Zinc in PDB 5kdw: Impa Metallopeptidase From Pseudomonas Aeruginosa

The structure of Impa Metallopeptidase From Pseudomonas Aeruginosa, PDB code: 5kdw 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)	100.09 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.920, 132.730, 103.070, 90.00, 103.81, 90.00
R / Rfree (%)	15.3 / 18.6

The binding sites of Zinc atom in the Impa Metallopeptidase From Pseudomonas Aeruginosa (pdb code 5kdw). 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 From Pseudomonas Aeruginosa, PDB code: 5kdw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Impa Metallopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Impa Metallopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1022 b:29.5 occ:0.50 O A:HOH1576 2.0 37.3 1.0 OE1 A:GLU716 2.1 22.7 1.0 NE2 A:HIS696 2.1 20.7 1.0 NE2 A:HIS700 2.2 20.2 1.0 CD A:GLU716 2.9 20.6 1.0 OH A:TYR776 2.9 46.1 1.0 OE2 A:GLU716 2.9 26.5 1.0 CD2 A:HIS696 3.1 19.2 1.0 CE1 A:HIS700 3.1 21.3 1.0 CE1 A:HIS696 3.1 19.6 1.0 CD2 A:HIS700 3.2 17.9 1.0 OE1 A:GLU697 3.8 20.5 1.0 CZ A:TYR776 4.1 37.1 1.0 ND2 A:ASN719 4.1 17.0 1.0 CG A:HIS696 4.2 16.2 1.0 ND1 A:HIS696 4.2 18.6 1.0 ND1 A:HIS700 4.2 18.6 1.0 OG A:SER677 4.3 14.7 0.6 CG A:HIS700 4.3 16.8 1.0 CG A:GLU716 4.3 17.6 1.0 CD A:GLU697 4.4 17.6 1.0 OE2 A:GLU697 4.5 17.9 1.0 CE1 A:TYR776 4.6 36.0 1.0 O A:HOH1939 4.9 47.6 1.0 CB A:GLU716 4.9 16.1 1.0

Zinc binding site 2 out of 2 in the Impa Metallopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Impa Metallopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1022 b:27.7 occ:0.50 O B:HOH1302 2.0 32.0 1.0 OE1 B:GLU716 2.0 23.5 1.0 NE2 B:HIS696 2.1 20.4 1.0 NE2 B:HIS700 2.2 19.3 1.0 CD B:GLU716 2.8 21.3 1.0 OE2 B:GLU716 2.8 24.6 1.0 OH B:TYR776 2.9 47.6 1.0 CD2 B:HIS696 3.0 19.9 1.0 CE1 B:HIS700 3.1 21.8 1.0 CE1 B:HIS696 3.1 20.3 1.0 CD2 B:HIS700 3.2 18.1 1.0 CZ B:TYR776 3.9 39.4 1.0 OE1 B:GLU697 4.0 19.5 1.0 CG B:HIS696 4.2 17.0 1.0 ND1 B:HIS696 4.2 19.6 1.0 ND2 B:ASN719 4.2 16.8 1.0 CG B:GLU716 4.2 18.2 1.0 ND1 B:HIS700 4.3 19.4 1.0 CG B:HIS700 4.3 17.7 1.0 CE1 B:TYR776 4.4 40.4 1.0 OG B:SER677 4.4 16.0 0.6 OE2 B:GLU697 4.5 18.2 1.0 CD B:GLU697 4.6 17.4 1.0 CB B:GLU716 4.8 17.1 1.0 O B:HOH1969 4.9 43.2 1.0 CE2 B:TYR776 4.9 33.1 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