Calcium in PDB 2p2k: Crystal Structure of A Lectin From Canavalia Gladiata Seeds (Cgl) in Complex with MAN1-4MAN-Ome

The structure of Crystal Structure of A Lectin From Canavalia Gladiata Seeds (Cgl) in Complex with MAN1-4MAN-Ome, PDB code: 2p2k was solved by F.B.M.B.Moreno, G.A.Bezerra, T.M.Oliveira, E.P.Souza, B.A.M.Rocha, G.B.Benevides, P.Delatorre, B.S.Cavada, W.F.Deazevedo Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.84 / 1.98
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	68.932, 68.932, 160.436, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 23.6

The structure of Crystal Structure of A Lectin From Canavalia Gladiata Seeds (Cgl) in Complex with MAN1-4MAN-Ome 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 (Cgl) in Complex with MAN1-4MAN-Ome (pdb code 2p2k). 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 (Cgl) in Complex with MAN1-4MAN-Ome, PDB code: 2p2k:
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 (Cgl) 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 A Lectin From Canavalia Gladiata Seeds (Cgl) in Complex with MAN1-4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:13.0 occ:1.00 O A:TYR12 2.2 12.7 1.0 O A:HOH257 2.3 10.2 1.0 O A:HOH243 2.3 12.6 1.0 OD2 A:ASP19 2.3 14.0 1.0 OD1 A:ASN14 2.3 11.8 1.0 OD2 A:ASP10 2.4 12.9 1.0 OD1 A:ASP10 2.4 13.6 1.0 CG A:ASP10 2.8 10.5 1.0 CG A:ASP19 3.4 12.4 1.0 C A:TYR12 3.4 11.7 1.0 CG A:ASN14 3.4 13.0 1.0 N A:ASN14 3.8 12.4 1.0 OD1 A:ASP19 3.8 13.3 1.0 CB A:ASN14 3.9 13.9 1.0 MN A:MN238 4.1 16.5 1.0 CA A:TYR12 4.3 12.1 1.0 CB A:ASP10 4.3 11.6 1.0 N A:PRO13 4.4 11.6 1.0 N A:TYR12 4.4 11.4 1.0 CB A:ARG228 4.4 11.7 1.0 CA A:PRO13 4.4 12.2 1.0 C A:PRO13 4.5 12.1 1.0 O A:ASP208 4.5 11.7 1.0 O A:HOH256 4.5 12.7 1.0 CB A:TYR12 4.5 13.0 1.0 CA A:ASN14 4.5 13.1 1.0 OD1 A:ASP208 4.5 9.6 1.0 CE1 A:HIS24 4.6 7.5 1.0 CA A:ARG228 4.6 11.8 1.0 ND2 A:ASN14 4.6 9.5 1.0 CB A:ASP19 4.6 12.9 1.0 O A:ARG228 4.7 13.8 1.0 CD2 A:TYR12 4.8 13.2 1.0 NE2 A:HIS24 4.9 7.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds (Cgl) 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 A Lectin From Canavalia Gladiata Seeds (Cgl) in Complex with MAN1-4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:11.8 occ:1.00 O B:HOH244 2.2 10.5 1.0 O B:TYR12 2.3 12.8 1.0 O B:HOH260 2.3 6.4 1.0 OD2 B:ASP10 2.3 12.1 1.0 OD1 B:ASN14 2.3 11.0 1.0 OD2 B:ASP19 2.4 14.0 1.0 OD1 B:ASP10 2.4 13.6 1.0 CG B:ASP10 2.7 10.3 1.0 CG B:ASN14 3.4 12.1 1.0 CG B:ASP19 3.4 13.9 1.0 C B:TYR12 3.5 11.3 1.0 N B:ASN14 3.8 13.1 1.0 OD1 B:ASP19 3.9 13.8 1.0 CB B:ASN14 3.9 14.7 1.0 MN B:MN238 4.1 16.9 1.0 CB B:ASP10 4.2 11.6 1.0 CA B:TYR12 4.3 11.7 1.0 N B:TYR12 4.3 10.1 1.0 N B:PRO13 4.4 12.1 1.0 CB B:TYR12 4.4 12.2 1.0 O B:HOH249 4.5 11.1 1.0 CA B:PRO13 4.5 13.1 1.0 CB B:ARG228 4.5 12.4 1.0 O B:ASP208 4.5 12.4 1.0 C B:PRO13 4.5 13.3 1.0 OD1 B:ASP208 4.5 9.5 1.0 CA B:ASN14 4.5 13.7 1.0 ND2 B:ASN14 4.6 10.3 1.0 CE1 B:HIS24 4.6 7.2 1.0 CA B:ARG228 4.6 12.4 1.0 O B:ARG228 4.6 12.9 1.0 CB B:ASP19 4.7 13.0 1.0 CD1 B:TYR12 4.8 11.4 1.0 NE2 B:HIS24 4.9 8.