Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Canavalia Gladiata Lectin Complexed with MAN1-3MAN-Ome, PDB code: 2ef6:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn239 b:17.9 occ:1.00 O A:HOH1118 2.1 17.5 1.0 OD2 A:ASP10 2.1 11.8 1.0 OE2 A:GLU8 2.1 12.5 1.0 NE2 A:HIS24 2.2 12.8 1.0 O A:HOH1063 2.4 16.1 1.0 OD1 A:ASP19 2.5 16.2 1.0 CE1 A:HIS24 3.0 13.3 1.0 CG A:ASP10 3.1 17.5 1.0 CD A:GLU8 3.2 14.6 1.0 CG A:ASP19 3.2 22.1 1.0 CD2 A:HIS24 3.2 16.9 1.0 CB A:ASP10 3.5 16.8 1.0 OD2 A:ASP19 3.5 23.2 1.0 OE1 A:GLU8 3.5 14.8 1.0 O A:HOH1037 3.7 13.8 1.0 CA A:CA238 4.0 18.2 1.0 O A:HOH1038 4.0 30.4 1.0 OG A:SER34 4.1 16.6 1.0 ND1 A:HIS24 4.2 12.4 1.0 O A:HOH1089 4.2 29.6 1.0 OD1 A:ASP10 4.2 16.2 1.0 O A:VAL32 4.3 14.3 1.0 CG A:HIS24 4.3 14.7 1.0 CG A:GLU8 4.5 12.9 1.0 CB A:ASP19 4.5 20.3 1.0 CA A:ASP19 4.8 20.4 1.0 CA A:ASP10 5.0 16.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn239 b:17.5 occ:1.00 O B:HOH1033 2.0 13.6 1.0 OD2 B:ASP10 2.1 11.4 1.0 NE2 B:HIS24 2.2 14.9 1.0 OE2 B:GLU8 2.2 10.0 1.0 O B:HOH1138 2.2 18.9 1.0 OD1 B:ASP19 2.3 18.4 1.0 CE1 B:HIS24 3.0 14.8 1.0 CG B:ASP19 3.1 21.1 1.0 CG B:ASP10 3.2 16.8 1.0 CD B:GLU8 3.2 13.3 1.0 CD2 B:HIS24 3.3 20.0 1.0 OD2 B:ASP19 3.5 23.1 1.0 OE1 B:GLU8 3.5 17.2 1.0 CB B:ASP10 3.5 15.7 1.0 O B:HOH1063 3.7 15.1 1.0 CA B:CA238 4.1 17.7 1.0 OG B:SER34 4.2 14.7 1.0 ND1 B:HIS24 4.2 15.0 1.0 OD1 B:ASP10 4.3 16.8 1.0 CG B:HIS24 4.4 16.0 1.0 O B:HOH1064 4.4 31.8 1.0 O B:VAL32 4.4 13.3 1.0 CB B:ASP19 4.4 21.4 1.0 CG B:GLU8 4.5 11.1 1.0 CA B:ASP19 4.7 20.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn239 b:22.7 occ:1.00 OD2 C:ASP10 2.2 19.7 1.0 OE2 C:GLU8 2.2 19.2 1.0 O C:HOH1078 2.3 21.6 1.0 O C:HOH1079 2.3 16.7 1.0 NE2 C:HIS24 2.3 15.7 1.0 OD1 C:ASP19 2.4 21.2 1.0 CG C:ASP19 3.1 25.1 1.0 CG C:ASP10 3.1 21.0 1.0 CD2 C:HIS24 3.2 18.3 1.0 CD C:GLU8 3.3 18.7 1.0 CE1 C:HIS24 3.3 16.5 1.0 OD2 C:ASP19 3.4 25.2 1.0 CB C:ASP10 3.5 19.2 1.0 OE1 C:GLU8 3.7 22.4 1.0 O C:HOH1032 3.9 12.1 1.0 CA C:CA238 4.1 20.0 1.0 CB C:ASP19 4.2 24.1 1.0 OG C:SER34 4.2 18.4 1.0 OD1 C:ASP10 4.2 19.5 1.0 O C:HOH1053 4.2 34.2 1.0 CG C:HIS24 4.4 17.0 1.0 ND1 C:HIS24 4.4 17.8 1.0 O C:VAL32 4.4 23.9 1.0 CA C:ASP19 4.5 25.1 1.0 CG C:GLU8 4.6 17.6 1.0 CD C:PRO20 5.0 24.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn239 b:23.9 occ:1.00 OD2 D:ASP10 2.0 20.4 1.0 O D:HOH1068 2.1 17.6 1.0 OE2 D:GLU8 2.2 18.8 1.0 NE2 D:HIS24 2.2 14.2 1.0 OD1 D:ASP19 2.4 23.7 1.0 CG D:ASP10 3.1 21.0 1.0 CG D:ASP19 3.1 26.7 1.0 CD2 D:HIS24 3.2 18.9 1.0 CE1 D:HIS24 3.2 15.6 1.0 CD D:GLU8 3.2 17.4 1.0 OD2 D:ASP19 3.5 24.9 1.0 CB D:ASP10 3.5 20.9 1.0 OE1 D:GLU8 3.6 22.1 1.0 O D:HOH1043 3.9 19.1 1.0 OD1 D:ASP10 4.1 18.4 1.0 CA D:CA238 4.1 21.6 1.0 OG D:SER34 4.2 18.4 1.0 CB D:ASP19 4.3 24.7 1.0 ND1 D:HIS24 4.3 17.3 1.0 CG D:HIS24 4.3 18.3 1.0 O D:VAL32 4.5 21.8 1.0 CG D:GLU8 4.5 16.0 1.0 CA D:ASP19 4.6 25.9 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