Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound, PDB code: 5njc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 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 Sodium with other atoms in the Na 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:Na504 b:54.8 occ:1.00 O A:HOH1027 2.3 23.0 1.0 O A:HOH936 2.8 27.2 1.0 O A:HOH1045 2.8 48.6 1.0 OG A:SER117 3.0 27.1 1.0 O A:HOH1086 3.1 35.3 1.0 CB A:SER117 3.7 23.6 1.0 O A:HOH869 4.1 21.5 1.0 O A:HOH727 4.2 19.9 1.0 N A:SER117 5.0 19.1 1.0 O A:HOH842 5.0 24.1 1.0 CA A:SER117 5.0 20.1 1.0

Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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 B:Na706 b:26.5 occ:1.00 O B:SER30 2.4 22.5 1.0 O B:HOH1184 2.4 32.9 1.0 O B:HOH1192 2.4 24.1 1.0 O B:HOH958 2.4 32.9 1.0 O B:SER33 2.5 18.6 1.0 C B:SER30 3.5 19.3 1.0 C B:SER33 3.8 17.8 1.0 CA B:SER30 4.1 16.2 1.0 O B:HOH1073 4.3 17.1 1.0 CA B:ASP34 4.4 14.6 1.0 N B:ASP34 4.5 14.6 1.0 C B:ASP34 4.5 14.7 1.0 O B:ASP34 4.6 19.2 1.0 N B:GLY31 4.6 21.8 1.0 CB B:SER30 4.6 18.1 1.0 N B:SER33 4.7 18.4 1.0 CA B:SER33 4.8 18.9 1.0 CA B:GLY31 4.9 23.3 1.0

Sodium binding site 3 out of 4 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 Sodium with other atoms in the Na binding site number 3 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:Na504 b:23.6 occ:1.00 O C:HOH980 2.3 27.9 1.0 O C:ILE84 2.5 19.5 1.0 O C:HOH879 2.6 22.9 1.0 OD1 C:ASN14 2.7 25.3 1.0 O C:HOH978 2.7 28.1 1.0 O C:HOH979 2.7 36.2 1.0 CG C:ASN14 3.4 16.9 1.0 C C:ILE84 3.6 14.4 1.0 CB C:ASN14 3.9 14.3 1.0 N C:ILE84 4.1 15.5 1.0 CA C:ILE84 4.3 15.0 1.0 ND2 C:ASN14 4.4 17.5 1.0 CA C:ASN14 4.5 17.0 1.0 CB C:ILE84 4.6 14.8 1.0 N C:SER85 4.6 13.8 1.0 CB C:SER85 4.7 14.8 1.0 O D:HOH1194 4.7 66.8 1.0 CA C:SER85 4.9 14.3 1.0 O C:HOH926 5.0 34.3 1.0

Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na binding site number 4 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 D:Na706 b:26.1 occ:1.00 O D:HOH1203 2.4 35.5 1.0 O D:SER30 2.4 26.0 0.5 O D:SER30 2.4 26.2 0.5 O D:SER33 2.4 15.7 1.0 O D:HOH1226 2.4 24.6 1.0 O D:HOH1219 2.5 26.9 1.0 C D:SER30 3.6 18.9 0.5 C D:SER30 3.6 19.6 0.5 C D:SER33 3.6 16.2 1.0 CA D:SER30 4.3 14.7 0.5 CA D:ASP34 4.3 15.2 1.0 CA D:SER30 4.4 15.9 0.5 O D:HOH1042 4.4 15.3 1.0 N D:ASP34 4.4 16.5 1.0 OG D:SER30 4.4 23.6 0.5 N D:SER33 4.5 16.9 1.0 O D:HOH1145 4.6 29.2 1.0 C D:ASP34 4.6 12.8 1.0 N D:GLY31 4.6 24.8 1.0 O D:ASP34 4.7 16.0 1.0 CA D:SER33 4.7 15.6 1.0 CA D:GLY31 4.8 23.2 1.0 O D:HOH872 4.8 31.4 1.0 CB D:SER30 4.8 13.1 0.5 C D:GLY31 4.9 24.9 1.0 O D:HOH1017 5.0 25.7 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