Calcium in PDB 4k1z: Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-Ome

The structure of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-Ome, PDB code: 4k1z 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)	41.15 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.810, 107.810, 157.910, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 22.2

The structure of Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-Ome also contains other interesting chemical elements:

Cadmium	(Cd)	9 atoms
Manganese	(Mn)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-Ome (pdb code 4k1z). 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- 4MAN-Ome, PDB code: 4k1z:
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- 4MAN-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- 4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:18.9 occ:1.00 O A:TYR12 2.4 23.9 1.0 OD2 A:ASP19 2.5 14.3 1.0 O A:HOH402 2.5 14.5 1.0 OD1 A:ASN14 2.5 20.4 1.0 OD2 A:ASP10 2.6 16.3 1.0 OD1 A:ASP10 2.6 18.1 1.0 O A:HOH401 2.6 8.1 1.0 CG A:ASP10 2.9 20.4 1.0 C A:TYR12 3.6 22.8 1.0 CG A:ASN14 3.6 24.2 1.0 CG A:ASP19 3.6 19.6 1.0 N A:ASN14 3.9 15.5 1.0 CB A:ASN14 4.1 17.1 1.0 OD1 A:ASP19 4.1 14.2 1.0 MN A:MN301 4.2 19.3 1.0 CB A:ASP10 4.4 14.8 1.0 CA A:TYR12 4.4 24.9 1.0 N A:TYR12 4.5 18.1 1.0 O A:HOH405 4.5 13.6 1.0 N A:PRO13 4.6 22.6 1.0 O A:ASP208 4.6 14.7 1.0 C A:PRO13 4.6 23.8 1.0 OD1 A:ASP208 4.6 17.0 1.0 CA A:ASN14 4.6 20.9 1.0 CA A:PRO13 4.6 20.1 1.0 CB A:TYR12 4.6 26.1 1.0 O A:ARG228 4.7 14.9 1.0 CB A:ARG228 4.8 17.0 1.0 ND2 A:ASN14 4.8 20.8 1.0 CE1 A:HIS24 4.8 18.1 1.0 CB A:ASP19 4.8 18.6 1.0 CA A:ARG228 4.8 15.2 1.0 CD1 A:TYR12 4.9 28.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:19.4 occ:1.00 O B:TYR12 2.5 22.1 1.0 OD2 B:ASP19 2.5 22.9 1.0 O B:HOH405 2.5 13.5 1.0 O B:HOH403 2.6 24.1 1.0 OD1 B:ASN14 2.6 27.6 1.0 OD1 B:ASP10 2.6 20.9 1.0 OD2 B:ASP10 2.6 17.5 1.0 CG B:ASP10 3.0 20.9 1.0 CG B:ASP19 3.6 22.8 1.0 CG B:ASN14 3.6 27.4 1.0 C B:TYR12 3.7 21.2 1.0 N B:ASN14 3.8 25.4 1.0 CB B:ASN14 4.0 21.0 1.0 OD1 B:ASP19 4.1 19.5 1.0 MN B:MN301 4.3 16.7 1.0 CB B:ASP10 4.5 18.9 1.0 CA B:TYR12 4.5 27.2 1.0 O B:HOH402 4.5 12.9 1.0 CA B:ASN14 4.5 28.6 1.0 C B:PRO13 4.6 25.6 1.0 N B:TYR12 4.6 23.5 1.0 N B:PRO13 4.6 24.4 1.0 CA B:PRO13 4.6 25.0 1.0 O B:ARG228 4.7 14.9 1.0 OD1 B:ASP208 4.7 21.0 1.0 CB B:TYR12 4.7 20.6 1.0 CB B:ARG228 4.7 24.5 1.0 CA B:ARG228 4.7 22.0 1.0 O B:ASP208 4.7 18.6 1.0 CE1 B:HIS24 4.8 17.0 1.0 ND2 B:ASN14 4.8 26.1 1.0 CB B:ASP19 4.8 22.1 1.0 CD1 B:TYR12 5.0 29.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:23.5 occ:1.00 OD2 C:ASP19 2.5 23.8 1.0 O C:TYR12 2.5 23.7 1.0 O C:HOH403 2.6 24.3 1.0 OD1 C:ASN14 2.6 29.1 1.0 O C:HOH409 2.7 20.3 1.0 OD2 C:ASP10 2.7 18.6 1.0 OD1 C:ASP10 2.7 20.4 1.0 CG C:ASP10 3.0 21.1 1.0 CG C:ASP19 3.5 24.6 1.0 CG C:ASN14 3.6 29.1 1.0 C C:TYR12 3.6 27.8 1.0 N C:ASN14 3.9 26.5 1.0 OD1 C:ASP19 4.0 21.4 1.0 CB C:ASN14 4.0 29.6 1.0 MN C:MN301 4.2 18.4 1.0 CA C:TYR12 4.5 27.0 1.0 CB C:ASP10 4.5 23.4 1.0 N C:TYR12 4.5 22.8 1.0 CA C:ASN14 4.6 28.8 1.0 O C:HOH408 4.6 13.9 1.0 O C:ASP208 4.6 19.0 1.0 CB C:TYR12 4.6 26.9 1.0 N C:PRO13 4.6 29.9 1.0 CB C:ARG228 4.6 21.0 1.0 C C:PRO13 4.6 29.1 1.0 OD1 C:ASP208 4.7 23.0 1.0 CA C:PRO13 4.7 26.8 1.0 CA C:ARG228 4.7 24.0 1.0 O C:ARG228 4.7 26.3 1.0 CE1 C:HIS24 4.8 18.2 1.0 CB C:ASP19 4.8 25.4 1.0 ND2 C:ASN14 4.8 24.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Canavalia Boliviana Lectin in Complex with MAN1- 4MAN-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- 4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:22.9 occ:1.00 O D:TYR12 2.5 27.3 1.0 OD2 D:ASP19 2.5 14.5 1.0 O D:HOH414 2.6 23.7 1.0 OD1 D:ASN14 2.6 23.9 1.0 OD2 D:ASP10 2.7 17.3 1.0 O D:HOH424 2.7 24.5 1.0 OD1 D:ASP10 2.7 21.2 1.0 CG D:ASP10 3.0 19.4 1.0 CG D:ASN14 3.7 31.9 1.0 CG D:ASP19 3.7 22.3 1.0 C D:TYR12 3.7 26.4 1.0 N D:ASN14 3.9 22.8 1.0 CB D:ASN14 4.1 25.4 1.0 OD1 D:ASP19 4.2 24.3 1.0 MN D:MN301 4.2 20.9 1.0 O D:HOH407 4.5 16.1 1.0 CB D:ASP10 4.5 21.5 1.0 C D:PRO13 4.5 28.3 1.0 CA D:TYR12 4.6 23.4 1.0 CA D:PRO13 4.6 27.7 1.0 N D:PRO13 4.6 26.5 1.0 OD1 D:ASP208 4.6 20.9 1.0 CB D:ARG228 4.6 21.7 1.0 O D:ARG228 4.6 16.5 1.0 CA D:ASN14 4.6 31.7 1.0 N D:TYR12 4.7 18.9 1.0 CA D:ARG228 4.7 21.2 1.0 O D:ASP208 4.7 19.0 1.0 CB D:TYR12 4.8 25.4 1.0 CE1 D:HIS24 4.8 20.4 1.0 ND2 D:ASN14 4.8 21.0 1.0 CB D:ASP19 4.9 22.0 1.0 CD1 D:TYR12 5.0 24.7 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