Zinc in PDB 5kdx: Impa Metallopeptidase in Complex with T-Antigen

The structure of Impa Metallopeptidase in Complex with T-Antigen, PDB code: 5kdx was solved by I.Noach, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.12 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	99.410, 133.100, 103.780, 90.00, 103.12, 90.00
R / Rfree (%)	20.1 / 25.4

The binding sites of Zinc atom in the Impa Metallopeptidase in Complex with T-Antigen (pdb code 5kdx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Impa Metallopeptidase in Complex with T-Antigen, PDB code: 5kdx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Impa Metallopeptidase in Complex with T-Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Impa Metallopeptidase in Complex with T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:22.4 occ:1.00 OE1 A:GLU716 1.9 19.8 1.0 O A:HOH1133 2.1 22.6 1.0 NE2 A:HIS696 2.1 17.9 1.0 NE2 A:HIS700 2.2 20.4 1.0 CD A:GLU716 2.7 20.8 1.0 OE2 A:GLU716 2.9 22.8 1.0 CD2 A:HIS696 3.0 18.0 1.0 O A:HOH1338 3.1 35.5 1.0 CE1 A:HIS700 3.1 20.1 1.0 CE1 A:HIS696 3.2 17.7 1.0 CD2 A:HIS700 3.2 20.1 1.0 OE2 A:GLU697 3.7 23.4 1.0 ND2 A:ASN719 4.0 19.9 1.0 OXT A:TNR1002 4.0 28.3 1.0 CG A:HIS696 4.1 18.3 1.0 ND1 A:HIS696 4.2 17.5 1.0 CG A:GLU716 4.2 20.2 1.0 ND1 A:HIS700 4.3 19.9 1.0 CG A:HIS700 4.3 19.7 1.0 OG A:SER677 4.4 23.4 1.0 CD A:GLU697 4.5 22.7 1.0 CB A:TNR1002 4.7 33.9 1.0 OE1 A:GLU697 4.8 25.1 1.0 CB A:GLU716 4.8 20.0 1.0 CE1 A:TYR776 4.9 31.2 1.0 C A:TNR1002 4.9 29.8 1.0

Zinc binding site 2 out of 2 in the Impa Metallopeptidase in Complex with T-Antigen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Impa Metallopeptidase in Complex with T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1006 b:24.3 occ:1.00 O B:HOH1125 2.0 20.4 1.0 OE1 B:GLU716 2.1 24.3 1.0 NE2 B:HIS700 2.2 21.9 1.0 NE2 B:HIS696 2.2 19.3 1.0 CD B:GLU716 2.8 23.7 1.0 OE2 B:GLU716 2.8 26.6 1.0 CD2 B:HIS696 3.0 19.8 1.0 CE1 B:HIS700 3.1 21.8 1.0 CD2 B:HIS700 3.2 22.3 1.0 CE1 B:HIS696 3.3 19.6 1.0 O B:TNR1002 3.9 40.5 1.0 ND2 B:ASN719 4.0 20.5 1.0 OE2 B:GLU697 4.0 24.6 1.0 CG B:HIS696 4.2 20.1 1.0 ND1 B:HIS700 4.2 21.6 1.0 CG B:GLU716 4.3 23.1 1.0 CG B:HIS700 4.3 21.8 1.0 ND1 B:HIS696 4.3 19.5 1.0 OG B:SER677 4.4 23.5 1.0 CB B:TNR1002 4.4 43.8 1.0 OE1 B:GLU697 4.5 25.8 1.0 CD B:GLU697 4.6 23.6 1.0 C B:TNR1002 4.8 40.9 1.0 CE1 B:TYR776 4.8 29.0 1.0 CB B:GLU716 4.9 22.6 1.0 O1 B:TNR1002 5.0 42.1 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