Manganese 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:

Calcium

(Ca)

4 atoms

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

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:14.7 occ:1.00 O A:HOH350 2.0 12.7 1.0 NE2 A:HIS24 2.1 8.2 1.0 OD2 A:ASP10 2.1 13.4 1.0 OE2 A:GLU8 2.1 13.5 1.0 O A:HOH328 2.3 11.9 1.0 OD1 A:ASP19 2.3 16.7 1.0 CE1 A:HIS24 3.1 9.7 1.0 CD2 A:HIS24 3.1 10.6 1.0 CG A:ASP10 3.1 12.5 1.0 CG A:ASP19 3.2 17.9 1.0 CD A:GLU8 3.2 11.6 1.0 CB A:ASP10 3.5 13.1 1.0 OE1 A:GLU8 3.6 10.8 1.0 OD2 A:ASP19 3.6 17.7 1.0 O A:HOH253 3.8 9.4 1.0 OG A:SER34 4.1 16.2 1.0 O A:HOH291 4.1 21.7 1.0 CA A:CA239 4.1 13.9 1.0 ND1 A:HIS24 4.2 10.6 1.0 OD1 A:ASP10 4.3 14.6 1.0 CG A:HIS24 4.3 8.9 1.0 O A:HOH338 4.3 25.0 1.0 CB A:ASP19 4.3 18.1 1.0 O A:VAL32 4.4 13.7 1.0 CG A:GLU8 4.4 10.9 1.0 CA A:ASP19 4.7 18.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:14.9 occ:1.00 O B:HOH343 2.0 13.8 1.0 OD2 B:ASP10 2.1 16.4 1.0 OE2 B:GLU8 2.1 8.4 1.0 NE2 B:HIS24 2.1 12.9 1.0 O B:HOH290 2.3 10.7 1.0 OD1 B:ASP19 2.3 18.5 1.0 CE1 B:HIS24 3.0 10.2 1.0 CG B:ASP10 3.1 14.3 1.0 CG B:ASP19 3.2 16.3 1.0 CD B:GLU8 3.2 9.6 1.0 CD2 B:HIS24 3.2 14.6 1.0 CB B:ASP10 3.5 13.6 1.0 OD2 B:ASP19 3.6 17.6 1.0 OE1 B:GLU8 3.6 9.7 1.0 O B:HOH250 3.9 6.4 1.0 ND1 B:HIS24 4.1 13.5 1.0 CA B:CA239 4.1 13.2 1.0 OG B:SER34 4.1 14.5 1.0 OD1 B:ASP10 4.2 17.2 1.0 O B:HOH330 4.2 26.1 1.0 O B:HOH317 4.2 25.6 1.0 CG B:HIS24 4.3 10.9 1.0 O B:VAL32 4.4 14.7 1.0 CB B:ASP19 4.4 18.1 1.0 CG B:GLU8 4.4 11.8 1.0 CA B:ASP19 4.6 17.7 1.0 CA B:ASP10 5.0 12.5 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:18.9 occ:1.00 O C:HOH313 2.1 15.9 1.0 OD2 C:ASP10 2.1 19.7 1.0 NE2 C:HIS24 2.1 12.1 1.0 OE2 C:GLU8 2.2 14.6 1.0 O C:HOH266 2.2 14.3 1.0 OD1 C:ASP19 2.2 17.1 1.0 CE1 C:HIS24 3.1 14.0 1.0 CG C:ASP19 3.1 20.9 1.0 CG C:ASP10 3.1 18.7 1.0 CD2 C:HIS24 3.2 16.8 1.0 CD C:GLU8 3.2 16.8 1.0 OD2 C:ASP19 3.5 25.4 1.0 OE1 C:GLU8 3.5 17.2 1.0 CB C:ASP10 3.5 15.2 1.0 O C:HOH270 3.9 13.7 1.0 CA C:CA239 4.1 16.7 1.0 OG C:SER34 4.1 14.9 1.0 ND1 C:HIS24 4.2 14.4 1.0 OD1 C:ASP10 4.2 18.4 1.0 CG C:HIS24 4.3 13.0 1.0 O C:HOH278 4.3 26.8 1.0 CB C:ASP19 4.3 21.1 1.0 O C:VAL32 4.4 19.8 1.0 CG C:GLU8 4.5 15.8 1.0 CA C:ASP19 4.6 21.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:21.2 occ:1.00 OD2 D:ASP10 2.2 16.9 1.0 NE2 D:HIS24 2.2 12.0 1.0 O D:HOH268 2.2 7.8 1.0 OE2 D:GLU8 2.3 18.2 1.0 OD1 D:ASP19 2.3 16.3 1.0 CD2 D:HIS24 3.1 14.8 1.0 CG D:ASP19 3.2 20.5 1.0 CG D:ASP10 3.2 17.8 1.0 CD D:GLU8 3.2 20.3 1.0 CE1 D:HIS24 3.2 16.4 1.0 OE1 D:GLU8 3.4 21.1 1.0 OD2 D:ASP19 3.5 20.0 1.0 CB D:ASP10 3.6 17.9 1.0 O D:HOH276 3.9 19.0 1.0 O D:HOH318 4.0 27.2 1.0 CA D:CA239 4.1 17.3 1.0 OG D:SER34 4.2 13.9 1.0 OD1 D:ASP10 4.3 16.3 1.0 CG D:HIS24 4.3 16.2 1.0 ND1 D:HIS24 4.3 16.4 1.0 O D:VAL32 4.3 20.9 1.0 CB D:ASP19 4.4 20.4 1.0 CG D:GLU8 4.6 16.6 1.0 CA D:ASP19 4.7 21.4 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