Calcium in PDB 1hkd: Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside

The structure of Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside, PDB code: 1hkd was solved by M.B.Shevtsov, I.N.Tsygannik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.95 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.793, 61.235, 136.005, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20.9

The structure of Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

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

Calcium binding site 1 out of 2 in the Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1182 b:14.3 occ:1.00 O A:PHE123 2.3 16.0 1.0 O A:HOH2077 2.4 14.8 1.0 OD1 A:ASN125 2.4 18.5 1.0 O A:HOH2060 2.4 10.5 1.0 OD2 A:ASP129 2.4 12.8 1.0 OD2 A:ASP121 2.5 13.5 1.0 OD1 A:ASP121 2.5 11.1 1.0 CG A:ASP121 2.9 13.1 1.0 C A:PHE123 3.5 16.5 1.0 CG A:ASN125 3.5 17.3 1.0 CG A:ASP129 3.5 15.0 1.0 OD1 A:ASP129 3.9 12.1 1.0 N A:ASN125 4.0 17.4 1.0 CB A:ASN125 4.1 16.7 1.0 MN A:MN1183 4.3 16.7 1.0 CA A:PHE123 4.3 16.6 1.0 CB A:ASP121 4.4 13.3 1.0 N A:PHE123 4.4 15.9 1.0 NE1 A:TRP128 4.4 16.2 1.0 N A:TYR124 4.5 16.8 1.0 O A:GLY99 4.5 14.8 1.0 ND2 A:ASN125 4.6 16.5 1.0 CB A:PHE123 4.6 15.8 1.0 CA A:TYR124 4.6 17.2 1.0 C A:TYR124 4.6 18.0 1.0 O A:HOH2127 4.6 8.5 1.0 O A:ASP81 4.7 21.6 1.0 CA A:ASN125 4.7 17.8 1.0 CA A:GLY99 4.7 14.8 1.0 CD1 A:PHE123 4.8 17.6 1.0 CB A:ASP129 4.8 14.5 1.0 OD2 A:ASP81 4.9 22.1 1.0

Calcium binding site 2 out of 2 in the Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1182 b:18.5 occ:1.00 O C:PHE123 2.3 18.9 1.0 OD2 C:ASP121 2.4 15.3 1.0 OD2 C:ASP129 2.4 16.2 1.0 OD1 C:ASN125 2.4 19.6 1.0 O C:HOH2060 2.4 15.0 1.0 OD1 C:ASP121 2.4 17.3 1.0 O C:HOH2049 2.5 17.4 1.0 CG C:ASP121 2.8 16.8 1.0 CG C:ASP129 3.4 19.3 1.0 C C:PHE123 3.5 19.6 1.0 CG C:ASN125 3.6 20.0 1.0 OD1 C:ASP129 3.7 12.6 1.0 N C:ASN125 4.1 19.1 1.0 MN C:MN1183 4.2 19.3 1.0 CB C:ASN125 4.2 19.7 1.0 CB C:ASP121 4.3 17.3 1.0 CA C:PHE123 4.4 19.2 1.0 NE1 C:TRP128 4.4 20.7 1.0 N C:PHE123 4.4 17.7 1.0 N C:TYR124 4.5 19.7 1.0 O C:GLY99 4.5 18.4 1.0 O C:HOH2106 4.6 12.6 1.0 O C:ASP81 4.6 25.0 1.0 CB C:PHE123 4.6 19.3 1.0 ND2 C:ASN125 4.7 16.8 1.0 CA C:TYR124 4.7 20.0 1.0 C C:TYR124 4.7 20.5 1.0 CB C:ASP129 4.8 18.2 1.0 CA C:ASN125 4.8 20.5 1.0 CA C:GLY99 4.9 18.1 1.0 CE1 C:HIS136 4.9 16.4 1.0 CD1 C:PHE123 4.9 20.6 1.0 OD1 C:ASP81 5.0 27.8 1.0

M.B.Shevtsov, I.N.Tsygannik. Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside To Be Published.