Calcium in PDB 1cvn: Concanavalin A Complexed to Trimannoside

The structure of Concanavalin A Complexed to Trimannoside, PDB code: 1cvn was solved by J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.650, 66.680, 108.320, 90.00, 97.79, 90.00
R / Rfree (%)	20.4 / 25.5

The structure of Concanavalin A Complexed to Trimannoside also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Concanavalin A Complexed to Trimannoside (pdb code 1cvn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Concanavalin A Complexed to Trimannoside, PDB code: 1cvn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Concanavalin A Complexed to Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A Complexed to Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:8.7 occ:1.00 O A:HOH251 2.0 12.2 1.0 O A:TYR12 2.2 9.2 1.0 OD2 A:ASP19 2.3 13.8 1.0 O A:HOH243 2.4 3.7 1.0 OD1 A:ASN14 2.4 5.0 1.0 OD1 A:ASP10 2.5 16.2 1.0 OD2 A:ASP10 2.6 18.2 1.0 CG A:ASP10 2.9 15.2 1.0 C A:TYR12 3.4 8.7 1.0 CG A:ASP19 3.4 13.0 1.0 CG A:ASN14 3.5 5.7 1.0 OD1 A:ASP19 4.0 14.0 1.0 N A:ASN14 4.0 5.5 1.0 CB A:ASN14 4.2 5.9 1.0 MN A:MN238 4.3 18.2 1.0 CA A:TYR12 4.3 8.5 1.0 N A:PRO13 4.3 5.1 1.0 CA A:PRO13 4.4 7.0 1.0 CB A:ASP10 4.4 12.9 1.0 N A:TYR12 4.4 9.4 1.0 C A:PRO13 4.5 6.4 1.0 ND2 A:ASN14 4.5 6.7 1.0 CB A:TYR12 4.5 8.2 1.0 CB A:ASP19 4.6 14.8 1.0 O A:ASP208 4.7 11.2 1.0 OD2 A:ASP208 4.7 9.8 1.0 CA A:ASN14 4.7 8.1 1.0 O A:HOH245 4.7 2.0 1.0 CA A:ARG228 4.7 6.0 1.0 CB A:ARG228 4.8 8.1 1.0 CE1 A:HIS24 4.8 5.9 1.0 CD2 A:TYR12 4.9 11.7 1.0 O A:ARG228 4.9 9.2 1.0

Calcium binding site 2 out of 4 in the Concanavalin A Complexed to Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A Complexed to Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:12.5 occ:1.00 O B:HOH250 2.1 11.2 1.0 O B:TYR12 2.3 18.8 1.0 OD2 B:ASP19 2.3 10.2 1.0 O B:HOH254 2.4 15.5 1.0 OD1 B:ASN14 2.4 10.5 1.0 OD1 B:ASP10 2.5 11.4 1.0 OD2 B:ASP10 2.6 12.1 1.0 CG B:ASP10 2.9 12.9 1.0 C B:TYR12 3.5 16.1 1.0 CG B:ASP19 3.5 11.4 1.0 CG B:ASN14 3.6 12.4 1.0 N B:ASN14 4.1 14.6 1.0 OD1 B:ASP19 4.1 14.0 1.0 CB B:ASN14 4.3 10.6 1.0 MN B:MN238 4.3 24.6 1.0 CB B:ASP10 4.4 13.5 1.0 CA B:PRO13 4.4 16.0 1.0 CA B:TYR12 4.4 15.3 1.0 N B:PRO13 4.4 14.7 1.0 N B:TYR12 4.5 18.0 1.0 C B:PRO13 4.5 14.7 1.0 OD1 B:ASP208 4.6 13.8 1.0 CB B:TYR12 4.6 16.2 1.0 O B:ASP208 4.6 10.1 1.0 ND2 B:ASN14 4.7 8.9 1.0 CB B:ASP19 4.7 13.9 1.0 CB B:ARG228 4.7 13.4 1.0 CA B:ASN14 4.8 12.4 1.0 CA B:ARG228 4.8 12.8 1.0 CE1 B:HIS24 4.8 12.1 1.0 O B:HOH248 4.9 9.6 1.0 CD2 B:TYR12 4.9 23.2 1.0 O B:ARG228 4.9 9.2 1.0

