Calcium 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:

Manganese	(Mn)	4 atoms
Chlorine	(Cl)	1 atom

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca240 b:14.9 occ:1.00 O A:TYR12 2.3 22.2 1.0 OD2 A:ASP19 2.3 13.6 1.0 O A:HOH247 2.4 19.7 1.0 O A:HOH248 2.4 14.1 1.0 OD1 A:ASP10 2.4 8.9 1.0 OD1 A:ASN14 2.5 12.8 1.0 OD2 A:ASP10 2.8 11.2 1.0 CG A:ASP10 2.9 17.8 1.0 CG A:ASP19 3.5 9.2 1.0 C A:TYR12 3.5 18.9 1.0 CG A:ASN14 3.6 15.2 1.0 OD1 A:ASP19 3.9 12.9 1.0 N A:ASN14 4.1 25.5 1.0 CB A:ASN14 4.2 17.5 1.0 MN A:MN239 4.2 20.0 1.0 CA A:TYR12 4.3 18.9 1.0 N A:TYR12 4.4 18.0 1.0 N A:PRO13 4.4 23.1 1.0 CB A:ASP10 4.5 12.4 1.0 CA A:PRO13 4.5 24.8 1.0 O A:HOH246 4.5 14.2 1.0 CB A:TYR12 4.5 21.3 1.0 ND2 A:ASN14 4.6 16.8 1.0 C A:PRO13 4.6 26.4 1.0 CB A:ASP19 4.7 13.0 1.0 O A:ASP208 4.7 13.7 1.0 OD2 A:ASP208 4.7 12.5 1.0 CA A:ASN14 4.7 20.7 1.0 CE1 A:HIS24 4.8 20.8 1.0 CB A:ARG228 4.8 13.1 1.0 CA A:ARG228 4.9 13.3 1.0 O A:ARG228 4.9 17.8 1.0 CD1 A:TYR12 5.0 19.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca240 b:19.9 occ:1.00 O B:HOH253 2.2 18.2 1.0 O B:HOH256 2.2 14.8 1.0 O B:TYR12 2.3 24.1 1.0 OD1 B:ASP10 2.3 19.3 1.0 OD2 B:ASP19 2.5 17.5 1.0 OD1 B:ASN14 2.6 21.8 1.0 OD2 B:ASP10 2.7 16.1 1.0 CG B:ASP10 2.9 24.8 1.0 C B:TYR12 3.5 18.9 1.0 CG B:ASP19 3.6 16.4 1.0 CG B:ASN14 3.7 21.7 1.0 OD1 B:ASP19 4.0 20.6 1.0 N B:ASN14 4.2 23.2 1.0 MN B:MN239 4.3 18.3 1.0 CB B:ASN14 4.3 19.6 1.0 CA B:TYR12 4.3 19.7 1.0 N B:PRO13 4.4 21.4 1.0 CB B:ASP10 4.4 19.2 1.0 N B:TYR12 4.4 22.6 1.0 CA B:PRO13 4.5 24.0 1.0 CB B:TYR12 4.5 23.7 1.0 O B:ASP208 4.5 17.7 1.0 OD2 B:ASP208 4.5 18.7 1.0 O B:HOH254 4.6 21.8 1.0 C B:PRO13 4.6 26.5 1.0 CB B:ARG228 4.8 19.4 1.0 CA B:ARG228 4.8 18.3 1.0 ND2 B:ASN14 4.8 15.5 1.0 CB B:ASP19 4.8 19.8 1.0 O B:ARG228 4.8 17.0 1.0 CE1 B:HIS24 4.9 26.9 1.0 CA B:ASN14 4.9 24.6 1.0 CD2 B:TYR12 4.9 23.8 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca240 b:39.9 occ:1.00 OD2 C:ASP19 2.2 36.5 1.0 O C:HOH245 2.2 34.2 1.0 OD1 C:ASN14 2.2 48.9 1.0 O C:HOH246 2.4 56.1 1.0 O C:TYR12 2.4 46.5 1.0 OD1 C:ASP10 2.6 39.1 1.0 OD2 C:ASP10 2.9 37.0 1.0 CG C:ASP10 3.1 42.8 1.0 CG C:ASN14 3.3 51.3 1.0 CG C:ASP19 3.4 45.4 1.0 C C:TYR12 3.6 49.8 1.0 OD1 C:ASP19 3.9 50.1 1.0 CB C:ASN14 4.0 47.5 1.0 N C:ASN14 4.0 54.1 1.0 CB C:TYR12 4.2 54.9 1.0 ND2 C:ASN14 4.3 59.0 1.0 OD1 C:ASP208 4.3 44.5 1.0 CA C:TYR12 4.3 49.2 1.0 N C:TYR12 4.4 48.4 1.0 CB C:ASP19 4.5 47.5 1.0 N C:PRO13 4.6 52.5 1.0 O C:HOH244 4.6 46.7 1.0 MN C:MN239 4.6 41.4 1.0 CA C:ASN14 4.6 49.1 1.0 CB C:ASP10 4.6 34.8 1.0 O C:ASP208 4.6 34.1 1.0 CA C:PRO13 4.7 53.6 1.0 O C:ARG228 4.7 40.7 1.0 C C:PRO13 4.7 55.6 1.0 CD2 C:TYR12 4.7 55.0 1.0 CA C:ARG228 4.7 46.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca240 b:23.9 occ:1.00 O D:HOH256 2.1 18.5 1.0 O D:HOH255 2.2 22.2 1.0 OD2 D:ASP19 2.3 34.1 1.0 O D:TYR12 2.3 29.7 1.0 OD1 D:ASP10 2.4 24.0 1.0 OD1 D:ASN14 2.5 29.6 1.0 OD2 D:ASP10 2.6 25.5 1.0 CG D:ASP10 2.8 30.7 1.0 CG D:ASP19 3.5 34.1 1.0 C D:TYR12 3.5 27.7 1.0 CG D:ASN14 3.6 27.0 1.0 OD1 D:ASP19 4.1 33.5 1.0 N D:ASN14 4.1 31.9 1.0 CB D:ASN14 4.1 24.2 1.0 MN D:MN239 4.3 26.5 1.0 CB D:ASP10 4.3 25.4 1.0 CA D:TYR12 4.4 28.4 1.0 N D:TYR12 4.4 29.1 1.0 N D:PRO13 4.5 29.5 1.0 CB D:TYR12 4.5 26.9 1.0 CA D:PRO13 4.6 28.5 1.0 O D:HOH252 4.6 22.1 1.0 ND2 D:ASN14 4.6 22.9 1.0 CB D:ASP19 4.7 33.1 1.0 OD1 D:ASP208 4.7 25.6 1.0 O D:ASP208 4.7 25.8 1.0 C D:PRO13 4.7 29.6 1.0 CA D:ASN14 4.8 27.0 1.0 CE1 D:HIS24 4.8 25.0 1.0 O D:ARG228 4.9 24.9 1.0 CA D:ARG228 4.9 25.8 1.0 CD2 D:TYR12 4.9 29.6 1.0 CB D:ARG228 4.9 27.1 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