Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:16.5 occ:1.00 OD2 A:ASP10 2.1 12.9 1.0 NE2 A:HIS24 2.2 7.4 1.0 OE2 A:GLU8 2.2 10.2 1.0 O A:HOH256 2.3 12.7 1.0 O A:HOH287 2.3 9.5 1.0 OD1 A:ASP19 2.3 13.3 1.0 CG A:ASP10 3.0 10.5 1.0 CE1 A:HIS24 3.1 7.5 1.0 CG A:ASP19 3.2 12.4 1.0 CD A:GLU8 3.2 8.8 1.0 CD2 A:HIS24 3.2 8.9 1.0 CB A:ASP10 3.4 11.6 1.0 OE1 A:GLU8 3.5 9.1 1.0 OD2 A:ASP19 3.6 14.0 1.0 O A:HOH257 3.8 10.2 1.0 OG A:SER34 4.0 15.0 1.0 CA A:CA239 4.1 13.0 1.0 O A:HOH381 4.1 24.6 1.0 OD1 A:ASP10 4.1 13.6 1.0 ND1 A:HIS24 4.2 5.9 1.0 O A:HOH383 4.3 23.7 1.0 O A:VAL32 4.3 10.2 1.0 CG A:HIS24 4.3 9.3 1.0 CB A:ASP19 4.3 12.9 1.0 CG A:GLU8 4.5 10.3 1.0 CA A:ASP19 4.6 14.1 1.0 CA A:ASP10 4.9 10.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:16.9 occ:1.00 NE2 B:HIS24 2.2 8.2 1.0 OD2 B:ASP10 2.2 12.1 1.0 O B:HOH249 2.2 11.1 1.0 OE2 B:GLU8 2.2 10.6 1.0 O B:HOH309 2.3 10.2 1.0 OD1 B:ASP19 2.3 13.8 1.0 CE1 B:HIS24 3.0 7.2 1.0 CG B:ASP10 3.1 10.3 1.0 CG B:ASP19 3.1 13.9 1.0 CD B:GLU8 3.2 9.5 1.0 CD2 B:HIS24 3.2 11.3 1.0 CB B:ASP10 3.4 11.6 1.0 OE1 B:GLU8 3.4 11.1 1.0 OD2 B:ASP19 3.6 14.0 1.0 O B:HOH260 3.9 6.4 1.0 OG B:SER34 4.0 13.6 1.0 O B:HOH292 4.1 23.0 1.0 CA B:CA239 4.1 11.8 1.0 ND1 B:HIS24 4.2 10.4 1.0 OD1 B:ASP10 4.2 13.6 1.0 O B:HOH377 4.3 22.4 1.0 CG B:HIS24 4.3 9.4 1.0 CB B:ASP19 4.3 13.0 1.0 O B:VAL32 4.4 11.5 1.0 CG B:GLU8 4.5 12.0 1.0 CA B:ASP19 4.7 13.7 1.0 CA B:ASP10 5.0 10.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:21.1 occ:1.00 OD2 C:ASP10 2.2 17.9 1.0 NE2 C:HIS24 2.2 11.7 1.0 O C:HOH242 2.2 14.2 1.0 OE2 C:GLU8 2.2 18.0 1.0 OD1 C:ASP19 2.3 16.4 1.0 O C:HOH278 2.4 15.7 1.0 CE1 C:HIS24 3.1 9.2 1.0 CG C:ASP10 3.1 17.4 1.0 CG C:ASP19 3.1 19.6 1.0 CD C:GLU8 3.2 18.0 1.0 CD2 C:HIS24 3.2 14.2 1.0 OD2 C:ASP19 3.4 20.0 1.0 OE1 C:GLU8 3.4 20.6 1.0 CB C:ASP10 3.5 16.2 1.0 O C:HOH273 3.8 11.9 1.0 OG C:SER34 4.0 15.1 1.0 CA C:CA239 4.1 17.7 1.0 O C:HOH277 4.2 22.2 1.0 OD1 C:ASP10 4.2 15.5 1.0 ND1 C:HIS24 4.2 11.8 1.0 CB C:ASP19 4.3 19.5 1.0 CG C:HIS24 4.3 15.7 1.0 O C:VAL32 4.4 18.1 1.0 CG C:GLU8 4.5 16.0 1.0 CA C:ASP19 4.6 20.5 1.0 CD C:PRO20 4.9 21.4 1.0 CA C:ASP10 5.0 15.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:21.0 occ:1.00 O D:HOH290 2.1 13.1 1.0 OE2 D:GLU8 2.1 15.7 1.0 OD2 D:ASP10 2.2 14.4 1.0 NE2 D:HIS24 2.2 10.3 1.0 O D:HOH251 2.4 16.1 1.0 OD1 D:ASP19 2.4 17.5 1.0 CE1 D:HIS24 3.0 7.0 1.0 CD D:GLU8 3.1 16.9 1.0 CG D:ASP10 3.1 17.5 1.0 CG D:ASP19 3.1 17.7 1.0 CD2 D:HIS24 3.3 14.4 1.0 OE1 D:GLU8 3.4 17.4 1.0 OD2 D:ASP19 3.4 17.6 1.0 CB D:ASP10 3.4 15.4 1.0 O D:HOH284 3.8 16.8 1.0 OG D:SER34 4.0 18.1 1.0 CA D:CA239 4.1 17.2 1.0 ND1 D:HIS24 4.2 8.0 1.0 O D:HOH297 4.2 25.8 1.0 OD1 D:ASP10 4.2 15.7 1.0 CG D:HIS24 4.3 13.8 1.0 CB D:ASP19 4.3 18.4 1.0 O D:VAL32 4.3 17.5 1.0 CG D:GLU8 4.4 15.3 1.0 CA D:ASP19 4.7 19.1 1.0 CA D:ASP10 5.0 14.9 1.0 CD D:PRO20 5.0 20.5 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