Calcium binding site 3 out of 4 in the Concanavalin A Complexed to Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Concanavalin A Complexed to Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca239 b:16.4 occ:1.00 O C:TYR12 2.3 20.2 1.0 OD2 C:ASP19 2.4 9.1 1.0 OD1 C:ASN14 2.4 14.4 1.0 O C:HOH243 2.4 10.3 1.0 O C:HOH249 2.5 4.0 1.0 OD1 C:ASP10 2.5 21.0 1.0 OD2 C:ASP10 2.6 13.6 1.0 CG C:ASP10 2.9 18.0 1.0 C C:TYR12 3.5 16.8 1.0 CG C:ASP19 3.5 9.7 1.0 CG C:ASN14 3.5 11.1 1.0 OD1 C:ASP19 4.0 14.9 1.0 N C:ASN14 4.1 14.2 1.0 CB C:ASN14 4.2 9.7 1.0 MN C:MN238 4.3 23.9 1.0 CA C:TYR12 4.4 16.2 1.0 CB C:ASP10 4.4 15.0 1.0 N C:PRO13 4.4 14.2 1.0 CA C:PRO13 4.5 13.7 1.0 N C:TYR12 4.5 18.8 1.0 CB C:TYR12 4.5 16.7 1.0 O C:ASP208 4.6 13.6 1.0 C C:PRO13 4.6 14.0 1.0 ND2 C:ASN14 4.6 14.4 1.0 O C:HOH253 4.6 10.0 1.0 OD2 C:ASP208 4.6 16.8 1.0 CB C:ARG228 4.6 12.7 1.0 CA C:ARG228 4.7 9.8 1.0 CB C:ASP19 4.7 16.4 1.0 CA C:ASN14 4.8 13.8 1.0 O C:ARG228 4.9 12.3 1.0 CE1 C:HIS24 4.9 9.4 1.0 CD2 C:TYR12 5.0 16.4 1.0

Calcium binding site 4 out of 4 in the Concanavalin A Complexed to Trimannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Concanavalin A Complexed to Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca239 b:7.5 occ:1.00 O D:TYR12 2.2 12.9 1.0 O D:HOH255 2.2 11.5 1.0 OD2 D:ASP19 2.3 13.2 1.0 OD1 D:ASN14 2.3 8.1 1.0 OD1 D:ASP10 2.4 2.0 1.0 O D:HOH245 2.5 3.4 1.0 OD2 D:ASP10 2.7 6.4 1.0 CG D:ASP10 2.9 5.6 1.0 C D:TYR12 3.4 11.0 1.0 CG D:ASN14 3.5 7.2 1.0 CG D:ASP19 3.5 10.7 1.0 N D:ASN14 3.9 11.2 1.0 OD1 D:ASP19 4.1 16.3 1.0 CB D:ASN14 4.2 8.1 1.0 MN D:MN238 4.2 14.8 1.0 CA D:PRO13 4.3 12.7 1.0 N D:PRO13 4.3 12.5 1.0 CA D:TYR12 4.4 7.4 1.0 CB D:ASP10 4.4 9.6 1.0 C D:PRO13 4.4 10.3 1.0 N D:TYR12 4.5 11.9 1.0 ND2 D:ASN14 4.5 3.6 1.0 CB D:TYR12 4.6 3.1 1.0 OD2 D:ASP208 4.6 9.8 1.0 O D:ASP208 4.6 8.2 1.0 CB D:ARG228 4.6 12.4 1.0 CB D:ASP19 4.6 11.5 1.0 O D:HOH244 4.6 4.8 1.0 CA D:ASN14 4.7 10.7 1.0 CD2 D:TYR12 4.8 5.5 1.0 CE1 D:HIS24 4.8 2.0 1.0 CA D:ARG228 4.9 7.6 1.0

J.H.Naismith, R.A.Field. Structural Basis of Trimannoside Recognition By Concanavalin A. J.Biol.Chem. V. 271 972 1996.
ISSN: ISSN 0021-9258
PubMed: 8557713
DOI: 10.1074/JBC.271.2.972