Zinc in PDB 5nj9: E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound, PDB code: 5nj9 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)	74.77 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.630, 173.530, 82.860, 90.00, 90.03, 90.00
R / Rfree (%)	14.9 / 18.2

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment 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 with Drvy Angiotensin Fragment Bound (pdb code 5nj9). 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 with Drvy Angiotensin Fragment Bound, PDB code: 5nj9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment 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 with Drvy Angiotensin Fragment Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:7.1 occ:1.00 NE2 A:HIS267 2.0 7.2 1.0 NE2 A:HIS262 2.1 8.2 1.0 OXT E:TYR604 2.1 3.2 0.7 SG A:CYS454 2.3 8.2 1.0 C E:TYR604 2.7 5.8 0.7 O E:TYR604 2.7 6.0 0.7 CE1 A:HIS267 2.9 7.3 1.0 CE1 A:HIS262 3.0 7.8 1.0 CD2 A:HIS262 3.1 7.7 1.0 CD2 A:HIS267 3.1 6.5 1.0 CB A:CYS454 3.3 7.6 1.0 CA A:CYS454 3.7 6.2 1.0 N A:GLY455 3.9 6.9 1.0 ND1 A:HIS267 4.0 7.2 1.0 CA E:TYR604 4.1 6.4 0.7 ND1 A:HIS262 4.1 8.7 1.0 CG A:HIS267 4.2 7.3 1.0 CE A:MET363 4.2 7.1 1.0 CG A:HIS262 4.2 7.5 1.0 O A:GLY455 4.2 8.9 1.0 C A:CYS454 4.2 6.7 1.0 N E:TYR604 4.4 6.5 0.7 O A:HOH608 4.7 7.3 1.0 C A:GLY455 4.8 7.9 1.0 CB E:TYR604 4.9 8.2 0.7 CA A:GLY455 5.0 6.3 1.0

Zinc binding site 2 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment 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 with Drvy Angiotensin Fragment Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:9.1 occ:1.00 OXT F:TYR604 2.0 3.9 0.7 NE2 C:HIS267 2.1 7.8 1.0 NE2 C:HIS262 2.1 8.7 1.0 SG C:CYS454 2.3 7.8 1.0 C F:TYR604 2.7 8.0 0.7 O F:TYR604 2.7 7.5 0.7 CE1 C:HIS267 2.9 6.8 1.0 CE1 C:HIS262 3.0 7.7 1.0 CD2 C:HIS262 3.1 7.1 1.0 CD2 C:HIS267 3.1 8.5 1.0 CB C:CYS454 3.3 7.9 1.0 CA C:CYS454 3.7 7.4 1.0 N C:GLY455 3.9 9.0 1.0 CA F:TYR604 4.1 7.3 0.7 ND1 C:HIS267 4.1 8.8 1.0 ND1 C:HIS262 4.2 7.5 1.0 CG C:HIS267 4.2 9.9 1.0 O C:GLY455 4.2 10.9 1.0 C C:CYS454 4.2 9.2 1.0 CG C:HIS262 4.2 6.7 1.0 CE C:MET363 4.2 8.3 1.0 N F:TYR604 4.4 7.8 0.7 O C:HOH641 4.7 8.1 1.0 C C:GLY455 4.8 9.1 1.0 CB F:TYR604 4.8 8.6 0.7 CA C:GLY455 5.0 8.6 1.0 N C:CYS454 5.0 7.5 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