Manganese in PDB 2d7f: Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid

The structure of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid, PDB code: 2d7f was solved by P.Delatorre, B.A.M.Rocha, E.P.Souza, B.T.Freitas, F.B.B.M.Moreno, A.H.Sampaio, W.F.Azevedo Jr., B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.99 / 2.31
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	100.915, 115.754, 241.626, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.7

The structure of Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid 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 Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid (pdb code 2d7f). 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 Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid, PDB code: 2d7f:
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 Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


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 Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn239 b:17.6 occ:1.00 OD2 A:ASP10 2.2 11.5 1.0 OE2 A:GLU8 2.2 13.6 1.0 NE2 A:HIS24 2.3 13.8 1.0 OD1 A:ASP19 2.3 11.3 1.0 CG A:ASP19 3.1 16.2 1.0 CD2 A:HIS24 3.2 16.2 1.0 CD A:GLU8 3.2 12.6 1.0 CG A:ASP10 3.2 15.6 1.0 CE1 A:HIS24 3.3 12.8 1.0 OE1 A:GLU8 3.5 14.8 1.0 OD2 A:ASP19 3.5 12.4 1.0 CB A:ASP10 3.7 15.9 1.0 O A:HOH1001 3.9 16.4 1.0 OG A:SER34 4.1 20.7 1.0 CA A:CA240 4.2 18.3 1.0 CB A:ASP19 4.2 16.0 1.0 OD1 A:ASP10 4.3 13.2 1.0 O A:VAL32 4.3 13.2 1.0 CG A:HIS24 4.4 16.1 1.0 ND1 A:HIS24 4.4 12.8 1.0 CA A:ASP19 4.5 17.3 1.0 CG A:GLU8 4.5 14.9 1.0 CD A:PRO20 4.9 18.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


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 Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn239 b:20.8 occ:1.00 OE2 F:GLU8 2.2 18.4 1.0 NE2 F:HIS24 2.2 18.9 1.0 OD2 F:ASP10 2.3 10.2 1.0 OD1 F:ASP19 2.3 15.2 1.0 CD F:GLU8 3.1 13.3 1.0 CG F:ASP19 3.2 16.3 1.0 CE1 F:HIS24 3.2 16.9 1.0 CD2 F:HIS24 3.2 17.8 1.0 CG F:ASP10 3.2 12.5 1.0 OE1 F:GLU8 3.4 17.2 1.0 OD2 F:ASP19 3.5 15.1 1.0 CB F:ASP10 3.6 14.5 1.0 O F:HOH930 4.2 16.5 1.0 CA F:CA240 4.2 19.2 1.0 OG F:SER34 4.3 13.0 1.0 ND1 F:HIS24 4.3 14.2 1.0 CB F:ASP19 4.3 16.5 1.0 OD1 F:ASP10 4.3 10.0 1.0 CG F:HIS24 4.3 17.7 1.0 O F:VAL32 4.4 15.1 1.0 CG F:GLU8 4.5 15.7 1.0 CA F:ASP19 4.6 17.8 1.0 CD F:PRO20 5.0 18.3 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


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 Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ L:Mn239 b:22.1 occ:1.00 OD2 L:ASP10 2.0 11.9 1.0 OE2 L:GLU8 2.2 26.2 1.0 NE2 L:HIS24 2.4 13.5 1.0 OD1 L:ASP19 2.4 20.1 1.0 CG L:ASP10 3.1 17.8 1.0 CD L:GLU8 3.2 19.3 1.0 CG L:ASP19 3.2 23.2 1.0 CD2 L:HIS24 3.3 15.3 1.0 CE1 L:HIS24 3.3 14.2 1.0 OE1 L:GLU8 3.5 18.5 1.0 OD2 L:ASP19 3.6 20.5 1.0 CB L:ASP10 3.6 16.5 1.0 O L:HOH1026 4.0 24.9 1.0 OG L:SER34 4.1 22.1 1.0 CA L:CA240 4.1 19.9 1.0 OD1 L:ASP10 4.1 10.3 1.0 CB L:ASP19 4.3 21.6 1.0 O L:VAL32 4.4 21.1 1.0 CG L:HIS24 4.4 15.0 1.0 ND1 L:HIS24 4.4 14.5 1.0 CG L:GLU8 4.5 19.5 1.0 CA L:ASP19 4.6 21.9 1.0 CD L:PRO20 4.9 22.5 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of A Lectin From Canavalia Gladiata Seeds Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid


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 Complexed with Alpha-Methyl-Mannoside and Alpha- Aminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ S:Mn239 b:21.9 occ:1.00 OD2 S:ASP10 2.1 12.8 1.0 NE2 S:HIS24 2.2 17.5 1.0 OE2 S:GLU8 2.2 20.3 1.0 OD1 S:ASP19 2.4 17.1 1.0 CG S:ASP10 3.1 18.4 1.0 CD S:GLU8 3.1 18.8 1.0 CE1 S:HIS24 3.2 15.6 1.0 CD2 S:HIS24 3.2 16.6 1.0 CG S:ASP19 3.2 21.6 1.0 OE1 S:GLU8 3.4 17.7 1.0 CB S:ASP10 3.6 16.3 1.0 OD2 S:ASP19 3.6 21.6 1.0 CA S:CA240 4.2 20.7 1.0 OD1 S:ASP10 4.2 14.1 1.0 OG S:SER34 4.2 17.4 1.0 ND1 S:HIS24 4.3 16.0 1.0 CB S:ASP19 4.3 22.9 1.0 CG S:HIS24 4.3 16.6 1.0 O S:VAL32 4.4 16.6 1.0 CG S:GLU8 4.5 17.5 1.0 CA S:ASP19 4.6 22.9 1.0 CA S:ASP10 5.0 17.5 1.0

P.Delatorre, B.A.M.Rocha, E.P.Souza, T.M.Oliveira, G.A.Bezerra, F.B.M.B.Moreno, B.T.Freitas, T.Santi-Gadelha, A.H.Sampaio, W.F.Azevedo Jr., B.S.Cavada. Structure of A Lectin From Canavalia Gladiata Seeds: New Structural Insights For Old Molecules Bmc Struct.Biol. V. 7 52 2007.
ISSN: ESSN 1472-6807
PubMed: 17683532
DOI: 10.1186/1472-6807-7-52