Zinc in PDB 6eke: Crystal Structure of A Pholiota Squarrosa Lectin Unliganded

The structure of Crystal Structure of A Pholiota Squarrosa Lectin Unliganded, PDB code: 6eke was solved by A.Cabanettes, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.83 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.229, 67.670, 30.985, 90.00, 97.25, 90.00
R / Rfree (%)	17.1 / 21.1

The binding sites of Zinc atom in the Crystal Structure of A Pholiota Squarrosa Lectin Unliganded (pdb code 6eke). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of A Pholiota Squarrosa Lectin Unliganded, PDB code: 6eke:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of A Pholiota Squarrosa Lectin Unliganded


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Pholiota Squarrosa Lectin Unliganded within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:22.9 occ:1.00 OXT A:ACT105 1.8 29.1 1.0 OD2 A:ASP25 1.9 22.7 1.0 O A:ACT102 2.0 29.8 1.0 NE2 C:HIS38 2.1 20.2 1.0 C A:ACT105 2.7 33.2 1.0 C A:ACT102 2.7 32.7 1.0 OXT A:ACT102 2.8 26.6 1.0 CG A:ASP25 2.9 25.0 1.0 CD2 C:HIS38 3.0 21.9 1.0 O A:ACT105 3.0 33.9 1.0 CE1 C:HIS38 3.1 23.1 1.0 OD1 A:ASP25 3.2 21.4 1.0 O A:HOH222 3.8 38.1 1.0 O A:HOH214 4.0 40.6 1.0 CG C:HIS38 4.1 19.8 1.0 CH3 A:ACT105 4.1 36.1 1.0 O A:HOH221 4.2 23.8 1.0 ND1 C:HIS38 4.2 20.3 1.0 CB A:ASP25 4.2 22.4 1.0 CH3 A:ACT102 4.2 31.6 1.0 CD A:ARG27 4.3 23.8 1.0 CB A:ARG27 4.5 21.8 1.0 NH2 A:ARG27 4.6 26.4 1.0 NE1 A:TRP28 4.7 26.1 1.0 CG A:ARG27 4.9 23.9 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of A Pholiota Squarrosa Lectin Unliganded


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Pholiota Squarrosa Lectin Unliganded within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:34.5 occ:0.50 OD2 A:ASP22 2.2 57.9 1.0 OD1 A:ASP22 2.6 45.4 1.0 CG A:ASP22 2.7 44.6 1.0 O A:HOH210 3.4 40.3 1.0 CB A:ASP22 4.2 37.7 1.0 O A:HOH235 4.6 40.2 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of A Pholiota Squarrosa Lectin Unliganded


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Pholiota Squarrosa Lectin Unliganded within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:11.3 occ:0.50 OD2 B:ASP25 1.5 20.8 1.0 NE2 A:HIS38 2.0 24.7 1.0 CG B:ASP25 2.6 25.5 1.0 CD2 A:HIS38 2.9 23.4 1.0 CE1 A:HIS38 3.0 27.4 1.0 OD1 B:ASP25 3.0 22.1 1.0 CB B:ASP25 4.0 27.3 1.0 CG A:HIS38 4.0 22.8 1.0 ND1 A:HIS38 4.1 21.1 1.0 CD B:ARG27 4.1 35.2 1.0 O B:HOH231 4.2 30.7 1.0 CB B:ARG27 4.5 26.8 1.0 CG B:ARG27 4.7 30.6 1.0 NE1 B:TRP28 4.8 21.3 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of A Pholiota Squarrosa Lectin Unliganded


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Pholiota Squarrosa Lectin Unliganded within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:27.0 occ:1.00 OD2 C:ASP25 1.8 29.8 1.0 OXT C:ACT103 1.9 35.4 1.0 NE2 B:HIS38 2.0 23.7 1.0 OXT C:ACT102 2.2 34.4 1.0 O C:ACT102 2.5 35.1 1.0 C C:ACT102 2.7 39.3 1.0 CG C:ASP25 2.8 28.2 1.0 C C:ACT103 2.8 40.2 1.0 CD2 B:HIS38 2.9 26.3 1.0 CE1 B:HIS38 3.0 25.4 1.0 O C:ACT103 3.0 41.3 1.0 OD1 C:ASP25 3.1 25.4 1.0 O C:HOH224 3.9 45.1 1.0 NE C:ARG27 4.0 41.8 1.0 ND1 B:HIS38 4.1 24.8 1.0 O C:HOH226 4.1 25.8 1.0 CG B:HIS38 4.1 23.6 1.0 CH3 C:ACT103 4.2 41.1 1.0 CB C:ASP25 4.2 26.8 1.0 CH3 C:ACT102 4.2 39.9 1.0 NH2 C:ARG27 4.4 42.0 1.0 CB C:ARG27 4.5 27.6 1.0 CZ C:ARG27 4.6 39.8 1.0 CD C:ARG27 4.8 38.3 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of A Pholiota Squarrosa Lectin Unliganded


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Pholiota Squarrosa Lectin Unliganded within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn104 b:22.7 occ:1.00 OD1 B:ASP13 1.8 25.3 1.0 O C:MET0 1.9 25.0 1.0 OD2 B:ASP11 2.1 33.5 1.0 OD1 B:ASP11 2.5 37.6 1.0 CG B:ASP11 2.6 30.6 1.0 CG B:ASP13 2.9 28.0 1.0 C C:MET0 3.1 28.6 1.0 OD2 B:ASP13 3.2 29.6 1.0 N C:MET0 3.6 29.5 1.0 CA C:MET0 3.8 29.5 1.0 CB C:MET0 4.0 38.4 1.0 CB B:ASP11 4.1 26.1 1.0 N C:ALA1 4.2 26.6 1.0 CB B:ASP13 4.2 24.6 1.0 O B:HOH213 4.2 27.1 1.0 C C:ALA1 4.3 24.9 1.0 CG2 B:THR14 4.3 19.9 1.0 CA C:ALA1 4.4 28.9 1.0 N C:PRO2 4.5 24.0 1.0 CD C:PRO2 4.5 27.7 1.0 C C:ALA-1 4.5 27.1 1.0 N B:ASP13 4.5 22.7 1.0 N B:THR14 4.5 21.1 1.0 O C:ALA1 4.7 23.9 1.0 CA B:ASP13 4.7 23.6 1.0 O6 B:BU1101 4.7 43.0 1.0 OG1 B:THR14 4.7 21.5 1.0 O B:HOH214 4.7 31.1 1.0 C B:ASP13 4.9 23.0 1.0 CB C:ALA-1 4.9 30.1 1.0 CA C:ALA-1 5.0 28.2 1.0

A.Cabanettes, L.Perkams, C.Spies, C.Unverzagt, A.Varrot. Recognition of Complex Core-Fucosylated N-Glycans By A Mini Lectin. Angew. Chem. Int. Ed. Engl. V. 57 10178 2018.
ISSN: ESSN 1521-3773
PubMed: 29956878
DOI: 10.1002/ANIE.201805165