Calcium in PDB 3nwk: A Second C2221 Form of Concanavalin A (Canavalia Ensiformis)

The structure of A Second C2221 Form of Concanavalin A (Canavalia Ensiformis), PDB code: 3nwk was solved by L.M.Foroughi, Y.N.Kang, A.J.Matzger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.66 / 2.09
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	101.518, 118.118, 250.113, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.2

The structure of A Second C2221 Form of Concanavalin A (Canavalia Ensiformis) also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the A Second C2221 Form of Concanavalin A (Canavalia Ensiformis) (pdb code 3nwk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the A Second C2221 Form of Concanavalin A (Canavalia Ensiformis), PDB code: 3nwk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the A Second C2221 Form of Concanavalin A (Canavalia Ensiformis)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Second C2221 Form of Concanavalin A (Canavalia Ensiformis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca238 b:17.6 occ:1.00 O A:HOH302 2.3 7.6 1.0 O A:TYR12 2.3 20.2 1.0 OD1 A:ASN14 2.3 17.9 1.0 OD2 A:ASP19 2.3 22.2 1.0 OD1 A:ASP10 2.4 17.0 1.0 O A:HOH265 2.5 3.8 1.0 OD2 A:ASP10 2.6 11.1 1.0 CG A:ASP10 2.8 19.4 1.0 CG A:ASN14 3.5 19.8 1.0 CG A:ASP19 3.5 17.3 1.0 C A:TYR12 3.5 18.6 1.0 N A:ASN14 3.9 19.8 1.0 OD1 A:ASP19 4.0 19.4 1.0 CB A:ASN14 4.1 17.5 1.0 MN A:MN239 4.2 14.5 1.0 CB A:ASP10 4.4 16.1 1.0 CA A:TYR12 4.4 17.0 1.0 O A:HOH444 4.4 6.2 1.0 N A:PRO13 4.5 19.8 1.0 CE1 A:HIS24 4.5 19.3 1.0 N A:TYR12 4.5 17.0 1.0 CA A:PRO13 4.6 21.4 1.0 ND2 A:ASN14 4.6 17.5 1.0 C A:PRO13 4.6 21.2 1.0 OD1 A:ASP208 4.6 14.4 1.0 CB A:TYR12 4.6 14.5 1.0 CA A:ASN14 4.7 19.0 1.0 O A:ASP208 4.7 16.9 1.0 CB A:ASP19 4.7 19.9 1.0 O A:ARG228 4.8 16.4 1.0 CA A:ARG228 4.8 16.7 1.0 NE2 A:HIS24 4.8 19.9 1.0 CD1 A:TYR12 4.8 19.1 1.0 CB A:ARG228 4.9 17.1 1.0

Calcium binding site 2 out of 4 in the A Second C2221 Form of Concanavalin A (Canavalia Ensiformis)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Second C2221 Form of Concanavalin A (Canavalia Ensiformis) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca238 b:16.4 occ:1.00 O B:HOH270 2.3 6.3 1.0 OD2 B:ASP19 2.3 22.9 1.0 O B:TYR12 2.3 16.6 1.0 OD1 B:ASP10 2.4 15.0 1.0 ND2 B:ASN14 2.4 12.7 1.0 O B:HOH244 2.4 4.9 1.0 OD2 B:ASP10 2.6 11.4 1.0 CG B:ASP10 2.8 17.5 1.0 CG B:ASP19 3.4 14.2 1.0 C B:TYR12 3.5 16.5 1.0 CG B:ASN14 3.6 17.1 1.0 OD1 B:ASP19 3.9 12.9 1.0 N B:ASN14 4.0 17.8 1.0 CB B:ASN14 4.2 14.5 1.0 MN B:MN239 4.2 13.5 1.0 CA B:TYR12 4.3 16.3 1.0 CB B:ASP10 4.4 16.2 1.0 N B:TYR12 4.4 15.0 1.0 CE1 B:HIS24 4.4 18.9 1.0 CB B:ARG228 4.5 15.3 1.0 N B:PRO13 4.5 16.9 1.0 CB B:TYR12 4.5 12.8 1.0 O B:HOH377 4.6 3.2 1.0 O B:ASP208 4.6 16.8 1.0 OD1 B:ASN14 4.6 15.0 1.0 CB B:ASP19 4.6 19.2 1.0 CA B:PRO13 4.7 16.9 1.0 OD1 B:ASP208 4.7 13.9 1.0 C B:PRO13 4.8 18.5 1.0 CA B:ARG228 4.8 16.4 1.0 NE2 B:HIS24 4.8 15.9 1.0 O B:ARG228 4.8 14.2 1.0 CA B:ASN14 4.8 17.0 1.0