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds (Cgl) 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 A Lectin From Canavalia Gladiata Seeds (Cgl) in Complex with MAN1-4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca239 b:17.7 occ:1.00 O C:TYR12 2.1 18.4 1.0 O C:HOH273 2.2 11.9 1.0 OD2 C:ASP19 2.3 20.0 1.0 OD1 C:ASN14 2.4 24.0 1.0 OD1 C:ASP10 2.4 15.5 1.0 O C:HOH243 2.5 15.4 1.0 OD2 C:ASP10 2.5 17.9 1.0 CG C:ASP10 2.8 17.4 1.0 C C:TYR12 3.4 17.5 1.0 CG C:ASP19 3.4 19.6 1.0 CG C:ASN14 3.5 20.9 1.0 N C:ASN14 3.8 20.5 1.0 OD1 C:ASP19 3.9 16.4 1.0 CB C:ASN14 4.0 20.4 1.0 MN C:MN238 4.1 21.1 1.0 CA C:TYR12 4.2 17.5 1.0 CB C:ASP10 4.3 16.2 1.0 N C:PRO13 4.4 18.9 1.0 O C:HOH242 4.4 14.2 1.0 N C:TYR12 4.4 16.8 1.0 CB C:TYR12 4.4 18.0 1.0 CE1 C:HIS24 4.5 9.2 1.0 CA C:PRO13 4.5 20.0 1.0 OD1 C:ASP208 4.5 16.5 1.0 C C:PRO13 4.5 20.3 1.0 CA C:ASN14 4.6 20.5 1.0 O C:ASP208 4.6 14.1 1.0 O C:ARG228 4.6 22.9 1.0 CB C:ARG228 4.6 21.5 1.0 CB C:ASP19 4.6 19.5 1.0 ND2 C:ASN14 4.7 13.7 1.0 CA C:ARG228 4.7 21.5 1.0 CD2 C:TYR12 4.8 20.1 1.0 NE2 C:HIS24 4.8 11.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds (Cgl) 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 A Lectin From Canavalia Gladiata Seeds (Cgl) in Complex with MAN1-4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca239 b:17.2 occ:1.00 O D:TYR12 2.2 18.0 1.0 O D:HOH284 2.2 16.8 1.0 OD2 D:ASP19 2.3 17.6 1.0 OD2 D:ASP10 2.4 14.4 1.0 OD1 D:ASP10 2.4 15.7 1.0 OD1 D:ASN14 2.4 24.1 1.0 O D:HOH245 2.4 14.6 1.0 CG D:ASP10 2.7 17.5 1.0 CG D:ASP19 3.4 17.7 1.0 C D:TYR12 3.4 16.6 1.0 CG D:ASN14 3.5 21.7 1.0 N D:ASN14 3.9 20.0 1.0 OD1 D:ASP19 3.9 17.5 1.0 MN D:MN238 4.1 21.0 1.0 CB D:ASN14 4.1 20.3 1.0 CA D:TYR12 4.2 17.0 1.0 CB D:ASP10 4.2 15.4 1.0 N D:TYR12 4.4 16.6 1.0 CB D:TYR12 4.4 17.8 1.0 O D:ASP208 4.4 15.4 1.0 O D:HOH290 4.4 13.1 1.0 N D:PRO13 4.4 17.9 1.0 CE1 D:HIS24 4.5 7.0 1.0 OD1 D:ASP208 4.5 17.2 1.0 CB D:ARG228 4.6 22.4 1.0 O D:ARG228 4.6 24.2 1.0 CA D:PRO13 4.6 19.2 1.0 C D:PRO13 4.6 19.3 1.0 CA D:ASN14 4.6 20.6 1.0 CB D:ASP19 4.6 18.4 1.0 ND2 D:ASN14 4.7 21.8 1.0 CA D:ARG228 4.7 23.0 1.0 CD1 D:TYR12 4.9 21.1 1.0 NE2 D:HIS24 4.9 10.3 1.0

G.A.Bezerra, T.M.Oliveira, F.B.Moreno, E.P.De Souza, B.A.Da Rocha, R.G.Benevides, P.Delatorre, W.F.De Azevedo, 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