Zinc in PDB 5nja: E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue Bound

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue Bound, PDB code: 5nja 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)	86.76 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.630, 173.530, 83.060, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 17.1

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue 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 Angiotensin Analogue Bound (pdb code 5nja). 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 Angiotensin Analogue Bound, PDB code: 5nja:
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 Angiotensin Analogue 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 Angiotensin Analogue Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:12.3 occ:1.00 OXT E:PHE604 1.9 8.7 0.5 NE2 A:HIS262 2.1 13.1 1.0 NE2 A:HIS267 2.1 12.0 1.0 OXT E:PHE604 2.1 13.2 0.5 SG A:CYS454 2.2 11.8 1.0 C E:PHE604 2.6 9.1 0.5 O E:PHE604 2.7 10.1 0.5 C E:PHE604 2.8 12.9 0.5 CE1 A:HIS267 2.9 10.8 1.0 O E:PHE604 3.0 23.0 0.5 CE1 A:HIS262 3.0 13.1 1.0 CD2 A:HIS262 3.1 14.8 1.0 CD2 A:HIS267 3.2 12.2 1.0 CB A:CYS454 3.3 10.4 1.0 CA A:CYS454 3.6 10.2 1.0 N A:GLY455 3.9 11.0 1.0 CA E:PHE604 4.1 9.6 0.5 CA E:PHE604 4.1 11.1 0.5 ND1 A:HIS267 4.1 12.4 1.0 ND1 A:HIS262 4.1 12.7 1.0 C A:CYS454 4.2 10.2 1.0 CE A:MET363 4.2 10.4 1.0 CG A:HIS262 4.2 12.2 1.0 CG A:HIS267 4.2 11.0 1.0 N E:PHE604 4.3 12.6 0.5 O A:GLY455 4.3 16.5 1.0 N E:PHE604 4.3 11.2 0.5 O A:HOH607 4.7 11.9 1.0 CB E:PHE604 4.8 18.1 0.5 C A:GLY455 4.8 13.7 1.0 N A:CYS454 5.0 11.6 1.0 CA A:GLY455 5.0 12.4 1.0

Zinc binding site 2 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue 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 Angiotensin Analogue Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:12.8 occ:1.00 OXT F:PHE604 2.0 15.2 0.5 NE2 C:HIS267 2.1 13.3 1.0 NE2 C:HIS262 2.1 14.2 1.0 OXT F:PHE604 2.1 10.7 0.5 O F:PHE604 2.1 19.3 0.5 SG C:CYS454 2.2 13.3 1.0 C F:PHE604 2.5 8.9 0.5 C F:PHE604 2.8 12.6 0.5 O F:PHE604 2.9 14.0 0.5 CE1 C:HIS267 2.9 12.5 1.0 CE1 C:HIS262 3.0 12.8 1.0 CD2 C:HIS262 3.1 14.5 1.0 CD2 C:HIS267 3.1 12.3 1.0 CB C:CYS454 3.3 12.9 1.0 CA C:CYS454 3.6 11.4 1.0 N C:GLY455 3.9 11.2 1.0 CA F:PHE604 3.9 10.5 0.5 ND1 C:HIS267 4.1 11.9 1.0 ND1 C:HIS262 4.1 13.2 1.0 C C:CYS454 4.1 10.3 1.0 CE C:MET363 4.1 12.1 1.0 CG C:HIS262 4.2 11.7 1.0 CG C:HIS267 4.2 12.7 1.0 O C:GLY455 4.2 15.6 1.0 CA F:PHE604 4.2 10.0 0.5 N F:PHE604 4.4 12.3 0.5 N F:PHE604 4.5 12.5 0.5 O C:HOH653 4.6 13.0 1.0 C C:GLY455 4.8 13.4 1.0 CB F:PHE604 4.9 13.9 0.5 CA C:GLY455 5.0 12.6 1.0 CB F:PHE604 5.0 13.9 0.5 N C:CYS454 5.0 11.3 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