Zinc in PDB 7yx8: Crystal Structure of the AM0627 (E326A) Inactive Mutant in Complex with Psgl-1-Like Bis-T Glycopeptide and ZN2+

The structure of Crystal Structure of the AM0627 (E326A) Inactive Mutant in Complex with Psgl-1-Like Bis-T Glycopeptide and ZN2+, PDB code: 7yx8 was solved by V.Taleb, Q.Liao, Y.Narimatsu, A.Garcia-Garcia, I.Companon, R.J.Borges, A.M.Gonzalez-Ramirez, F.Corzana, H.Clausen, C.Rovira, R.Hurtado-Guerrero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.30 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.145, 82.687, 172.608, 90, 90, 90
R / Rfree (%)	16.7 / 18.2

The binding sites of Zinc atom in the Crystal Structure of the AM0627 (E326A) Inactive Mutant in Complex with Psgl-1-Like Bis-T Glycopeptide and ZN2+ (pdb code 7yx8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the AM0627 (E326A) Inactive Mutant in Complex with Psgl-1-Like Bis-T Glycopeptide and ZN2+, PDB code: 7yx8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the AM0627 (E326A) Inactive Mutant in Complex with Psgl-1-Like Bis-T Glycopeptide and ZN2+


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 the AM0627 (E326A) Inactive Mutant in Complex with Psgl-1-Like Bis-T Glycopeptide and ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn609 b:19.3 occ:1.00 OE1 A:GLU343 1.9 19.8 1.0 NE2 A:HIS325 2.0 16.8 1.0 O H:THR5 2.0 33.7 1.0 NE2 A:HIS329 2.0 19.1 1.0 CD A:GLU343 2.6 21.1 1.0 OE2 A:GLU343 2.6 22.4 1.0 O H:HOH101 2.8 30.3 1.0 CE1 A:HIS329 3.0 17.1 1.0 CD2 A:HIS325 3.0 17.7 1.0 CE1 A:HIS325 3.0 19.0 1.0 CD2 A:HIS329 3.1 18.1 1.0 C H:THR5 3.2 43.9 1.0 O H:HOH107 4.0 24.5 1.0 ND2 A:ASN346 4.0 18.6 1.0 N H:THR5 4.1 37.5 1.0 CG A:GLU343 4.1 20.3 1.0 ND1 A:HIS325 4.1 18.8 1.0 ND1 A:HIS329 4.1 17.7 1.0 CG A:HIS325 4.1 18.0 1.0 CA H:THR5 4.1 41.0 1.0 CG A:HIS329 4.2 17.4 1.0 N H:THR6 4.2 43.0 1.0 C H:GLN4 4.5 35.5 1.0 CB H:THR6 4.7 30.4 1.0 CA H:THR6 4.7 36.5 1.0 CB A:GLU343 4.7 19.7 1.0 OH A:TYR470 4.7 29.0 1.0 C8 E:A2G1 4.8 56.1 1.0 CA A:GLU343 4.8 18.7 1.0 O H:GLN4 4.9 23.9 1.0 CB H:GLN4 4.9 39.0 1.0 CG A:ASN346 5.0 17.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the AM0627 (E326A) Inactive Mutant in Complex with Psgl-1-Like Bis-T Glycopeptide and ZN2+


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 the AM0627 (E326A) Inactive Mutant in Complex with Psgl-1-Like Bis-T Glycopeptide and ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:22.4 occ:1.00 O F:THR5 1.9 41.8 1.0 OE1 B:GLU343 2.0 22.4 1.0 NE2 B:HIS325 2.0 20.9 1.0 NE2 B:HIS329 2.0 22.9 1.0 CD B:GLU343 2.6 23.9 1.0 OE2 B:GLU343 2.7 25.6 1.0 O F:HOH102 2.9 39.6 1.0 CE1 B:HIS329 2.9 20.4 1.0 CE1 B:HIS325 3.0 22.3 1.0 CD2 B:HIS325 3.0 22.0 1.0 CD2 B:HIS329 3.1 21.1 1.0 C F:THR5 3.1 45.1 1.0 O F:HOH105 3.9 28.4 1.0 ND2 B:ASN346 4.0 23.4 1.0 ND1 B:HIS329 4.1 20.9 1.0 ND1 B:HIS325 4.1 21.5 1.0 N F:THR5 4.1 37.5 1.0 CG B:GLU343 4.1 23.4 1.0 N F:THR6 4.1 47.7 1.0 CG B:HIS325 4.1 21.6 1.0 CA F:THR5 4.2 40.3 1.0 CG B:HIS329 4.2 20.2 1.0 C F:GLN4 4.5 34.3 1.0 CA F:THR6 4.6 46.7 1.0 C8 C:A2G1 4.7 51.6 1.0 CB F:THR6 4.7 42.2 1.0 OH B:TYR470 4.7 27.0 1.0 CB B:GLU343 4.7 23.4 1.0 O F:GLN4 4.8 26.1 1.0 CA B:GLU343 4.8 22.8 1.0 CB F:GLN4 4.9 35.5 1.0 CG B:ASN346 4.9 22.4 1.0 N2 C:A2G1 4.9 51.2 1.0

V.Taleb, Q.Liao, Y.Narimatsu, A.Garcia-Garcia, I.Companon, R.J.Borges, A.M.Gonzalez-Ramirez, F.Corzana, H.Clausen, C.Rovira, R.Hurtado-Guerrero. Structural and Mechanistic Insights Into the Cleavage of Clustered O-Glycan Patches-Containing Glycoproteins By Mucinases of the Human Gut. Nat Commun V. 13 4324 2022.
ISSN: ESSN 2041-1723
PubMed: 35882872
DOI: 10.1038/S41467-022-32021-9