Calcium in PDB 6eyj: E-Selectin Lectin, Egf-Like and Two Scr Domains Complexed with Glycomimetic Ligand NV354

The structure of E-Selectin Lectin, Egf-Like and Two Scr Domains Complexed with Glycomimetic Ligand NV354, PDB code: 6eyj was solved by R.P.Jakob, P.Zihlmann, R.C.Preston, N.Varga, B.Ernst, T.Maier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.22 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.580, 71.040, 92.160, 90.00, 93.73, 90.00
R / Rfree (%)	21.9 / 25.9

The structure of E-Selectin Lectin, Egf-Like and Two Scr Domains Complexed with Glycomimetic Ligand NV354 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Calcium atom in the E-Selectin Lectin, Egf-Like and Two Scr Domains Complexed with Glycomimetic Ligand NV354 (pdb code 6eyj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the E-Selectin Lectin, Egf-Like and Two Scr Domains Complexed with Glycomimetic Ligand NV354, PDB code: 6eyj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the E-Selectin Lectin, Egf-Like and Two Scr Domains Complexed with Glycomimetic Ligand NV354


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E-Selectin Lectin, Egf-Like and Two Scr Domains Complexed with Glycomimetic Ligand NV354 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca309 b:58.4 occ:1.00 OD1 A:ASP106 2.2 73.3 1.0 OBD A:C5H308 2.3 69.2 1.0 OE1 A:GLU88 2.4 72.6 1.0 O A:ASP106 2.5 63.9 1.0 OD1 A:ASN105 2.6 56.8 1.0 OD1 A:ASN82 2.6 73.2 1.0 OBB A:C5H308 2.6 68.2 1.0 OE1 A:GLU80 2.8 61.7 1.0 CG A:ASP106 3.2 69.4 1.0 CBC A:C5H308 3.3 70.5 1.0 CD A:GLU88 3.4 79.4 1.0 CBA A:C5H308 3.4 69.8 1.0 C A:ASP106 3.6 60.4 1.0 CG A:ASN82 3.6 77.9 1.0 CG A:ASN105 3.6 63.9 1.0 CD A:GLU80 3.7 81.7 1.0 OE2 A:GLU88 3.8 76.7 1.0 N A:ASP106 3.8 54.4 1.0 CBE A:C5H308 3.9 72.4 1.0 OD2 A:ASP106 4.0 72.4 1.0 CA A:ASP106 4.0 54.5 1.0 OE2 A:GLU80 4.0 84.9 1.0 ND2 A:ASN105 4.1 53.0 1.0 ND2 A:ASN82 4.1 69.7 1.0 CB A:ASP106 4.2 57.9 1.0 N A:ASN82 4.2 65.5 1.0 N A:ASN83 4.2 69.2 1.0 OBF A:C5H308 4.5 71.5 1.0 CG A:GLU88 4.6 65.4 1.0 C A:ASN105 4.7 52.8 1.0 OE2 A:GLU107 4.7 84.4 1.0 CB A:ASN82 4.7 67.3 1.0 N A:GLU107 4.7 54.7 1.0 CA A:ASN82 4.8 68.8 1.0 CG A:GLU80 4.8 57.9 1.0 N A:ARG84 4.8 77.5 1.0 CB A:GLU88 4.9 63.4 1.0 CAZ A:C5H308 4.9 71.9 1.0 CB A:ASN105 4.9 47.2 1.0 C A:ASN82 4.9 74.5 1.0 CA A:ASN83 5.0 69.2 1.0

Calcium binding site 2 out of 2 in the E-Selectin Lectin, Egf-Like and Two Scr Domains Complexed with Glycomimetic Ligand NV354


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E-Selectin Lectin, Egf-Like and Two Scr Domains Complexed with Glycomimetic Ligand NV354 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca309 b:47.1 occ:1.00 OBD B:C5H308 2.2 56.9 1.0 OE1 B:GLU88 2.4 61.4 1.0 OBB B:C5H308 2.4 56.8 1.0 OD1 B:ASP106 2.4 53.7 1.0 OD1 B:ASN105 2.5 56.4 1.0 OD1 B:ASN82 2.6 44.8 1.0 O B:ASP106 2.6 50.8 1.0 OE1 B:GLU80 2.7 71.5 1.0 CBC B:C5H308 3.2 56.7 1.0 CBA B:C5H308 3.2 59.1 1.0 CG B:ASP106 3.5 55.3 1.0 CD B:GLU88 3.5 66.2 1.0 CG B:ASN82 3.5 66.4 1.0 CD B:GLU80 3.6 69.1 1.0 CG B:ASN105 3.6 64.7 1.0 C B:ASP106 3.7 48.8 1.0 CBE B:C5H308 3.8 55.5 1.0 OE2 B:GLU88 3.9 62.8 1.0 N B:ASP106 3.9 43.3 1.0 OE2 B:GLU80 3.9 60.0 1.0 ND2 B:ASN82 4.0 63.4 1.0 ND2 B:ASN105 4.1 55.6 1.0 CA B:ASP106 4.2 41.6 1.0 OD2 B:ASP106 4.2 62.7 1.0 N B:ASN82 4.3 56.3 1.0 N B:ASN83 4.3 58.5 1.0 CB B:ASP106 4.4 43.7 1.0 OBF B:C5H308 4.5 52.2 1.0 CB B:ASN82 4.7 54.7 1.0 CAZ B:C5H308 4.7 62.8 1.0 C B:ASN105 4.7 43.5 1.0 CG B:GLU88 4.8 57.6 1.0 CG B:GLU80 4.8 50.6 1.0 CA B:ASN82 4.8 59.4 1.0 N B:ARG84 4.8 69.9 1.0 CB B:ASN105 4.9 44.6 1.0 N B:GLU107 4.9 42.4 1.0 OE2 B:GLU107 4.9 47.8 1.0 C B:ASN82 5.0 63.7 1.0 CB B:GLU88 5.0 57.5 1.0

N.Varga, P.Zihlmann, R.C.Preston, R.P.Jakob, T.Maier, B.Ernst. E-Selectin Lectin with Different Glycomimetic Ligands To Be Published.