Zinc in PDB 5kdj: Zmpb Metallopeptidase From Clostridium Perfringens

The structure of Zmpb Metallopeptidase From Clostridium Perfringens, PDB code: 5kdj was solved by I.Noach, E.Ficko-Blean, C.Stuart, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.82 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.620, 95.800, 187.220, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.9

The structure of Zmpb Metallopeptidase From Clostridium Perfringens also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Zmpb Metallopeptidase From Clostridium Perfringens (pdb code 5kdj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Zmpb Metallopeptidase From Clostridium Perfringens, PDB code: 5kdj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Zmpb Metallopeptidase From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zmpb Metallopeptidase From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1103 b:27.9 occ:1.00 NE2 B:HIS756 2.1 16.1 1.0 NE2 B:HIS760 2.2 15.9 1.0 OE1 B:GLU771 2.2 27.1 1.0 O B:HOH1544 2.7 32.0 1.0 CD B:GLU771 3.0 26.3 1.0 CE1 B:HIS756 3.0 15.9 1.0 CD2 B:HIS760 3.0 15.6 1.0 CD2 B:HIS756 3.1 15.6 1.0 OE2 B:GLU771 3.1 28.2 1.0 CE1 B:HIS760 3.3 16.5 1.0 O B:HOH1542 4.1 23.0 1.0 ND1 B:HIS756 4.2 15.3 1.0 CG B:HIS756 4.2 15.1 1.0 CG B:HIS760 4.3 15.1 1.0 ND1 B:HIS760 4.3 16.1 1.0 OE2 B:GLU757 4.4 16.9 1.0 ND2 B:ASN774 4.5 17.1 1.0 CG B:GLU771 4.5 25.2 1.0 OE1 B:GLU757 4.5 15.6 1.0 CD B:GLU757 4.8 15.1 1.0 CA B:GLU771 4.8 21.2 1.0

Zinc binding site 2 out of 2 in the Zmpb Metallopeptidase From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zmpb Metallopeptidase From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:39.5 occ:1.00 NE2 A:HIS756 2.0 20.0 1.0 OE1 A:GLU771 2.2 35.2 1.0 NE2 A:HIS760 2.3 25.8 1.0 O A:HOH1417 2.5 30.4 1.0 O A:HOH1252 2.6 25.6 1.0 CE1 A:HIS756 3.0 19.5 1.0 CD A:GLU771 3.1 35.3 1.0 CD2 A:HIS756 3.1 19.7 1.0 CD2 A:HIS760 3.1 24.2 1.0 OE2 A:GLU771 3.3 35.6 1.0 CE1 A:HIS760 3.4 26.6 1.0 O A:HOH1414 4.1 31.8 1.0 ND1 A:HIS756 4.1 19.9 1.0 CG A:HIS756 4.2 18.5 1.0 CG A:HIS760 4.4 24.2 1.0 OE1 A:GLU757 4.5 20.6 1.0 ND1 A:HIS760 4.5 25.4 1.0 CG A:GLU771 4.5 34.1 1.0 OE2 A:GLU757 4.5 21.1 1.0 ND2 A:ASN774 4.6 23.7 1.0 CA A:GLU771 4.8 28.3 1.0 CD A:GLU757 4.8 19.5 1.0 O A:HOH1287 5.0 36.8 1.0

I.Noach, E.Ficko-Blean, B.Pluvinage, C.Stuart, M.L.Jenkins, D.Brochu, N.Buenbrazo, W.Wakarchuk, J.E.Burke, M.Gilbert, A.B.Boraston. Recognition of Protein-Linked Glycans As A Determinant of Peptidase Activity. Proc. Natl. Acad. Sci. V. 114 E679 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28096352
DOI: 10.1073/PNAS.1615141114