Calcium in PDB 2ef6: Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome

The structure of Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome, PDB code: 2ef6 was solved by F.B.M.B.Moreno, G.A.Bezerra, T.M.Oliveira, E.P.De Souza, B.A.M.Da Rocha, R.G.Benevides, P.Delatorre, B.S.Cavada, W.F.De Azevedo Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.92 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	69.391, 69.391, 161.298, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 24.5

The structure of Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome (pdb code 2ef6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome, PDB code: 2ef6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Canavalia Gladiata Lectin Complexed 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 Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca238 b:18.2 occ:1.00 O A:HOH1037 2.2 13.8 1.0 OD1 A:ASN14 2.2 18.4 1.0 OD2 A:ASP19 2.3 23.2 1.0 O A:TYR12 2.3 17.9 1.0 OD2 A:ASP10 2.3 11.8 1.0 O A:HOH1004 2.5 11.9 1.0 OD1 A:ASP10 2.5 16.2 1.0 CG A:ASP10 2.7 17.5 1.0 CG A:ASN14 3.4 21.1 1.0 CG A:ASP19 3.4 22.1 1.0 C A:TYR12 3.5 16.8 1.0 OD1 A:ASP19 3.8 16.2 1.0 N A:ASN14 3.9 18.3 1.0 CB A:ASN14 4.0 18.4 1.0 MN A:MN239 4.0 17.9 1.0 CB A:ASP10 4.3 16.8 1.0 CA A:TYR12 4.4 15.6 1.0 N A:TYR12 4.4 15.1 1.0 CE1 A:HIS24 4.5 13.3 1.0 CA A:PRO13 4.5 18.9 1.0 N A:PRO13 4.5 18.7 1.0 ND2 A:ASN14 4.5 19.1 1.0 O A:ASP208 4.5 14.9 1.0 O A:HOH1118 4.5 17.5 1.0 C A:PRO13 4.6 19.3 1.0 CA A:ASN14 4.6 18.3 1.0 OD1 A:ASP208 4.6 11.8 1.0 CB A:TYR12 4.7 15.4 1.0 O A:ARG228 4.7 17.8 1.0 CB A:ASP19 4.7 20.3 1.0 CA A:ARG228 4.7 16.4 1.0 CB A:ARG228 4.7 15.7 1.0 NE2 A:HIS24 4.9 12.8 1.0 CD2 A:TYR12 5.0 15.5 1.0

Calcium binding site 2 out of 4 in the Canavalia Gladiata Lectin Complexed 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 Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca238 b:17.7 occ:1.00 OD1 B:ASN14 2.2 19.9 1.0 O B:HOH1063 2.2 15.1 1.0 O B:HOH1013 2.2 14.6 1.0 O B:TYR12 2.3 19.6 1.0 OD2 B:ASP10 2.4 11.4 1.0 OD2 B:ASP19 2.4 23.1 1.0 OD1 B:ASP10 2.5 16.8 1.0 CG B:ASP10 2.7 16.8 1.0 CG B:ASN14 3.3 18.6 1.0 CG B:ASP19 3.5 21.1 1.0 C B:TYR12 3.5 17.4 1.0 N B:ASN14 3.9 17.4 1.0 OD1 B:ASP19 3.9 18.4 1.0 CB B:ASN14 3.9 17.1 1.0 MN B:MN239 4.1 17.5 1.0 CB B:ASP10 4.3 15.7 1.0 CA B:TYR12 4.4 16.2 1.0 O B:HOH1033 4.4 13.6 1.0 N B:TYR12 4.4 16.1 1.0 OD1 B:ASP208 4.5 11.6 1.0 ND2 B:ASN14 4.5 19.9 1.0 CB B:TYR12 4.5 16.1 1.0 O B:ASP208 4.5 13.5 1.0 CA B:PRO13 4.5 18.2 1.0 N B:PRO13 4.5 17.8 1.0 C B:PRO13 4.5 18.9 1.0 CA B:ASN14 4.5 17.3 1.0 O B:ARG228 4.6 16.0 1.0 CE1 B:HIS24 4.6 14.8 1.0 CB B:ARG228 4.6 15.7 1.0 CA B:ARG228 4.7 15.5 1.0 CB B:ASP19 4.8 21.4 1.0 CD1 B:TYR12 4.8 16.7 1.0

