Zinc in PDB 5njf: E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd H262A Mutant) with Pentapeptide Bound

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd H262A Mutant) with Pentapeptide Bound, PDB code: 5njf 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)	65.16 / 1.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.160, 174.480, 83.650, 90.00, 90.04, 90.00
R / Rfree (%)	13.9 / 17.1

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd H262A Mutant) with Pentapeptide 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 H262A Mutant) with Pentapeptide Bound (pdb code 5njf). 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 H262A Mutant) with Pentapeptide Bound, PDB code: 5njf:
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 H262A Mutant) with Pentapeptide 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 H262A Mutant) with Pentapeptide Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:16.5 occ:1.00 OE2 A:GLU263 2.0 20.9 1.0 NE2 A:HIS267 2.1 15.9 1.0 O A:HOH749 2.1 16.5 0.5 SG A:CYS454 2.3 15.0 1.0 OE1 A:GLU263 2.6 22.8 1.0 CD A:GLU263 2.6 23.0 1.0 CE1 A:HIS267 3.0 15.0 1.0 CD2 A:HIS267 3.1 17.1 1.0 CB A:CYS454 3.4 14.7 1.0 CA A:CYS454 3.8 12.7 1.0 O A:GLY455 3.9 15.9 1.0 CB E:ALA603 3.9 25.9 1.0 N A:GLY455 4.0 14.7 1.0 CG A:GLU263 4.1 20.5 1.0 ND1 A:HIS267 4.1 15.4 1.0 CE A:MET363 4.2 15.8 1.0 CG A:HIS267 4.2 15.1 1.0 C A:CYS454 4.3 13.4 1.0 O A:HOH935 4.5 26.1 1.0 N E:ALA603 4.5 19.5 0.5 C A:GLY455 4.6 14.4 1.0 C E:ALA602 4.7 19.0 0.5 N E:ALA602 4.7 18.6 0.5 CA E:ALA603 4.7 20.7 0.5 O A:HOH654 4.8 15.7 1.0 O E:ALA602 4.9 22.5 0.5 CA A:GLY455 4.9 14.9 1.0 CB A:GLU263 4.9 19.4 1.0

Zinc binding site 2 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd H262A Mutant) with Pentapeptide 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 H262A Mutant) with Pentapeptide Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:17.5 occ:1.00 O C:HOH737 1.9 14.5 0.5 OE2 C:GLU263 2.0 24.7 1.0 NE2 C:HIS267 2.1 17.8 1.0 SG C:CYS454 2.3 16.5 1.0 OE1 C:GLU263 2.6 26.5 1.0 CD C:GLU263 2.7 23.6 1.0 CE1 C:HIS267 3.0 16.0 1.0 CD2 C:HIS267 3.1 17.6 1.0 CB C:CYS454 3.4 15.9 1.0 CA C:CYS454 3.8 14.0 1.0 O C:GLY455 3.8 17.6 1.0 N C:GLY455 3.9 15.3 1.0 CB F:ALA603 3.9 27.4 1.0 ND1 C:HIS267 4.1 17.8 1.0 CG C:GLU263 4.1 22.9 1.0 CE C:MET363 4.2 16.6 1.0 C C:CYS454 4.2 14.5 1.0 CG C:HIS267 4.2 17.8 1.0 O C:HOH742 4.3 28.4 1.0 C F:ALA602 4.6 19.0 0.5 C C:GLY455 4.6 14.9 1.0 N F:ALA602 4.6 19.4 0.5 N F:ALA603 4.6 19.2 0.5 O F:ALA602 4.6 20.6 0.5 CA F:ALA603 4.7 20.8 0.5 O C:HOH656 4.8 16.3 1.0 CA C:GLY455 4.9 15.2 1.0 CB C:GLU263 5.0 22.3 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