Calcium in PDB 1dgl: Lectin From Dioclea Grandiflora Complexed to Trimannoside

The structure of Lectin From Dioclea Grandiflora Complexed to Trimannoside, PDB code: 1dgl was solved by D.A.Rozwarski, B.M.Swami, C.F.Brewer, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.110, 92.110, 202.820, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 25.2

The structure of Lectin From Dioclea Grandiflora Complexed to Trimannoside also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Lectin From Dioclea Grandiflora Complexed to Trimannoside (pdb code 1dgl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Lectin From Dioclea Grandiflora Complexed to Trimannoside, PDB code: 1dgl:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Lectin From Dioclea Grandiflora 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 Lectin From Dioclea Grandiflora Complexed to Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:26.0 occ:1.00 OD1 A:ASN14 1.7 46.1 1.0 O A:HOH501 2.0 26.4 1.0 O A:HOH502 2.0 11.0 1.0 O A:TYR12 2.2 11.4 1.0 OD1 A:ASN10 2.4 12.5 1.0 ND2 A:ASN10 2.5 23.2 1.0 OD2 A:ASP19 2.6 31.8 1.0 CG A:ASN10 2.8 21.7 1.0 CG A:ASN14 3.0 37.0 1.0 C A:TYR12 3.4 17.6 1.0 CG A:ASP19 3.6 35.4 1.0 ND2 A:ASN14 3.8 41.0 1.0 CB A:ASN14 4.0 30.9 1.0 N A:ASN14 4.0 22.9 1.0 OD1 A:ASP19 4.1 35.3 1.0 CA A:TYR12 4.3 19.8 1.0 CB A:ASN10 4.3 20.8 1.0 N A:PRO13 4.4 17.0 1.0 CB A:TYR12 4.4 22.4 1.0 O A:ARG228 4.4 25.7 1.0 OD1 A:ASP208 4.5 45.0 1.0 CB A:ARG228 4.5 30.3 1.0 C A:PRO13 4.5 21.2 1.0 CA A:PRO13 4.5 17.4 1.0 CA A:ARG228 4.5 27.3 1.0 N A:TYR12 4.5 19.7 1.0 CA A:ASN14 4.6 27.2 1.0 O A:HOH503 4.6 22.7 1.0 MN A:MN302 4.7 37.6 1.0 CD2 A:TYR12 4.7 30.0 1.0 CB A:ASP19 4.8 31.3 1.0 O A:ASP208 4.8 40.5 1.0 CE1 A:HIS24 5.0 7.1 1.0 C A:ARG228 5.0 25.9 1.0

Calcium binding site 2 out of 2 in the Lectin From Dioclea Grandiflora 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 Lectin From Dioclea Grandiflora Complexed to Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:38.1 occ:1.00 O B:HOH501 2.0 41.8 1.0 O B:HOH502 2.0 35.0 1.0 OD1 B:ASN14 2.0 38.9 1.0 O B:TYR12 2.1 26.8 1.0 ND2 B:ASN10 2.5 18.8 1.0 OD1 B:ASN10 2.5 20.9 1.0 OD2 B:ASP19 2.6 28.4 1.0 CG B:ASN10 2.9 24.1 1.0 CG B:ASN14 3.3 28.5 1.0 C B:TYR12 3.3 28.7 1.0 CG B:ASP19 3.7 26.9 1.0 N B:ASN14 4.0 16.5 1.0 CB B:ASN14 4.1 24.3 1.0 OD1 B:ASP208 4.1 34.5 1.0 OD1 B:ASP19 4.1 31.4 1.0 CA B:TYR12 4.2 28.9 1.0 ND2 B:ASN14 4.3 24.3 1.0 N B:PRO13 4.3 25.8 1.0 O B:HOH503 4.3 21.8 1.0 CB B:ARG228 4.4 31.9 1.0 CB B:TYR12 4.4 31.4 1.0 CB B:ASN10 4.4 22.6 1.0 CA B:ARG228 4.5 25.6 1.0 C B:PRO13 4.5 18.1 1.0 N B:TYR12 4.5 28.5 1.0 CA B:PRO13 4.5 21.4 1.0 O B:ARG228 4.5 21.3 1.0 MN B:MN302 4.6 37.1 1.0 O B:ASP208 4.6 29.5 1.0 CA B:ASN14 4.7 22.9 1.0 CD2 B:TYR12 4.7 31.1 1.0 CB B:ASP19 4.8 28.6 1.0 CE1 B:HIS24 4.9 6.0 1.0

D.A.Rozwarski, B.M.Swami, C.F.Brewer, J.C.Sacchettini. Crystal Structure of the Lectin From Dioclea Grandiflora Complexed with Core Trimannoside of Asparagine-Linked Carbohydrates. J.Biol.Chem. V. 273 32818 1998.
ISSN: ISSN 0021-9258
PubMed: 9830028
DOI: 10.1074/JBC.273.49.32818