Manganese in PDB 4pf5: Crystal Structure of Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain

The structure of Crystal Structure of Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain, PDB code: 4pf5 was solved by P.Lafite, R.Daniellou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.99 / 2.04
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	125.901, 125.901, 181.972, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 22.7

The binding sites of Manganese atom in the Crystal Structure of Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain (pdb code 4pf5). 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 Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain, PDB code: 4pf5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain


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 Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:28.9 occ:1.00 OD2 A:ASP10 2.2 23.1 1.0 O A:HOH436 2.3 21.4 1.0 OE2 A:GLU8 2.3 24.1 1.0 OD1 A:ASP19 2.4 24.3 1.0 NE2 A:HIS24 2.4 20.5 1.0 O A:HOH435 2.4 27.9 1.0 CG A:ASP10 3.2 23.8 1.0 CD A:GLU8 3.2 23.2 1.0 CG A:ASP19 3.2 28.2 1.0 CE1 A:HIS24 3.3 21.7 1.0 CD2 A:HIS24 3.4 18.8 1.0 OE1 A:GLU8 3.4 24.2 1.0 CB A:ASP10 3.6 21.6 1.0 OD2 A:ASP19 3.6 22.4 1.0 O A:HOH433 4.1 25.1 1.0 O A:HOH437 4.1 32.3 1.0 MN A:MN302 4.2 34.4 1.0 OG A:SER34 4.2 22.7 1.0 OD1 A:ASP10 4.3 24.1 1.0 CB A:ASP19 4.4 22.9 1.0 ND1 A:HIS24 4.5 24.1 1.0 O A:HOH505 4.5 35.1 1.0 O A:VAL32 4.5 24.9 1.0 CG A:HIS24 4.5 21.8 1.0 CG A:GLU8 4.6 18.3 1.0 CA A:ASP19 4.7 24.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain


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 Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:34.4 occ:1.00 O A:TYR12 2.4 26.4 1.0 OD2 A:ASP19 2.4 22.4 1.0 O A:HOH434 2.4 23.1 1.0 OD1 A:ASP10 2.5 24.1 1.0 O A:HOH433 2.5 25.1 1.0 OD2 A:ASP10 2.5 23.1 1.0 OD1 A:ASN14 2.5 27.4 1.0 CG A:ASP10 2.8 23.8 1.0 CG A:ASP19 3.5 28.2 1.0 CG A:ASN14 3.6 30.3 1.0 C A:TYR12 3.6 27.6 1.0 N A:ASN14 4.0 25.2 1.0 OD1 A:ASP19 4.0 24.3 1.0 CB A:ASN14 4.0 26.6 1.0 MN A:MN301 4.2 28.9 1.0 CB A:ASP10 4.3 21.6 1.0 CA A:TYR12 4.4 25.6 1.0 N A:TYR12 4.4 25.4 1.0 N A:PRO13 4.6 27.0 1.0 O A:ASP208 4.6 24.2 1.0 CA A:PRO13 4.6 27.3 1.0 CB A:TYR12 4.6 30.7 1.0 O A:HOH435 4.6 27.9 1.0 C A:PRO13 4.6 33.4 1.0 CA A:ASN14 4.6 26.4 1.0 OD1 A:ASP208 4.7 27.3 1.0 O A:ARG228 4.7 28.3 1.0 CE1 A:HIS24 4.7 21.7 1.0 CB A:ARG228 4.7 27.8 1.0 CB A:ASP19 4.7 22.9 1.0 ND2 A:ASN14 4.8 30.2 1.0 CA A:ARG228 4.8 29.3 1.0 CD1 A:TYR12 4.9 27.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain


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 Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:31.7 occ:1.00 OD2 B:ASP10 2.2 23.3 1.0 O B:HOH423 2.3 24.4 1.0 O B:HOH424 2.4 27.3 1.0 OE2 B:GLU8 2.4 26.4 1.0 NE2 B:HIS24 2.4 29.8 1.0 OD1 B:ASP19 2.4 27.9 1.0 CD B:GLU8 3.2 28.9 1.0 CG B:ASP10 3.2 26.0 1.0 CG B:ASP19 3.2 33.7 1.0 CE1 B:HIS24 3.3 24.5 1.0 OE1 B:GLU8 3.3 28.0 1.0 CD2 B:HIS24 3.5 24.9 1.0 CB B:ASP10 3.6 30.1 1.0 OD2 B:ASP19 3.6 27.8 1.0 O B:HOH421 4.0 30.5 1.0 OG B:SER34 4.1 28.7 1.0 MN B:MN303 4.2 36.8 1.0 OD1 B:ASP10 4.3 31.9 1.0 ND1 B:HIS24 4.4 30.0 1.0 CB B:ASP19 4.5 29.2 1.0 O B:VAL32 4.5 29.5 1.0 CG B:HIS24 4.6 32.7 1.0 CG B:GLU8 4.6 26.0 1.0 CA B:ASP19 4.7 30.3 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain


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 Concanavalin A Complexed with A Synthetic Derivative of High-Mannose Chain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:36.8 occ:1.00 O B:TYR12 2.4 30.9 1.0 OD2 B:ASP19 2.4 27.8 1.0 O B:HOH422 2.4 24.4 1.0 OD2 B:ASP10 2.4 23.3 1.0 OD1 B:ASN14 2.5 30.9 1.0 OD1 B:ASP10 2.5 31.9 1.0 O B:HOH421 2.5 30.5 1.0 CG B:ASP10 2.8 26.0 1.0 CG B:ASP19 3.5 33.7 1.0 CG B:ASN14 3.6 36.5 1.0 C B:TYR12 3.6 29.2 1.0 N B:ASN14 3.9 31.3 1.0 OD1 B:ASP19 4.0 27.9 1.0 CB B:ASN14 4.1 34.0 1.0 MN B:MN302 4.2 31.7 1.0 CB B:ASP10 4.3 30.1 1.0 CA B:TYR12 4.4 31.2 1.0 N B:TYR12 4.5 30.2 1.0 O B:HOH424 4.6 27.3 1.0 N B:PRO13 4.6 30.7 1.0 CA B:PRO13 4.6 29.4 1.0 CB B:TYR12 4.6 30.3 1.0 C B:PRO13 4.6 34.1 1.0 O B:ARG228 4.6 27.9 1.0 O B:ASP208 4.7 27.5 1.0 CA B:ASN14 4.7 33.6 1.0 OD1 B:ASP208 4.7 28.4 1.0 ND2 B:ASN14 4.7 32.8 1.0 CB B:ARG228 4.7 27.8 1.0 CB B:ASP19 4.7 29.2 1.0 CE1 B:HIS24 4.8 24.5 1.0 CA B:ARG228 4.8 31.3 1.0 CD1 B:TYR12 4.9 33.5 1.0

M.Francois-Heude, A.Mendez-Ardoy, V.Cendret, P.Lafite, R.Daniellou, C.Ortiz Mellet, J.M.Garcia Fernandez, V.Moreau, F.Djedaini-Pilard. Synthesis of High-Mannose Oligosaccharide Analogues Through Click Chemistry: True Functional Mimics of Their Natural Counterparts Against Lectins? Chemistry 2014.
ISSN: ISSN 0947-6539
PubMed: 25483029
DOI: 10.1002/CHEM.201405481