.9 37.7 1.0 CB D:ASN14 4.0 39.3 1.0 OD1 D:ASP208 4.1 40.0 1.0 O D:HOH432 4.3 26.4 1.0 O D:ARG228 4.3 32.4 1.0 MN D:MN301 4.5 30.5 1.0 CA D:ASN14 4.5 38.6 1.0 N D:PRO13 4.6 42.1 1.0 CA D:ARG228 4.6 32.9 1.0 CA D:TYR12 4.6 30.7 1.0 CB D:TYR12 4.7 35.9 1.0 C D:PRO13 4.7 35.2 1.0 CB D:ASP10 4.7 28.0 1.0 OD1 D:ASP19 4.7 35.3 1.0 CA D:PRO13 4.7 36.0 1.0 CB D:ARG228 4.7 35.1 1.0 CB D:ASP19 4.7 38.0 1.0 O D:ASP208 4.8 29.4 1.0 CD1 D:ILE17 4.9 35.0 1.0 CB D:ASP208 4.9 29.2 1.0 N D:TYR12 4.9 33.3 1.0 CG D:ASP208 4.9 41.5 1.0 CD1 D:TYR12 5.0 36.8 1.0 C D:ARG228 5.0 33.0 1.0 CD2 D:LEU230 5.0 30.9 1.0

G.A.Bezerra, R.Viertlmayr, T.R.Moura, P.Delatorre, B.A.Rocha, K.S.Do Nascimento, J.G.Figueiredo, I.G.Bezerra, C.S.Teixeira, R.C.Simoes, C.S.Nagano, N.M.De Alencar, K.Gruber, B.S.Cavada. Structural Studies of An Anti-Inflammatory Lectin From Canavalia Boliviana Seeds in Complex with Dimannosides. Plos One V. 9 97015 2014.
ISSN: ESSN 1932-6203
PubMed: 24865454
DOI: 10.1371/JOURNAL.PONE.0097015