Zinc in PDB 5njc: E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound, PDB code: 5njc was solved by D.Ghilarov, M.Serebryakova, C.E.M.Stevenson, S.J.Hearnshaw, D.Volkov, A.Maxwell, D.M.Lawson, K.Severinov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.29 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.290, 175.440, 84.330, 90.00, 90.01, 90.00
R / Rfree (%)	14.5 / 18.3

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Zinc atom in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound (pdb code 5njc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound, PDB code: 5njc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:18.6 occ:1.00 OD1 E:ASP603 2.0 27.2 1.0 NE2 A:HIS262 2.1 17.0 1.0 NE2 A:HIS267 2.2 16.8 1.0 SG A:CYS454 2.3 16.6 1.0 CG E:ASP603 2.7 29.4 1.0 OD2 E:ASP603 2.9 29.1 1.0 CE1 A:HIS267 3.0 13.9 1.0 CD2 A:HIS262 3.1 19.1 1.0 CE1 A:HIS262 3.1 18.8 1.0 CD2 A:HIS267 3.2 15.3 1.0 CB A:CYS454 3.4 15.4 1.0 CA A:CYS454 3.9 11.8 1.0 CB E:ASP603 4.1 27.4 1.0 ND1 A:HIS267 4.2 14.7 1.0 ND1 A:HIS262 4.2 18.2 1.0 CG A:HIS262 4.2 19.1 1.0 CG A:HIS267 4.3 15.4 1.0 CE A:MET363 4.4 14.2 1.0 N A:GLY455 4.4 14.2 1.0 O E:GLU602 4.4 27.4 1.0 C A:CYS454 4.5 12.6 1.0 O A:GLY455 4.7 15.9 1.0 CA E:ASP603 4.8 20.9 1.0 C E:GLU602 4.8 20.5 1.0 O A:HOH635 4.8 13.3 1.0 N E:ASP603 5.0 20.7 1.0

Zinc binding site 2 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:19.4 occ:1.00 OD1 F:ASP603 2.0 30.9 1.0 NE2 C:HIS267 2.1 18.7 1.0 NE2 C:HIS262 2.2 21.6 1.0 SG C:CYS454 2.3 16.1 1.0 CG F:ASP603 2.7 19.6 1.0 OD2 F:ASP603 2.8 25.0 1.0 CE1 C:HIS267 3.0 17.0 1.0 CD2 C:HIS262 3.2 17.6 1.0 CE1 C:HIS262 3.2 18.1 1.0 CD2 C:HIS267 3.2 15.3 1.0 CB C:CYS454 3.4 16.0 1.0 CA C:CYS454 3.9 12.3 1.0 ND1 C:HIS267 4.1 15.0 1.0 CB F:ASP603 4.2 15.2 1.0 CG C:HIS267 4.3 15.5 1.0 ND1 C:HIS262 4.3 20.0 1.0 CG C:HIS262 4.3 18.0 1.0 N C:GLY455 4.4 13.8 1.0 CE C:MET363 4.4 15.2 1.0 C C:CYS454 4.5 13.3 1.0 O F:GLU602 4.5 15.6 1.0 O C:GLY455 4.7 17.3 1.0 O C:HOH654 4.7 14.6 1.0 CA F:ASP603 4.8 15.8 1.0 C F:GLU602 5.0 13.6 1.0

D.Ghilarov, M.Serebryakova, C.E.M.Stevenson, S.J.Hearnshaw, D.S.Volkov, A.Maxwell, D.M.Lawson, K.Severinov. The Origins of Specificity in the Microcin-Processing Protease Tldd/E. Structure V. 25 1549 2017.
ISSN: ISSN 1878-4186
PubMed: 28943336
DOI: 10.1016/J.STR.2017.08.006