Calcium in PDB 2p34: Crystal Structure of A Lectin From Canavalia Maritima Seeds (Cml) in Complex with MAN1-4MAN-Ome

The structure of Crystal Structure of A Lectin From Canavalia Maritima Seeds (Cml) in Complex with MAN1-4MAN-Ome, PDB code: 2p34 was solved by F.B.M.B.Moreno, G.A.Bezerra, T.M.Oliveira, E.P.Souza, B.A.M.Rocha, R.G.Benevides, P.Delatorre, B.S.Cavada, W.Deazevedo Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.52 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	69.446, 69.446, 161.454, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 23.9

The structure of Crystal Structure of A Lectin From Canavalia Maritima Seeds (Cml) 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 Maritima Seeds (Cml) in Complex with MAN1-4MAN-Ome (pdb code 2p34). 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 Maritima Seeds (Cml) in Complex with MAN1-4MAN-Ome, PDB code: 2p34:
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 Maritima Seeds (Cml) 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 Maritima Seeds (Cml) in Complex with MAN1-4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:13.9 occ:1.00 O A:TYR12 2.2 15.0 1.0 OD1 A:ASN14 2.3 16.3 1.0 O A:HOH253 2.3 9.4 1.0 O A:HOH245 2.4 10.2 1.0 OD2 A:ASP19 2.4 17.7 1.0 OD2 A:ASP10 2.5 13.4 1.0 OD1 A:ASP10 2.5 14.6 1.0 CG A:ASP10 2.8 12.5 1.0 CG A:ASN14 3.4 16.5 1.0 C A:TYR12 3.4 13.9 1.0 CG A:ASP19 3.5 17.9 1.0 OD1 A:ASP19 3.9 16.7 1.0 N A:ASN14 3.9 15.8 1.0 CB A:ASN14 4.0 15.9 1.0 MN A:MN238 4.1 14.7 1.0 CA A:TYR12 4.3 13.5 1.0 CB A:ASP10 4.3 13.1 1.0 N A:PRO13 4.4 14.7 1.0 N A:TYR12 4.4 14.4 1.0 CB A:ARG228 4.4 14.3 1.0 CA A:PRO13 4.4 15.2 1.0 CB A:TYR12 4.5 15.4 1.0 O A:HOH350 4.5 12.7 1.0 ND2 A:ASN14 4.5 15.4 1.0 CE1 A:HIS24 4.5 9.7 1.0 O A:ASP208 4.5 13.5 1.0 C A:PRO13 4.5 15.8 1.0 CA A:ARG228 4.6 14.4 1.0 CA A:ASN14 4.6 15.8 1.0 OD1 A:ASP208 4.6 11.7 1.0 O A:ARG228 4.7 15.1 1.0 CB A:ASP19 4.8 18.1 1.0 NE2 A:HIS24 4.8 8.2 1.0 CD2 A:TYR12 4.8 14.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A Lectin From Canavalia Maritima Seeds (Cml) 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 Maritima Seeds (Cml) in Complex with MAN1-4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:13.2 occ:1.00 OD1 B:ASP10 2.2 17.2 1.0 O B:HOH250 2.2 6.4 1.0 O B:TYR12 2.3 14.1 1.0 O B:HOH242 2.3 11.9 1.0 OD1 B:ASN14 2.4 15.0 1.0 OD2 B:ASP10 2.5 16.4 1.0 OD2 B:ASP19 2.5 17.6 1.0 CG B:ASP10 2.7 14.3 1.0 C B:TYR12 3.5 13.1 1.0 CG B:ASN14 3.5 16.0 1.0 CG B:ASP19 3.6 16.3 1.0 OD1 B:ASP19 3.9 18.5 1.0 N B:ASN14 3.9 13.7 1.0 CB B:ASN14 4.0 14.9 1.0 MN B:MN238 4.1 14.9 1.0 CB B:ASP10 4.2 13.6 1.0 CA B:TYR12 4.3 12.0 1.0 N B:TYR12 4.3 12.4 1.0 