Calcium in PDB 1bqp: The Structure of the Pea Lectin-D-Mannopyranose Complex

The structure of The Structure of the Pea Lectin-D-Mannopyranose Complex, PDB code: 1bqp was solved by S.N.Ruzeinikov, I.Y.Mikhailova, I.N.Tsygannik, W.Pangborn, W.Duax, V.Z.Pletnev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.926, 104.083, 64.837, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.8

The structure of The Structure of the Pea Lectin-D-Mannopyranose Complex also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the The Structure of the Pea Lectin-D-Mannopyranose Complex (pdb code 1bqp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Structure of the Pea Lectin-D-Mannopyranose Complex, PDB code: 1bqp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Structure of the Pea Lectin-D-Mannopyranose Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of the Pea Lectin-D-Mannopyranose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca300 b:19.7 occ:1.00 O A:HOH303 2.2 18.6 1.0 O A:PHE123 2.3 26.9 1.0 OD1 A:ASN125 2.3 19.0 1.0 O A:HOH304 2.3 20.7 1.0 OD2 A:ASP129 2.5 20.8 1.0 OD1 A:ASP121 2.5 12.7 1.0 OD2 A:ASP121 2.5 14.4 1.0 CG A:ASP121 2.8 14.5 1.0 CG A:ASN125 3.5 17.2 1.0 CG A:ASP129 3.5 19.4 1.0 C A:PHE123 3.5 22.1 1.0 OD1 A:ASP129 3.9 19.4 1.0 N A:ASN125 4.1 19.0 1.0 CB A:ASN125 4.1 18.2 1.0 MN A:MN301 4.2 20.9 1.0 O A:HOH302 4.2 32.4 1.0 CA A:PHE123 4.3 19.1 1.0 CB A:ASP121 4.3 15.1 1.0 N A:PHE123 4.3 16.0 1.0 NE1 A:TRP128 4.4 22.2 1.0 CB A:PHE123 4.5 17.0 1.0 N A:TYR124 4.5 21.4 1.0 O A:ASP81 4.5 13.0 1.0 ND2 A:ASN125 4.5 15.1 1.0 O A:GLY99 4.5 16.2 1.0 OD1 A:ASP81 4.6 18.2 1.0 CA A:TYR124 4.7 19.9 1.0 C A:TYR124 4.7 20.1 1.0 CA A:ASN125 4.7 20.5 1.0 CD1 A:PHE123 4.8 19.2 1.0 CB A:ASP129 4.8 19.8 1.0 CA A:GLY99 4.9 13.1 1.0

Calcium binding site 2 out of 2 in the The Structure of the Pea Lectin-D-Mannopyranose Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of the Pea Lectin-D-Mannopyranose Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:11.9 occ:1.00 OD1 C:ASN125 2.1 13.9 1.0 O C:HOH408 2.2 14.9 1.0 O C:PHE123 2.2 12.2 1.0 O C:HOH405 2.2 16.9 1.0 OD2 C:ASP129 2.4 17.5 1.0 OD1 C:ASP121 2.4 17.1 1.0 OD2 C:ASP121 2.7 16.6 1.0 CG C:ASP121 2.9 18.1 1.0 CG C:ASN125 3.3 13.2 1.0 C C:PHE123 3.4 11.3 1.0 CG C:ASP129 3.5 16.0 1.0 OD1 C:ASP129 3.8 18.2 1.0 N C:ASN125 4.0 14.2 1.0 CB C:ASN125 4.1 15.1 1.0 CA C:PHE123 4.2 12.8 1.0 NE1 C:TRP128 4.3 16.9 1.0 ND2 C:ASN125 4.3 10.6 1.0 N C:PHE123 4.3 16.5 1.0 MN C:MN303 4.3 21.4 1.0 CB C:PHE123 4.4 12.2 1.0 CB C:ASP121 4.4 15.2 1.0 N C:TYR124 4.4 11.9 1.0 O C:HOH407 4.4 11.9 1.0 OD1 C:ASP81 4.5 20.7 1.0 O C:ASP81 4.6 16.3 1.0 O C:GLY99 4.6 17.7 1.0 CA C:TYR124 4.6 15.4 1.0 C C:TYR124 4.6 13.9 1.0 CA C:ASN125 4.7 16.6 1.0 CD1 C:PHE123 4.8 12.7 1.0 CB C:ASP129 4.8 21.4 1.0 CA C:GLY99 4.9 16.2 1.0

S.N.Ruzheinikov, I.Y.Mikhailova, I.N.Tsygannik, W.Pangborn, W.Duax, V.Z.Pletnev. The Structure of the Pea Lectin-D-Mannopyranose Complex at A 2.1 A Resolution Russ.J.Bioorganic Chem. V. 24 277 1998.
ISSN: ISSN 1068-1620