Calcium binding site 3 out of 4 in the Canavalia Gladiata Lectin Complexed 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 Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca238 b:20.0 occ:1.00 O C:TYR12 2.2 20.1 1.0 OD2 C:ASP19 2.3 25.2 1.0 O C:HOH1032 2.3 12.1 1.0 OD1 C:ASP10 2.3 19.5 1.0 OD2 C:ASP10 2.4 19.7 1.0 O C:HOH1010 2.4 15.7 1.0 OD1 C:ASN14 2.4 21.7 1.0 CG C:ASP10 2.7 21.0 1.0 C C:TYR12 3.4 20.5 1.0 CG C:ASP19 3.4 25.1 1.0 CG C:ASN14 3.6 21.2 1.0 N C:ASN14 3.9 21.8 1.0 OD1 C:ASP19 3.9 21.2 1.0 MN C:MN239 4.1 22.7 1.0 CB C:ASN14 4.1 21.7 1.0 CB C:ASP10 4.2 19.2 1.0 CA C:TYR12 4.2 20.7 1.0 CB C:TYR12 4.3 19.9 1.0 N C:TYR12 4.4 21.1 1.0 N C:PRO13 4.4 21.7 1.0 OD1 C:ASP208 4.5 25.4 1.0 CA C:PRO13 4.5 21.6 1.0 O C:ASP208 4.5 20.8 1.0 CB C:ARG228 4.5 23.3 1.0 O C:HOH1078 4.5 21.6 1.0 CE1 C:HIS24 4.6 16.5 1.0 C C:PRO13 4.6 22.0 1.0 O C:ARG228 4.6 22.2 1.0 CA C:ARG228 4.6 23.3 1.0 CB C:ASP19 4.6 24.1 1.0 CA C:ASN14 4.7 22.4 1.0 ND2 C:ASN14 4.7 25.8 1.0 CD2 C:TYR12 4.7 18.6 1.0 NE2 C:HIS24 4.8 15.7 1.0 O C:HOH1054 4.9 68.8 1.0

Calcium binding site 4 out of 4 in the Canavalia Gladiata Lectin Complexed 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 Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca238 b:21.6 occ:1.00 O D:TYR12 2.2 22.1 1.0 OD1 D:ASN14 2.2 23.5 1.0 OD1 D:ASP10 2.3 18.4 1.0 O D:HOH1015 2.3 17.6 1.0 OD2 D:ASP19 2.4 24.9 1.0 O D:HOH1043 2.4 19.1 1.0 OD2 D:ASP10 2.5 20.4 1.0 CG D:ASP10 2.8 21.0 1.0 CG D:ASN14 3.4 24.4 1.0 C D:TYR12 3.4 20.7 1.0 CG D:ASP19 3.5 26.7 1.0 N D:ASN14 3.9 22.7 1.0 CB D:ASN14 4.0 22.5 1.0 OD1 D:ASP19 4.0 23.7 1.0 MN D:MN239 4.1 23.9 1.0 CA D:TYR12 4.2 20.3 1.0 N D:TYR12 4.3 20.3 1.0 CB D:ASP10 4.3 20.9 1.0 CB D:TYR12 4.3 19.6 1.0 N D:PRO13 4.5 21.3 1.0 O D:HOH1068 4.5 17.6 1.0 ND2 D:ASN14 4.5 22.4 1.0 O D:ASP208 4.5 19.6 1.0 OD1 D:ASP208 4.5 23.6 1.0 CA D:ASN14 4.6 23.2 1.0 O D:ARG228 4.6 20.2 1.0 CB D:ARG228 4.6 22.4 1.0 CE1 D:HIS24 4.6 15.6 1.0 CA D:PRO13 4.6 21.6 1.0 CA D:ARG228 4.7 22.2 1.0 C D:PRO13 4.7 22.6 1.0 CD1 D:TYR12 4.7 19.1 1.0 CB D:ASP19 4.8 24.7 1.0 NE2 D:HIS24 4.8 14.2 1.0

G.A.Bezerra, T.M.Oliveira, F.B.M.B.Moreno, E.P.De Souza, B.A.M.Da Rocha, R.G.Benevides, P.Delatorre, W.F.De Azevedo Jr., B.S.Cavada. Structural Analysis of Canavalia Maritima and Canavalia Gladiata Lectins Complexed with Different Dimannosides: New Insights Into the Understanding of the Structure-Biological Activity Relationship in Legume Lectins J.Struct.Biol. V. 160 168 2007.
ISSN: ISSN 1047-8477
PubMed: 17881248
DOI: 10.1016/J.JSB.2007.07.012