Zinc in PDB 6xsz: The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc

The structure of The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc, PDB code: 6xsz 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)	38.98 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	109.694, 99.991, 118.587, 90, 95.95, 90
R / Rfree (%)	20.1 / 24.4

The binding sites of Zinc atom in the The Structure of the M60 Catalytic Domain From Clostridium Perfringens Zmpc (pdb code 6xsz). 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, PDB code: 6xsz:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:41.7 occ:1.00 NE2 A:HIS751 2.2 29.5 1.0 OE2 A:GLU766 2.2 43.7 1.0 NE2 A:HIS755 2.4 25.7 1.0 O A:HOH1306 2.5 25.0 1.0 O A:HOH1330 2.6 40.4 1.0 O A:HOH1343 2.8 24.3 1.0 CD A:GLU766 3.1 39.4 1.0 CE1 A:HIS751 3.1 27.8 1.0 CD2 A:HIS751 3.2 28.2 1.0 CD2 A:HIS755 3.2 25.7 1.0 OE1 A:GLU766 3.3 42.7 1.0 CE1 A:HIS755 3.5 25.7 1.0 ND1 A:HIS751 4.3 29.5 1.0 O A:HOH1328 4.3 36.7 1.0 CG A:HIS751 4.3 27.8 1.0 CG A:HIS755 4.4 25.1 1.0 CG A:GLU766 4.5 36.5 1.0 ND1 A:HIS755 4.5 24.9 1.0 ND2 A:ASN769 4.6 25.8 1.0 O A:HOH1296 4.6 33.8 1.0 CA A:GLU766 4.9 31.9 1.0 OE1 A:GLU752 5.0 27.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:41.8 occ:1.00 OE1 B:GLU766 2.1 47.0 1.0 NE2 B:HIS751 2.2 28.4 1.0 NE2 B:HIS755 2.3 30.9 1.0 O B:HOH1242 2.5 26.6 1.0 O B:HOH1310 2.7 32.4 1.0 CD B:GLU766 2.9 45.8 1.0 OE2 B:GLU766 3.0 51.9 1.0 CE1 B:HIS751 3.1 27.6 1.0 CD2 B:HIS751 3.1 27.2 1.0 CD2 B:HIS755 3.1 31.4 1.0 CE1 B:HIS755 3.4 31.3 1.0 O B:HOH1184 4.2 41.0 1.0 ND1 B:HIS751 4.2 28.1 1.0 CG B:HIS751 4.3 26.8 1.0 CG B:GLU766 4.3 41.0 1.0 ND2 B:ASN769 4.3 25.4 1.0 CG B:HIS755 4.4 30.6 1.0 ND1 B:HIS755 4.5 31.4 1.0 OE1 B:GLU752 4.9 23.7 1.0 CA B:GLU766 4.9 33.4 1.0 OE2 B:GLU752 4.9 25.4 1.0 CB B:GLU766 4.9 37.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:40.7 occ:1.00 OE2 C:GLU766 2.1 40.3 1.0 NE2 C:HIS755 2.1 26.6 1.0 NE2 C:HIS751 2.2 25.9 1.0 O C:HOH1271 2.4 36.0 1.0 O C:HOH1297 2.7 40.8 1.0 O C:HOH1188 2.8 28.0 1.0 CD C:GLU766 2.9 41.6 1.0 OE1 C:GLU766 3.0 47.3 1.0 CD2 C:HIS755 3.1 25.8 1.0 CD2 C:HIS751 3.1 26.0 1.0 CE1 C:HIS751 3.2 25.4 1.0 CE1 C:HIS755 3.2 26.7 1.0 CG C:HIS755 4.2 26.7 1.0 ND1 C:HIS751 4.3 25.6 1.0 CG C:HIS751 4.3 26.9 1.0 ND1 C:HIS755 4.3 27.2 1.0 CG C:GLU766 4.3 37.5 1.0 ND2 C:ASN769 4.4 24.6 1.0 O C:HOH1241 4.5 30.1 1.0 OE1 C:GLU752 4.8 28.3 1.0 OE2 C:GLU752 4.8 29.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:38.4 occ:1.00 NE2 D:HIS755 2.2 26.9 1.0 OE1 D:GLU766 2.2 39.6 1.0 NE2 D:HIS751 2.2 29.6 1.0 O D:HOH1277 2.5 31.4 1.0 O D:HOH1242 2.6 26.0 1.0 O D:HOH1295 2.8 35.1 1.0 OE2 D:GLU766 2.8 42.7 1.0 CD D:GLU766 2.9 38.7 1.0 CD2 D:HIS755 3.1 25.2 1.0 CD2 D:HIS751 3.1 28.3 1.0 CE1 D:HIS755 3.2 27.2 1.0 CE1 D:HIS751 3.3 29.6 1.0 CG D:HIS755 4.3 25.7 1.0 ND2 D:ASN769 4.3 23.0 1.0 ND1 D:HIS755 4.3 25.9 1.0 CG D:HIS751 4.3 28.1 1.0 CG D:GLU766 4.3 35.6 1.0 ND1 D:HIS751 4.4 29.4 1.0 O D:HOH1268 4.6 36.2 1.0 OE1 D:GLU752 4.8 26.2 1.0 OE2 D:GLU752 4.9 27.6 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