Calcium in PDB 4wn0: Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate

The structure of Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate, PDB code: 4wn0 was solved by K.Wangkanont, L.L.Kiessling, K.T.Forest, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.94 / 2.20
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	124.628, 124.628, 55.585, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / 16.9

The binding sites of Calcium atom in the Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate (pdb code 4wn0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate, PDB code: 4wn0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:15.8 occ:1.00 O A:GLY121 2.3 17.4 1.0 O A:HOH570 2.3 14.4 1.0 OE1 A:GLU116 2.4 15.7 1.0 OD2 A:ASP127 2.4 16.6 1.0 O A:HOH530 2.4 14.6 1.0 O A:ASN118 2.5 17.1 1.0 OD1 A:ASP127 2.5 16.6 1.0 CG A:ASP127 2.8 14.9 1.0 CD A:GLU116 3.3 18.2 1.0 C A:GLY121 3.5 19.0 1.0 C A:ASN118 3.5 18.8 1.0 OE2 A:GLU116 3.5 15.1 1.0 CA A:GLY121 4.1 17.8 1.0 N A:GLY121 4.2 21.1 1.0 N A:ASN118 4.2 14.2 1.0 O A:HOH559 4.3 13.0 1.0 CA A:ASN118 4.3 16.5 1.0 OG1 A:THR124 4.3 14.6 1.0 CB A:ASP127 4.4 14.8 1.0 OD1 A:ASN117 4.4 17.1 1.0 N A:MET119 4.4 18.3 1.0 CA A:GLY310 4.5 15.8 1.0 CB A:ASN118 4.5 17.3 1.0 N A:CYS123 4.5 14.8 1.0 N A:LYS122 4.6 17.7 1.0 CA A:MET119 4.6 20.8 1.0 N A:ASP311 4.6 15.7 1.0 CG A:GLU116 4.7 16.8 1.0 C A:MET119 4.7 20.6 1.0 CA A:LYS122 4.8 17.9 1.0 O A:HOH562 4.8 17.5 1.0 O A:MET119 4.8 20.9 1.0 N A:THR124 5.0 15.2 1.0

Calcium binding site 2 out of 3 in the Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:15.5 occ:1.00 O A:HIS115 2.2 14.3 1.0 OD2 A:ASP311 2.3 18.8 1.0 O A:HOH576 2.3 17.6 1.0 O A:GLY126 2.4 17.9 1.0 OD2 A:ASP162 2.4 16.8 1.0 O A:HOH559 2.4 13.0 1.0 OD1 A:ASP162 2.4 17.6 1.0 CG A:ASP162 2.7 17.9 1.0 CG A:ASP311 3.4 19.4 1.0 C A:HIS115 3.4 16.4 1.0 C A:GLY126 3.5 15.7 1.0 CB A:ASP311 4.1 15.2 1.0 N A:ARG128 4.2 17.6 1.0 CA A:ASP127 4.2 14.4 1.0 CB A:ASP162 4.2 16.6 1.0 N A:HIS115 4.2 16.8 1.0 CA A:HIS115 4.3 17.3 1.0 N A:ASP127 4.3 14.3 1.0 N A:GLU116 4.4 16.7 1.0 OD1 A:ASN117 4.4 17.1 1.0 OD1 A:ASP311 4.4 17.1 1.0 CA A:GLU116 4.4 15.0 1.0 N A:ASN117 4.5 14.5 1.0 CB A:HIS115 4.5 14.8 1.0 CA A:GLY126 4.6 16.8 1.0 ND1 A:HIS115 4.6 19.8 1.0 NH1 A:ARG128 4.7 18.5 1.0 CD1 A:TRP129 4.7 14.2 1.0 C A:ASP127 4.7 18.0 1.0 N A:ASP162 4.7 16.6 1.0 OD1 A:ASP127 4.7 16.6 1.0 CA A:ASP162 4.9 16.9 1.0 C A:GLU116 4.9 18.7 1.0 O A:HOH595 5.0 25.7 1.0

Calcium binding site 3 out of 3 in the Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xenopus Laevis Embryonic Epidermal Lectin in Complex with Glycerol Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:20.6 occ:1.00 O1 A:G3P409 2.3 22.7 1.0 OD1 A:ASN289 2.3 22.7 1.0 O A:HOH580 2.4 21.4 1.0 OE1 A:GLU303 2.4 19.1 1.0 OE2 A:GLU291 2.4 19.9 1.0 O A:HOH588 2.5 20.8 1.0 O2 A:G3P409 2.5 21.6 1.0 C2 A:G3P409 3.2 29.1 1.0 C1 A:G3P409 3.2 22.5 1.0 CD A:GLU303 3.3 23.2 1.0 CG A:ASN289 3.4 24.6 1.0 OE2 A:GLU303 3.5 24.8 1.0 CD A:GLU291 3.6 22.4 1.0 CB A:ASN289 3.9 21.7 1.0 O A:HOH624 4.0 43.3 1.0 OG A:SER272 4.1 31.8 1.0 OE1 A:GLU291 4.1 19.4 1.0 CA A:ASN289 4.3 21.0 1.0 OE2 A:GLU273 4.3 23.0 1.0 NE2 A:GLN308 4.4 19.3 1.0 OE1 A:GLU273 4.4 23.9 1.0 ND2 A:ASN289 4.5 24.5 1.0 NE2 A:HIS292 4.6 19.2 1.0 C3 A:G3P409 4.6 30.8 1.0 CG A:GLU303 4.7 21.5 1.0 CD A:GLU273 4.8 23.8 1.0 CG A:GLU291 4.8 19.2 1.0 O A:HOH551 5.0 43.2 1.0 CB A:SER272 5.0 23.8 1.0

K.Wangkanont, D.A.Wesener, J.A.Vidani, L.L.Kiessling, K.T.Forest. Structures of Xenopus Embryonic Epidermal Lectin Reveal A Conserved Mechanism of Microbial Glycan Recognition. J.Biol.Chem. V. 291 5596 2016.
ISSN: ESSN 1083-351X
PubMed: 26755729
DOI: 10.1074/JBC.M115.709212