Manganese 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:

Calcium

(Ca)

2 atoms

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

Manganese 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 Manganese with other atoms in the Mn binding site number 1 of Lectin From Dioclea Grandiflora Complexed to Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:37.6 occ:1.00 O A:HOH503 2.0 22.7 1.0 O A:HOH504 2.0 29.5 1.0 OD1 A:ASP19 2.1 35.3 1.0 OE2 A:GLU8 2.2 28.6 1.0 NE2 A:HIS24 2.2 3.2 1.0 OD1 A:ASN10 2.5 12.5 1.0 CD A:GLU8 3.2 27.7 1.0 CE1 A:HIS24 3.2 7.1 1.0 CG A:ASN10 3.2 21.7 1.0 CG A:ASP19 3.3 35.4 1.0 CD2 A:HIS24 3.3 10.3 1.0 CB A:ASN10 3.4 20.8 1.0 OE1 A:GLU8 3.5 19.5 1.0 OD2 A:ASP19 3.8 31.8 1.0 O A:HOH553 3.9 37.4 1.0 OG A:SER34 3.9 25.2 1.0 O A:HOH502 4.1 11.0 1.0 O A:HOH551 4.4 38.5 1.0 ND1 A:HIS24 4.4 9.2 1.0 CB A:ASP19 4.5 31.3 1.0 CG A:HIS24 4.5 10.2 1.0 ND2 A:ASN10 4.5 23.2 1.0 CG A:GLU8 4.5 24.4 1.0 O A:ILE32 4.6 29.4 1.0 CA A:CA301 4.7 26.0 1.0 CA A:ASP19 4.8 28.8 1.0 CA A:ASN10 4.9 25.9 1.0

Manganese 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 Manganese with other atoms in the Mn binding site number 2 of Lectin From Dioclea Grandiflora Complexed to Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:37.1 occ:1.00 NE2 B:HIS24 1.9 8.0 1.0 O B:HOH503 2.0 21.8 1.0 O B:HOH504 2.0 38.9 1.0 OD1 B:ASP19 2.1 31.4 1.0 OE2 B:GLU8 2.2 36.3 1.0 OD1 B:ASN10 2.4 20.9 1.0 CE1 B:HIS24 2.9 6.0 1.0 CD2 B:HIS24 3.1 7.7 1.0 CG B:ASN10 3.2 24.1 1.0 CG B:ASP19 3.2 26.9 1.0 CD B:GLU8 3.3 32.2 1.0 CB B:ASN10 3.4 22.6 1.0 O B:HOH551 3.6 58.6 1.0 O B:HOH553 3.7 41.0 1.0 OE1 B:GLU8 3.7 22.1 1.0 OD2 B:ASP19 3.8 28.4 1.0 O B:HOH502 3.8 35.0 1.0 ND1 B:HIS24 4.1 7.3 1.0 OG B:SER34 4.1 19.6 1.0 CG B:HIS24 4.2 6.0 1.0 CB B:ASP19 4.4 28.6 1.0 ND2 B:ASN10 4.4 18.8 1.0 CG B:GLU8 4.5 28.6 1.0 CA B:CA301 4.6 38.1 1.0 CA B:ASP19 4.7 26.4 1.0 O B:ILE32 4.8 27.5 1.0 CA B:ASN10 4.9 25.8 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