Calcium in PDB 3d4k: Concanavalin A Complexed to A Synthetic Analog of the Trimannoside

The structure of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside, PDB code: 3d4k was solved by R.Kadirvelraj, B.L.Foley, J.D.Dyekjaer, R.J.Woods, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.015, 63.547, 126.215, 90.00, 86.91, 90.00
R / Rfree (%)	20.5 / 23.8

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

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside (pdb code 3d4k). 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 A Synthetic Analog of the Trimannoside, PDB code: 3d4k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the 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 A Synthetic Analog of the Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:20.1 occ:1.00 O A:TYR12 2.5 21.8 1.0 OD1 A:ASN14 2.6 19.8 1.0 OD1 A:ASP10 2.6 15.9 1.0 OD2 A:ASP10 2.6 14.0 1.0 O A:HOH447 2.6 15.7 1.0 OD1 A:ASP19 2.6 26.2 1.0 O A:HOH250 2.7 18.4 1.0 CG A:ASP10 2.9 14.4 1.0 CG A:ASN14 3.6 24.4 1.0 C A:TYR12 3.7 22.2 1.0 CG A:ASP19 3.9 26.0 1.0 N A:ASN14 4.0 23.3 1.0 CB A:ASN14 4.1 23.0 1.0 MN A:MN238 4.2 18.6 1.0 CB A:ASP10 4.4 14.8 1.0 CA A:PRO13 4.5 23.6 1.0 CA A:TYR12 4.5 22.9 1.0 C A:PRO13 4.6 24.1 1.0 O A:HOH307 4.6 20.6 1.0 OD2 A:ASP19 4.6 26.9 1.0 N A:TYR12 4.6 20.4 1.0 N A:PRO13 4.6 24.0 1.0 CA A:ASN14 4.7 24.5 1.0 OD1 A:ASP208 4.7 19.0 1.0 O A:ASP208 4.7 17.4 1.0 CB A:ARG228 4.7 19.7 1.0 CE1 A:HIS24 4.8 20.9 1.0 CB A:TYR12 4.8 23.3 1.0 ND2 A:ASN14 4.8 21.3 1.0 CB A:ASP19 4.8 27.8 1.0 CA A:ARG228 4.8 20.7 1.0 O A:ARG228 4.9 20.4 1.0 CD1 A:TYR12 4.9 25.0 1.0

Calcium binding site 2 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the 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 A Synthetic Analog of the Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:18.3 occ:1.00 O B:TYR12 2.4 18.8 1.0 OD2 B:ASP19 2.5 19.9 1.0 OD1 B:ASN14 2.5 17.1 1.0 O B:HOH444 2.6 18.9 1.0 OD1 B:ASP10 2.6 16.3 1.0 OD2 B:ASP10 2.6 14.1 1.0 O B:HOH257 2.6 18.8 1.0 CG B:ASP10 2.9 16.3 1.0 CG B:ASP19 3.6 21.4 1.0 C B:TYR12 3.6 20.6 1.0 CG B:ASN14 3.6 20.9 1.0 N B:ASN14 4.0 22.8 1.0 OD1 B:ASP19 4.1 16.5 1.0 CB B:ASN14 4.1 22.2 1.0 MN B:MN238 4.2 18.8 1.0 CB B:ASP10 4.4 17.0 1.0 CA B:PRO13 4.5 23.3 1.0 CA B:TYR12 4.5 20.7 1.0 O B:HOH306 4.5 20.7 1.0 N B:PRO13 4.6 22.7 1.0 C B:PRO13 4.6 23.8 1.0 N B:TYR12 4.6 20.4 1.0 CB B:ARG228 4.6 17.2 1.0 O B:ASP208 4.7 14.9 1.0 CB B:TYR12 4.7 21.7 1.0 CA B:ASN14 4.7 22.7 1.0 OD2 B:ASP208 4.7 19.7 1.0 CB B:ASP19 4.8 21.7 1.0 CA B:ARG228 4.8 16.5 1.0 ND2 B:ASN14 4.8 18.6 1.0 CE1 B:HIS24 4.8 20.5 1.0 O B:ARG228 4.9 17.4 1.0 CD1 B:TYR12 5.0 23.8 1.0

