Zinc in PDB 5kdn: Zmpb Metallopeptidase From Clostridium Perfringens

The structure of Zmpb Metallopeptidase From Clostridium Perfringens, PDB code: 5kdn 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)	43.09 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.890, 68.020, 170.860, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18

The binding sites of Zinc atom in the Zmpb Metallopeptidase From Clostridium Perfringens (pdb code 5kdn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Zmpb Metallopeptidase From Clostridium Perfringens, PDB code: 5kdn:

Zinc binding site 1 out of 1 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 A:Zn1106 b:18.8 occ:0.50 OE1 A:GLU771 2.0 32.2 1.0 O A:HOH1312 2.0 37.4 1.0 O A:HOH1300 2.1 34.9 1.0 NE2 A:HIS760 2.2 29.2 1.0 NE2 A:HIS756 2.2 26.2 1.0 CD A:GLU771 2.9 34.4 1.0 CD2 A:HIS756 3.1 22.4 1.0 OE2 A:GLU771 3.1 37.4 1.0 CD2 A:HIS760 3.1 25.6 1.0 CE1 A:HIS760 3.2 28.7 1.0 CE1 A:HIS756 3.2 24.4 1.0 O A:HOH1670 4.1 46.3 1.0 OE2 A:GLU757 4.2 25.9 1.0 O A:HOH1633 4.3 32.9 1.0 ND1 A:HIS760 4.3 28.1 1.0 CG A:HIS756 4.3 21.6 1.0 ND1 A:HIS756 4.3 23.6 1.0 CG A:HIS760 4.3 25.3 1.0 CG A:GLU771 4.4 28.7 1.0 ND2 A:ASN774 4.4 22.9 1.0 OE1 A:GLU757 4.5 24.9 1.0 CD A:GLU757 4.7 21.4 1.0 CA A:GLU771 4.8 24.0 1.0 CB A:GLU771 4.8 25.4 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