Calcium in PDB 1sbd: Soybean Agglutinin Complexed with 2,4-Pentasaccharide

The structure of Soybean Agglutinin Complexed with 2,4-Pentasaccharide, PDB code: 1sbd was solved by A.Dessen, L.R.Olsen, D.Gupta, S.Sabesan, 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)	15.00 / 2.52
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	144.600, 144.600, 107.200, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / n/a

The structure of Soybean Agglutinin Complexed with 2,4-Pentasaccharide also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Soybean Agglutinin Complexed with 2,4-Pentasaccharide (pdb code 1sbd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Soybean Agglutinin Complexed with 2,4-Pentasaccharide, PDB code: 1sbd:

Calcium binding site 1 out of 1 in the Soybean Agglutinin Complexed with 2,4-Pentasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Soybean Agglutinin Complexed with 2,4-Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:12.6 occ:1.00 OD2 A:ASP133 2.1 4.9 1.0 O A:HOH868 2.1 11.7 1.0 O A:PHE128 2.3 7.0 1.0 OD2 A:ASP126 2.3 22.4 1.0 OD1 A:ASN130 2.4 71.1 1.0 O A:HOH890 2.5 7.4 1.0 OD1 A:ASP126 2.6 26.6 1.0 CG A:ASP126 2.8 14.4 1.0 CG A:ASN130 3.1 19.5 1.0 CG A:ASP133 3.2 11.3 1.0 C A:PHE128 3.4 14.4 1.0 ND2 A:ASN130 3.9 1.0 1.0 OD1 A:ASP133 3.9 1.0 1.0 N A:ASN130 3.9 7.2 1.0 CB A:ASN130 3.9 13.0 1.0 NE1 A:TRP132 4.1 21.9 1.0 CA A:PHE128 4.1 19.2 1.0 MN A:MN600 4.1 27.0 1.0 O A:HOH867 4.2 1.0 1.0 CB A:ASP126 4.2 2.9 1.0 CB A:PHE128 4.2 20.9 1.0 N A:PHE128 4.2 18.5 1.0 CB A:ASP133 4.4 3.0 1.0 O A:GLY106 4.5 4.5 1.0 N A:ARG129 4.5 9.0 1.0 CA A:ASN130 4.5 7.7 1.0 CZ2 A:TRP132 4.6 24.5 1.0 OD1 A:ASP88 4.6 16.2 1.0 CE2 A:TRP132 4.6 22.8 1.0 C A:ARG129 4.7 14.0 1.0 O A:ASP88 4.8 8.2 1.0 CD2 A:PHE128 4.8 13.7 1.0 CA A:ARG129 4.8 11.1 1.0 CA A:GLY106 4.8 11.8 1.0

L.R.Olsen, A.Dessen, D.Gupta, S.Sabesan, J.C.Sacchettini, C.F.Brewer. X-Ray Crystallographic Studies of Unique Cross-Linked Lattices Between Four Isomeric Biantennary Oligosaccharides and Soybean Agglutinin. Biochemistry V. 36 15073 1997.
ISSN: ISSN 0006-2960
PubMed: 9398234
DOI: 10.1021/BI971828+