Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd H262A Mutant) with Pentapeptide Bound, PDB code: 5njf:
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 H262A Mutant) with Pentapeptide 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 H262A Mutant) with Pentapeptide Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:25.9 occ:1.00 O A:HOH1078 2.3 33.9 1.0 O A:HOH1015 2.5 20.6 1.0 O A:HOH1032 2.5 29.5 1.0 OG A:SER117 2.6 24.0 1.0 O A:HOH963 2.8 27.4 1.0 O A:HOH1072 3.2 35.7 1.0 CB A:SER117 3.5 23.9 1.0 O A:HOH803 4.4 23.1 1.0 O A:HOH763 4.5 25.2 1.0 O A:HOH1056 4.5 41.7 1.0 N A:SER117 4.7 22.8 1.0 CA A:SER117 4.7 21.5 1.0

Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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 B:Na705 b:29.4 occ:1.00 O B:HOH1163 2.3 51.3 1.0 O B:HOH1172 2.3 34.6 1.0 O B:SER30 2.5 29.4 1.0 O B:HOH1202 2.5 50.2 1.0 O B:SER33 2.5 24.3 1.0 C B:SER30 3.6 25.2 1.0 C B:SER33 3.7 19.6 1.0 CA B:SER30 4.3 23.4 1.0 O B:HOH941 4.3 22.2 1.0 CA B:ASP34 4.3 19.7 1.0 N B:ASP34 4.5 21.4 1.0 O B:ASP34 4.6 21.9 1.0 C B:ASP34 4.6 19.5 1.0 N B:SER33 4.6 22.9 1.0 N B:GLY31 4.7 24.2 1.0 CB B:SER30 4.8 25.1 1.0 CA B:SER33 4.8 21.3 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 H262A Mutant) with Pentapeptide 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 H262A Mutant) with Pentapeptide Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Na504 b:22.6 occ:1.00 O C:HOH953 2.3 30.3 1.0 O C:HOH942 2.3 36.2 1.0 O C:HOH948 2.4 25.7 1.0 O C:ILE84 2.4 17.5 1.0 O C:HOH819 2.6 21.1 1.0 OD1 C:ASN14 2.7 24.6 1.0 CG C:ASN14 3.5 18.8 1.0 C C:ILE84 3.6 15.4 1.0 CB C:ASN14 3.9 19.7 1.0 N C:ILE84 4.1 15.6 1.0 O C:HOH974 4.2 37.0 1.0 CA C:ILE84 4.3 16.2 1.0 CA C:ASN14 4.5 21.1 1.0 ND2 C:ASN14 4.5 19.4 1.0 CB C:ILE84 4.6 15.8 1.0 N C:SER85 4.6 15.1 1.0 CB C:SER85 4.7 18.1 1.0 CA C:SER85 4.8 16.1 1.0 O C:ASN14 4.9 24.3 1.0

Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na binding site number 4 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 D:Na706 b:25.8 occ:1.00 O D:HOH1158 2.4 46.6 1.0 O D:SER30 2.4 20.4 0.5 O D:SER30 2.4 21.0 0.5 O D:HOH1230 2.5 33.6 1.0 O D:SER33 2.5 16.2 1.0 O D:HOH1205 2.5 25.1 1.0 C D:SER30 3.6 20.3 0.5 C D:SER30 3.6 21.0 0.5 C D:SER33 3.7 16.1 1.0 OG D:SER30 4.1 23.6 0.5 CA D:SER30 4.2 18.6 0.5 CA D:SER30 4.2 20.2 0.5 O D:HOH1079 4.3 16.5 1.0 CA D:ASP34 4.3 15.6 1.0 N D:ASP34 4.5 15.7 1.0 C D:ASP34 4.6 12.7 1.0 O D:HOH1144 4.6 34.4 1.0 O D:ASP34 4.6 18.2 1.0 N D:SER33 4.6 17.9 1.0 O D:HOH891 4.6 38.1 1.0 N D:GLY31 4.7 21.9 1.0 CB D:SER30 4.7 15.7 0.5 CB D:SER30 4.8 22.1 0.5 CA D:SER33 4.8 17.9 1.0 CA D:GLY31 4.9 21.5 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