Manganese in PDB 5cna: Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure

The structure of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure, PDB code: 5cna was solved by J.H.Naismith, C.Emmerich, J.Habash, S.J.Harrop, J.R.Helliwell, W.N.Hunter, J.Raftery, A.J.Kalb(Gilboa), J.Yariv, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	123.700, 128.600, 67.200, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / n/a

The structure of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	4 atoms

The binding sites of Manganese atom in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure (pdb code 5cna). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure, PDB code: 5cna:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn239 b:20.0 occ:1.00 OD2 A:ASP10 2.0 11.2 1.0 O A:HOH245 2.1 12.6 1.0 OD1 A:ASP19 2.2 12.9 1.0 O A:HOH246 2.2 14.2 1.0 OE2 A:GLU8 2.3 20.0 1.0 NE2 A:HIS24 2.5 22.6 1.0 CG A:ASP19 3.0 9.2 1.0 CG A:ASP10 3.1 17.8 1.0 CD A:GLU8 3.3 22.9 1.0 CD2 A:HIS24 3.4 21.4 1.0 OD2 A:ASP19 3.5 13.6 1.0 CE1 A:HIS24 3.5 20.8 1.0 OE1 A:GLU8 3.5 19.6 1.0 CB A:ASP10 3.7 12.4 1.0 O A:HOH248 4.0 14.1 1.0 O A:HOH298 4.0 37.6 1.0 OG A:SER34 4.1 16.5 1.0 OD1 A:ASP10 4.1 8.9 1.0 CB A:ASP19 4.2 13.0 1.0 CA A:CA240 4.2 14.9 1.0 CG A:HIS24 4.5 24.5 1.0 CA A:ASP19 4.5 16.5 1.0 O A:VAL32 4.6 21.5 1.0 ND1 A:HIS24 4.6 22.4 1.0 CG A:GLU8 4.6 17.4 1.0 O A:HOH299 4.8 52.7 1.0

Manganese binding site 2 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn239 b:18.3 occ:1.00 OD2 B:ASP10 2.0 16.1 1.0 O B:HOH255 2.2 12.2 1.0 OE2 B:GLU8 2.2 17.8 1.0 O B:HOH254 2.3 21.8 1.0 OD1 B:ASP19 2.3 20.6 1.0 NE2 B:HIS24 2.5 30.5 1.0 CG B:ASP10 3.1 24.8 1.0 CG B:ASP19 3.2 16.4 1.0 CD B:GLU8 3.2 26.3 1.0 CD2 B:HIS24 3.4 23.3 1.0 CE1 B:HIS24 3.4 26.9 1.0 OD2 B:ASP19 3.5 17.5 1.0 OE1 B:GLU8 3.5 27.4 1.0 CB B:ASP10 3.6 19.2 1.0 OG B:SER34 4.0 21.5 1.0 O B:HOH253 4.0 18.2 1.0 OD1 B:ASP10 4.1 19.3 1.0 O B:HOH257 4.1 38.6 1.0 CA B:CA240 4.3 19.9 1.0 CB B:ASP19 4.4 19.8 1.0 ND1 B:HIS24 4.5 27.4 1.0 O B:VAL32 4.6 20.4 1.0 CG B:HIS24 4.6 26.4 1.0 CG B:GLU8 4.6 17.6 1.0 CA B:ASP19 4.7 24.6 1.0

Manganese binding site 3 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn239 b:41.4 occ:1.00 O C:HOH244 2.0 46.7 1.0 OD2 C:ASP10 2.1 37.0 1.0 O C:HOH243 2.1 24.1 1.0 OD1 C:ASP19 2.3 50.1 1.0 OE2 C:GLU8 2.4 39.8 1.0 NE2 C:HIS24 2.4 46.9 1.0 CG C:ASP19 3.0 45.4 1.0 CE1 C:HIS24 3.2 48.6 1.0 CG C:ASP10 3.2 42.8 1.0 CD C:GLU8 3.3 41.2 1.0 OD2 C:ASP19 3.4 36.5 1.0 CD2 C:HIS24 3.5 43.4 1.0 OE1 C:GLU8 3.6 37.4 1.0 CB C:ASP10 3.6 34.8 1.0 CB C:ASP19 4.0 47.5 1.0 OG C:SER34 4.1 34.0 1.0 OD1 C:ASP10 4.2 39.1 1.0 O C:HOH245 4.3 34.2 1.0 ND1 C:HIS24 4.3 45.8 1.0 CA C:ASP19 4.4 51.5 1.0 CG C:HIS24 4.5 44.1 1.0 CA C:CA240 4.6 39.9 1.0 O C:VAL32 4.6 42.2 1.0 CG C:GLU8 4.7 32.2 1.0

Manganese binding site 4 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn239 b:26.5 occ:1.00 O D:HOH254 2.1 19.4 1.0 O D:HOH252 2.1 22.1 1.0 OE2 D:GLU8 2.2 19.5 1.0 OD2 D:ASP10 2.2 25.5 1.0 NE2 D:HIS24 2.3 25.8 1.0 OD1 D:ASP19 2.5 33.5 1.0 CG D:ASP19 3.1 34.1 1.0 CD D:GLU8 3.2 26.2 1.0 CG D:ASP10 3.2 30.7 1.0 CD2 D:HIS24 3.2 21.2 1.0 CE1 D:HIS24 3.3 25.0 1.0 OD2 D:ASP19 3.4 34.1 1.0 OE1 D:GLU8 3.5 25.4 1.0 CB D:ASP10 3.6 25.4 1.0 O D:HOH255 3.9 22.2 1.0 CB D:ASP19 4.2 33.1 1.0 OG D:SER34 4.2 22.6 1.0 OD1 D:ASP10 4.3 24.0 1.0 CA D:CA240 4.3 23.9 1.0 ND1 D:HIS24 4.4 28.2 1.0 CG D:HIS24 4.4 25.6 1.0 O D:HOH299 4.5 44.6 1.0 CG D:GLU8 4.5 25.1 1.0 O D:VAL32 4.7 24.3 1.0 CA D:ASP19 4.7 36.5 1.0

J.H.Naismith, C.Emmerich, J.Habash, S.J.Harrop, J.R.Helliwell, W.N.Hunter, J.Raftery, A.J.Kalb, J.Yariv. Refined Structure of Concanavalin A Complexed with Methyl Alpha-D-Mannopyranoside at 2.0 A Resolution and Comparison with the Saccharide-Free Structure. Acta Crystallogr.,Sect.D V. 50 847 1994.
ISSN: ISSN 0907-4449
PubMed: 15299352
DOI: 10.1107/S0907444994005287