Calcium binding site 3 out of 4 in the A Second C2221 Form of Concanavalin A (Canavalia Ensiformis)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Second C2221 Form of Concanavalin A (Canavalia Ensiformis) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca238 b:20.1 occ:1.00 O C:TYR12 2.3 23.9 1.0 O C:HOH290 2.3 9.2 1.0 OD2 C:ASP19 2.3 30.1 1.0 OD1 C:ASP10 2.3 22.2 1.0 OD1 C:ASN14 2.4 23.3 1.0 O C:HOH274 2.4 9.0 1.0 OD2 C:ASP10 2.6 14.3 1.0 CG C:ASP10 2.8 22.5 1.0 CG C:ASP19 3.5 25.0 1.0 C C:TYR12 3.5 22.7 1.0 CG C:ASN14 3.5 25.4 1.0 N C:ASN14 3.9 26.8 1.0 OD1 C:ASP19 4.0 28.0 1.0 CB C:ASN14 4.2 26.5 1.0 MN C:MN239 4.2 19.0 1.0 CA C:TYR12 4.3 20.7 1.0 CB C:ASP10 4.4 19.5 1.0 N C:TYR12 4.4 21.0 1.0 N C:PRO13 4.5 22.9 1.0 CE1 C:HIS24 4.6 23.1 1.0 O C:ASP208 4.6 18.6 1.0 CA C:PRO13 4.6 24.5 1.0 OD1 C:ASP208 4.6 21.8 1.0 O C:HOH301 4.6 11.2 1.0 CB C:TYR12 4.6 19.7 1.0 C C:PRO13 4.6 26.4 1.0 ND2 C:ASN14 4.6 20.2 1.0 O C:ARG228 4.7 22.7 1.0 CB C:ASP19 4.7 26.3 1.0 CA C:ASN14 4.7 27.5 1.0 CA C:ARG228 4.7 26.1 1.0 CB C:ARG228 4.8 23.9 1.0

Calcium binding site 4 out of 4 in the A Second C2221 Form of Concanavalin A (Canavalia Ensiformis)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A Second C2221 Form of Concanavalin A (Canavalia Ensiformis) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca238 b:18.8 occ:1.00 O D:TYR12 2.3 23.2 1.0 OD2 D:ASP19 2.3 25.1 1.0 OD1 D:ASN14 2.3 18.4 1.0 OD1 D:ASP10 2.4 18.4 1.0 O D:HOH442 2.4 11.2 1.0 O D:HOH287 2.4 8.4 1.0 OD2 D:ASP10 2.7 13.8 1.0 CG D:ASP10 2.9 20.1 1.0 CG D:ASP19 3.5 16.1 1.0 CG D:ASN14 3.5 20.6 1.0 C D:TYR12 3.5 21.3 1.0 OD1 D:ASP19 3.9 20.1 1.0 N D:ASN14 4.0 22.7 1.0 CB D:ASN14 4.2 19.9 1.0 MN D:MN239 4.2 17.8 1.0 CA D:TYR12 4.3 19.7 1.0 CB D:ASP10 4.4 19.1 1.0 N D:TYR12 4.4 18.8 1.0 N D:PRO13 4.5 22.1 1.0 CB D:TYR12 4.5 19.3 1.0 CE1 D:HIS24 4.6 17.4 1.0 O D:ASP208 4.6 17.4 1.0 O D:HOH426 4.6 8.8 1.0 ND2 D:ASN14 4.6 18.1 1.0 CA D:PRO13 4.6 23.8 1.0 CB D:ARG228 4.7 18.3 1.0 OD1 D:ASP208 4.7 20.9 1.0 C D:PRO13 4.7 23.4 1.0 CB D:ASP19 4.7 21.1 1.0 O D:ARG228 4.7 19.0 1.0 CA D:ASN14 4.8 20.2 1.0 CA D:ARG228 4.8 18.5 1.0 CD1 D:TYR12 4.9 20.1 1.0 NE2 D:HIS24 4.9 19.5 1.0

L.M.Foroughi, Y.N.Kang, A.J.Matzger. Polymer-Induced Heteronucleation For Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms Cryst.Growth Des. V. 11 1294 2011.
ISSN: ISSN 1528-7483
DOI: 10.1021/CG101518F