CB B:TYR12 4.4 13.2 1.0 N B:PRO13 4.5 13.7 1.0 O B:ASP208 4.5 12.6 1.0 O B:HOH343 4.5 13.8 1.0 CE1 B:HIS24 4.5 10.2 1.0 CA B:PRO13 4.5 14.1 1.0 OD1 B:ASP208 4.6 12.7 1.0 C B:PRO13 4.6 13.9 1.0 CB B:ARG228 4.6 14.1 1.0 ND2 B:ASN14 4.6 16.0 1.0 CA B:ASN14 4.6 14.1 1.0 O B:ARG228 4.7 15.7 1.0 CA B:ARG228 4.7 13.8 1.0 CB B:ASP19 4.8 18.1 1.0 CD1 B:TYR12 4.9 12.5 1.0 NE2 B:HIS24 4.9 12.9 1.0 CA B:ASP10 5.0 12.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A Lectin From Canavalia Maritima Seeds (Cml) 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 Maritima Seeds (Cml) in Complex with MAN1-4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca239 b:16.7 occ:1.00 O C:HOH270 2.2 13.7 1.0 O C:TYR12 2.3 21.0 1.0 OD1 C:ASP10 2.3 18.4 1.0 OD2 C:ASP10 2.4 19.7 1.0 OD1 C:ASN14 2.4 25.6 1.0 O C:HOH242 2.4 12.2 1.0 OD2 C:ASP19 2.4 25.4 1.0 CG C:ASP10 2.7 18.7 1.0 C C:TYR12 3.5 20.1 1.0 CG C:ASN14 3.5 21.8 1.0 CG C:ASP19 3.5 20.9 1.0 N C:ASN14 3.9 23.0 1.0 OD1 C:ASP19 4.0 17.1 1.0 MN C:MN238 4.1 18.9 1.0 CB C:ASN14 4.2 22.5 1.0 CB C:ASP10 4.2 15.2 1.0 CA C:TYR12 4.3 19.3 1.0 OD1 C:ASP208 4.4 20.8 1.0 CB C:TYR12 4.4 19.0 1.0 N C:TYR12 4.4 18.1 1.0 N C:PRO13 4.5 21.1 1.0 CE1 C:HIS24 4.5 14.0 1.0 O C:HOH266 4.5 14.3 1.0 CA C:PRO13 4.6 21.8 1.0 O C:ASP208 4.6 17.0 1.0 C C:PRO13 4.6 22.5 1.0 ND2 C:ASN14 4.6 21.5 1.0 CB C:ARG228 4.6 21.8 1.0 O C:ARG228 4.7 21.3 1.0 CA C:ASN14 4.7 22.2 1.0 CA C:ARG228 4.7 22.3 1.0 CB C:ASP19 4.8 21.1 1.0 NE2 C:HIS24 4.8 12.1 1.0 CD2 C:TYR12 4.8 21.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A Lectin From Canavalia Maritima Seeds (Cml) 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 Maritima Seeds (Cml) in Complex with MAN1-4MAN-Ome within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca239 b:17.3 occ:1.00 O D:HOH276 2.2 19.0 1.0 O D:TYR12 2.3 19.8 1.0 OD2 D:ASP10 2.3 16.9 1.0 OD1 D:ASP10 2.3 16.3 1.0 O D:HOH240 2.3 11.3 1.0 OD1 D:ASN14 2.3 24.1 1.0 OD2 D:ASP19 2.4 20.0 1.0 CG D:ASP10 2.6 17.8 1.0 C D:TYR12 3.5 19.1 1.0 CG D:ASN14 3.5 22.6 1.0 CG D:ASP19 3.5 20.5 1.0 OD1 D:ASP19 3.9 16.3 1.0 N D:ASN14 4.0 21.9 1.0 MN D:MN238 4.1 21.2 1.0 CB D:ASN14 4.1 21.9 1.0 CB D:ASP10 4.2 17.9 1.0 CA D:TYR12 4.3 19.2 1.0 N D:TYR12 4.4 18.8 1.0 CE1 D:HIS24 4.4 16.4 1.0 CB D:TYR12 4.4 19.0 1.0 OD1 D:ASP208 4.5 22.0 1.0 N D:PRO13 4.5 20.1 1.0 O D:ASP208 4.5 18.3 1.0 ND2 D:ASN14 4.6 17.1 1.0 O D:HOH268 4.6 7.8 1.0 CA D:PRO13 4.6 20.6 1.0 C D:PRO13 4.6 21.0 1.0 CA D:ASN14 4.6 21.8 1.0 O D:ARG228 4.7 22.4 1.0 NE2 D:HIS24 4.7 12.0 1.0 CB D:ARG228 4.7 22.7 1.0 CA D:ARG228 4.8 23.2 1.0 CB D:ASP19 4.8 20.4 1.0 CD1 D:TYR12 4.8 22.8 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