Calcium in PDB 2bqp: The Structure of the Pea Lectin-D-Glucopyranose Complex

The structure of The Structure of the Pea Lectin-D-Glucopyranose Complex, PDB code: 2bqp was solved by S.N.Ruzeinikov, I.Mikhailova Yu, 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 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.838, 135.246, 54.781, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.8

The structure of The Structure of the Pea Lectin-D-Glucopyranose 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-Glucopyranose Complex (pdb code 2bqp). 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-Glucopyranose Complex, PDB code: 2bqp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Structure of the Pea Lectin-D-Glucopyranose 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-Glucopyranose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca235 b:10.7 occ:1.00 O A:HOH419 2.1 18.3 1.0 O A:PHE123 2.1 19.4 1.0 O A:HOH397 2.2 8.2 1.0 OD1 A:ASN125 2.4 8.7 1.0 OD1 A:ASP121 2.4 4.7 1.0 OD2 A:ASP129 2.5 10.9 1.0 OD2 A:ASP121 2.6 6.6 1.0 CG A:ASP121 2.8 9.8 1.0 C A:PHE123 3.4 14.7 1.0 CG A:ASP129 3.5 6.9 1.0 H A:PHE123 3.5 0.0 0.0 CG A:ASN125 3.5 6.0 1.0 H A:ASN125 3.6 0.0 0.0 HE1 A:TRP128 3.7 0.0 0.0 OD1 A:ASP129 3.8 2.6 1.0 N A:ASN125 4.0 10.1 1.0 CB A:ASN125 4.2 12.6 1.0 N A:PHE123 4.2 13.3 1.0 CA A:PHE123 4.2 10.4 1.0 MN A:MN236 4.2 12.2 1.0 CB A:ASP121 4.3 10.3 1.0 N A:TYR124 4.4 13.7 1.0 CB A:PHE123 4.4 9.0 1.0 NE1 A:TRP128 4.5 8.0 1.0 CA A:TYR124 4.5 11.4 1.0 C A:TYR124 4.5 9.1 1.0 ND2 A:ASN125 4.5 5.9 1.0 O A:GLY99 4.6 6.9 1.0 O A:HOH358 4.6 6.4 1.0 HD22 A:ASN125 4.6 0.0 0.0 CD2 A:PHE123 4.6 8.8 1.0 O A:ASP81 4.6 18.1 1.0 CA A:ASN125 4.7 10.2 1.0 OD1 A:ASP81 4.7 11.8 1.0 CB A:ASP129 4.8 8.4 1.0 CA A:GLY99 4.9 2.8 1.0

Calcium binding site 2 out of 2 in the The Structure of the Pea Lectin-D-Glucopyranose 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-Glucopyranose Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca235 b:13.9 occ:1.00 O B:HOH358 2.1 13.8 1.0 OD1 B:ASN125 2.2 17.0 1.0 O B:PHE123 2.3 16.8 1.0 OD2 B:ASP129 2.3 14.4 1.0 O B:HOH360 2.5 14.0 1.0 OD2 B:ASP121 2.5 12.5 1.0 OD1 B:ASP121 2.5 13.8 1.0 CG B:ASP121 2.8 15.5 1.0 CG B:ASP129 3.4 14.0 1.0 CG B:ASN125 3.4 16.4 1.0 C B:PHE123 3.5 19.0 1.0 HE1 B:TRP128 3.6 0.0 0.0 H B:ASN125 3.6 0.0 0.0 H B:PHE123 3.8 0.0 0.0 OD1 B:ASP129 3.8 13.0 1.0 N B:ASN125 4.1 10.5 1.0 CB B:ASN125 4.1 12.3 1.0 MN B:MN236 4.2 15.7 1.0 CA B:PHE123 4.3 17.5 1.0 CB B:ASP121 4.3 11.4 1.0 NE1 B:TRP128 4.4 20.9 1.0 CB B:PHE123 4.4 21.6 1.0 HD22 B:ASN125 4.4 0.0 0.0 N B:PHE123 4.4 14.9 1.0 ND2 B:ASN125 4.4 16.9 1.0 N B:TYR124 4.4 20.1 1.0 O B:GLY99 4.6 16.7 1.0 CA B:TYR124 4.6 16.7 1.0 C B:TYR124 4.6 14.3 1.0 CB B:ASP129 4.7 17.5 1.0 O B:ASP81 4.7 17.2 1.0 CD2 B:PHE123 4.7 23.4 1.0 CA B:GLY99 4.7 14.1 1.0 O B:HOH359 4.7 17.1 1.0 CA B:ASN125 4.7 13.0 1.0 OD1 B:ASP81 4.8 14.8 1.0 CE1 B:HIS136 4.9 16.4 1.0

V.Z.Pletnev, S.N.Ruzheinikov, I.N.Tsygannik, I.Mikhailova Yu, W.Duax, D.Ghosh, W.Pangborn. The Structure of Pea Lectin-D-Glucopyranose Complex at A 1.9 A Resolution Russ.J.Bioorganic Chem. V. 23 469 1997.
ISSN: ISSN 1068-1620