Calcium binding site 3 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the 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 A Synthetic Analog of the Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca239 b:20.0 occ:1.00 O C:TYR12 2.5 23.6 1.0 OD2 C:ASP19 2.6 27.7 1.0 OD1 C:ASP10 2.6 16.0 1.0 OD1 C:ASN14 2.6 20.0 1.0 OD2 C:ASP10 2.6 13.6 1.0 O C:HOH449 2.6 18.5 1.0 O C:HOH281 2.7 18.9 1.0 CG C:ASP10 2.9 16.8 1.0 CG C:ASP19 3.6 24.3 1.0 CG C:ASN14 3.6 24.6 1.0 C C:TYR12 3.6 23.5 1.0 N C:ASN14 3.9 23.7 1.0 CB C:ASN14 4.0 22.9 1.0 OD1 C:ASP19 4.1 19.3 1.0 MN C:MN238 4.2 17.3 1.0 CB C:ASP10 4.4 15.5 1.0 CA C:PRO13 4.5 24.9 1.0 O C:HOH256 4.5 17.2 1.0 C C:PRO13 4.5 25.5 1.0 N C:PRO13 4.5 25.8 1.0 CA C:TYR12 4.5 23.2 1.0 CA C:ASN14 4.6 25.0 1.0 N C:TYR12 4.6 21.7 1.0 CB C:ASP19 4.6 23.1 1.0 O C:ASP208 4.7 17.6 1.0 OD1 C:ASP208 4.7 18.6 1.0 CB C:ARG228 4.8 20.7 1.0 CE1 C:HIS24 4.8 22.1 1.0 ND2 C:ASN14 4.8 21.1 1.0 CB C:TYR12 4.8 22.3 1.0 CA C:ARG228 4.9 19.6 1.0 O C:ARG228 4.9 19.3 1.0 CD1 C:TYR12 4.9 22.6 1.0

Calcium binding site 4 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the 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 A Synthetic Analog of the Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca239 b:17.2 occ:1.00 O D:TYR12 2.4 18.4 1.0 OD1 D:ASN14 2.5 16.9 1.0 OD2 D:ASP19 2.5 21.6 1.0 O D:HOH253 2.5 16.1 1.0 OD2 D:ASP10 2.6 14.8 1.0 OD1 D:ASP10 2.6 18.4 1.0 O D:HOH445 2.6 18.4 1.0 CG D:ASP10 2.9 17.5 1.0 CG D:ASN14 3.6 20.3 1.0 C D:TYR12 3.6 18.9 1.0 CG D:ASP19 3.6 22.4 1.0 N D:ASN14 4.0 20.2 1.0 CB D:ASN14 4.1 19.4 1.0 OD1 D:ASP19 4.1 20.8 1.0 MN D:MN238 4.2 16.6 1.0 CB D:ASP10 4.4 16.6 1.0 O D:HOH270 4.4 20.4 1.0 CA D:TYR12 4.4 19.0 1.0 N D:TYR12 4.5 18.7 1.0 N D:PRO13 4.5 21.0 1.0 C D:PRO13 4.6 21.7 1.0 CA D:PRO13 4.6 21.3 1.0 CA D:ASN14 4.6 20.2 1.0 CB D:TYR12 4.7 20.3 1.0 O D:ASP208 4.7 16.7 1.0 CB D:ARG228 4.7 15.8 1.0 OD2 D:ASP208 4.7 20.9 1.0 ND2 D:ASN14 4.7 17.0 1.0 CB D:ASP19 4.7 22.2 1.0 CE1 D:HIS24 4.7 20.3 1.0 CA D:ARG228 4.8 16.2 1.0 O D:ARG228 4.9 15.8 1.0 CD1 D:TYR12 4.9 20.9 1.0

R.Kadirvelraj, B.L.Foley, J.D.Dyekjaer, R.J.Woods. Involvement of Water in Carbohydrate-Protein Binding: Concanavalin A Revisited. J.Am.Chem.Soc. V. 130 16933 2008.
ISSN: ISSN 0002-7863
PubMed: 19053475
DOI: 10.1021/JA8039663