Calcium in PDB 2sba: Soybean Agglutinin Complexed with 2,6-Pentasaccharide

The structure of Soybean Agglutinin Complexed with 2,6-Pentasaccharide, PDB code: 2sba was solved by A.Dessen, 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)	90.00 / 2.60
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	144.900, 144.900, 109.400, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The structure of Soybean Agglutinin Complexed with 2,6-Pentasaccharide also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Soybean Agglutinin Complexed with 2,6-Pentasaccharide (pdb code 2sba). 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 2,6-Pentasaccharide, PDB code: 2sba:

Calcium binding site 1 out of 1 in the Soybean Agglutinin Complexed with 2,6-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 2,6-Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca541 b:37.0 occ:1.00 OD2 A:ASP133 1.8 11.9 1.0 O A:HOH954 2.0 13.7 1.0 O A:PHE128 2.0 12.8 1.0 OD1 A:ASN130 2.1 79.2 1.0 OD2 A:ASP126 2.3 38.4 1.0 OD1 A:ASP126 2.5 33.3 1.0 CG A:ASP126 2.7 25.5 1.0 O A:HOH866 2.8 20.5 1.0 CG A:ASP133 3.0 27.0 1.0 O A:HOH887 3.1 27.5 1.0 CG A:ASN130 3.2 29.5 1.0 C A:PHE128 3.2 14.8 1.0 N A:ASN130 3.6 11.4 1.0 OD1 A:ASP133 3.7 8.5 1.0 CB A:ASN130 3.8 10.1 1.0 CA A:PHE128 4.1 21.3 1.0 CB A:ASP126 4.1 10.8 1.0 N A:PHE128 4.2 19.3 1.0 MN A:MN540 4.2 37.5 1.0 N A:ARG129 4.2 15.6 1.0 CB A:ASP133 4.2 14.1 1.0 ND2 A:ASN130 4.3 1.0 1.0 CA A:ASN130 4.3 13.8 1.0 CA A:ARG129 4.3 17.7 1.0 CD1 A:PHE128 4.4 24.6 1.0 C A:ARG129 4.4 24.1 1.0 CB A:PHE128 4.5 26.4 1.0 NE1 A:TRP132 4.6 47.0 1.0 CE1 A:HIS138 4.7 21.1 1.0 CZ2 A:TRP132 4.7 50.2 1.0 OD2 A:ASP88 4.7 30.4 1.0 CE2 A:TRP132 4.9 48.5 1.0 NE2 A:HIS138 4.9 18.5 1.0 CG A:PHE128 4.9 25.9 1.0

A.Dessen, D.Gupta, S.Sabesan, C.F.Brewer, J.C.Sacchettini. X-Ray Crystal Structure of the Soybean Agglutinin Cross-Linked with A Biantennary Analog of the Blood Group I Carbohydrate Antigen. Biochemistry V. 34 4933 1995.
ISSN: ISSN 0006-2960
PubMed: 7711015
DOI: 10.1021/BI00015A004