Zinc in PDB 6xt1: The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen

The structure of The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen, PDB code: 6xt1 was solved by B.Pluvinage, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.07 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	109.615, 100.93, 119.024, 90, 95.91, 90
R / Rfree (%)	23.5 / 28

The binding sites of Zinc atom in the The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen (pdb code 6xt1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen, PDB code: 6xt1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:52.4 occ:1.00 OXT A:SER1004 2.2 60.8 1.0 OE2 A:GLU766 2.2 43.5 1.0 NE2 A:HIS751 2.2 39.0 1.0 NE2 A:HIS755 2.3 37.7 1.0 N A:SER1004 2.5 60.9 1.0 CD A:GLU766 3.0 43.0 1.0 C A:SER1004 3.0 60.9 1.0 OE1 A:GLU766 3.0 43.1 1.0 CD2 A:HIS751 3.1 38.7 1.0 CA A:SER1004 3.1 61.6 1.0 CD2 A:HIS755 3.2 37.5 1.0 CE1 A:HIS751 3.3 38.9 1.0 CE1 A:HIS755 3.4 37.6 1.0 CB A:SER1004 3.6 63.2 1.0 O A:SER1004 4.1 60.9 1.0 CG A:HIS751 4.3 38.2 1.0 ND1 A:HIS751 4.3 38.6 1.0 OG A:SER1004 4.4 65.8 1.0 CG A:HIS755 4.4 37.2 1.0 O A:HOH1142 4.4 39.5 1.0 CG A:GLU766 4.4 42.4 1.0 ND1 A:HIS755 4.5 37.5 1.0 OD1 A:ASN769 4.7 34.6 1.0 CA A:GLU766 4.8 40.7 1.0 CB A:GLU766 5.0 41.5 1.0 C1 F:A2G1 5.0 67.6 1.0

Zinc binding site 2 out of 4 in the The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:52.3 occ:1.00 OE1 B:GLU766 2.1 44.5 1.0 NE2 B:HIS755 2.2 34.3 1.0 OXT B:SER1006 2.2 51.3 1.0 NE2 B:HIS751 2.2 36.1 1.0 N B:SER1006 2.5 51.5 1.0 CD B:GLU766 3.0 43.9 1.0 C B:SER1006 3.0 51.4 1.0 CD2 B:HIS751 3.1 35.9 1.0 CD2 B:HIS755 3.1 34.0 1.0 OE2 B:GLU766 3.2 44.6 1.0 CA B:SER1006 3.2 51.8 1.0 CE1 B:HIS755 3.2 34.3 1.0 CE1 B:HIS751 3.3 36.1 1.0 CB B:SER1006 3.9 52.8 1.0 O B:SER1006 4.2 51.3 1.0 CG B:HIS751 4.3 35.5 1.0 CG B:HIS755 4.3 33.8 1.0 ND1 B:HIS755 4.3 34.1 1.0 ND2 B:ASN769 4.3 33.3 1.0 ND1 B:HIS751 4.4 35.8 1.0 CG B:GLU766 4.4 42.7 1.0 OG B:SER1006 4.5 54.3 1.0 CA B:GLU766 4.8 39.5 1.0 OE1 B:GLU752 4.8 34.1 1.0 CB B:GLU766 4.9 41.2 1.0 OE2 B:GLU752 4.9 34.5 1.0

Zinc binding site 3 out of 4 in the The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:46.5 occ:1.00 OE2 C:GLU766 2.2 39.0 1.0 NE2 C:HIS751 2.3 31.9 1.0 NE2 C:HIS755 2.3 33.3 1.0 O C:HOH1115 2.7 20.2 1.0 O C:HOH1217 2.8 46.0 1.0 CD C:GLU766 3.0 38.9 1.0 OE1 C:GLU766 3.0 39.4 1.0 CD2 C:HIS751 3.0 32.0 1.0 CD2 C:HIS755 3.0 33.0 1.0 CE1 C:HIS751 3.4 31.9 1.0 CE1 C:HIS755 3.5 33.3 1.0 CG C:HIS751 4.3 32.0 1.0 CG C:HIS755 4.3 32.7 1.0 ND1 C:HIS751 4.4 32.0 1.0 CG C:GLU766 4.4 38.4 1.0 ND1 C:HIS755 4.5 33.1 1.0 OE2 C:GLU752 4.6 34.4 1.0 ND2 C:ASN769 4.6 29.8 1.0 OE1 C:GLU752 4.7 34.3 1.0 CD C:GLU752 4.9 34.0 1.0

Zinc binding site 4 out of 4 in the The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc in Complex the Sialyl T Antigen within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:49.3 occ:1.00 NE2 D:HIS751 2.2 32.0 1.0 OE1 D:GLU766 2.2 40.2 1.0 NE2 D:HIS755 2.3 34.9 1.0 O D:HOH1213 2.6 32.6 1.0 O D:HOH1187 2.8 28.8 1.0 O D:HOH1218 2.9 35.4 1.0 CD D:GLU766 3.0 39.8 1.0 OE2 D:GLU766 3.0 40.5 1.0 CD2 D:HIS751 3.1 32.0 1.0 CD2 D:HIS755 3.2 34.6 1.0 CE1 D:HIS751 3.2 32.0 1.0 CE1 D:HIS755 3.4 34.9 1.0 O D:HOH1125 3.9 42.5 1.0 ND1 D:HIS751 4.3 32.1 1.0 CG D:HIS751 4.3 32.0 1.0 CG D:HIS755 4.4 34.3 1.0 CG D:GLU766 4.4 39.1 1.0 ND1 D:HIS755 4.5 34.7 1.0 ND2 D:ASN769 4.5 30.0 1.0 OE2 D:GLU752 4.7 33.5 1.0 OE1 D:GLU752 4.8 33.4 1.0

B.Pluvinage, E.Ficko-Blean, I.Noach, C.Stuart, N.Thompson, H.Mcclure, N.Buenbrazo, W.Wakarchuck, A.B.Boraston. Molecular Insights Into Architecturally Complex Glycopeptidases Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490