Sodium in PDB 7am8: Crystal Structure of Omniligase Mutant W189F

All present enzymatic activity of Crystal Structure of Omniligase Mutant W189F:
3.4.21.62;

The structure of Crystal Structure of Omniligase Mutant W189F, PDB code: 7am8 was solved by H.J.Rozeboom, D.J.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.11 / 2.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.49, 60.697, 78.927, 90, 90, 90
R / Rfree (%)	18 / 22.8

The structure of Crystal Structure of Omniligase Mutant W189F also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Omniligase Mutant W189F (pdb code 7am8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Omniligase Mutant W189F, PDB code: 7am8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Omniligase Mutant W189F


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Omniligase Mutant W189F within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:19.6 occ:1.00 O A:SER37 2.3 20.7 1.0 O A:LEU42 2.4 24.4 1.0 O A:HIS39 2.4 22.9 1.0 O A:HOH482 2.4 16.6 1.0 O A:HOH496 2.5 19.0 1.0 C A:HIS39 3.4 21.7 1.0 C A:SER37 3.5 18.8 1.0 C A:LEU42 3.5 22.4 1.0 C A:SER38 4.0 21.4 1.0 O A:SER38 4.0 21.1 1.0 N A:HIS39 4.1 20.5 1.0 CA A:PRO40 4.1 23.8 1.0 N A:LEU42 4.2 22.7 1.0 N A:PRO40 4.2 23.6 1.0 O A:HOH491 4.2 21.0 1.0 CA A:LEU42 4.3 21.7 1.0 O A:PRO40 4.3 23.0 1.0 C A:PRO40 4.3 23.7 1.0 CA A:HIS39 4.4 21.0 1.0 N A:SER38 4.4 19.7 1.0 CA A:SER38 4.4 20.2 1.0 CA A:SER37 4.4 18.7 1.0 ND2 A:ASN43 4.4 28.0 1.0 N A:ASN43 4.6 21.3 1.0 CB A:LEU42 4.6 21.0 1.0 CA A:ASN43 4.9 22.3 1.0 CB A:SER37 4.9 18.8 1.0 N A:ASP41 5.0 23.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Omniligase Mutant W189F


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Omniligase Mutant W189F within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:20.6 occ:1.00 O A:ALA169 2.2 20.1 1.0 O A:HOH456 2.3 17.2 1.0 O A:VAL174 2.3 17.7 1.0 O A:HOH514 2.4 15.1 1.0 O A:TYR171 2.4 20.5 1.0 C A:TYR171 3.2 21.2 1.0 C A:VAL174 3.4 16.7 1.0 C A:ALA169 3.4 21.3 1.0 C A:LYS170 3.9 22.1 1.0 N A:TYR171 3.9 20.8 1.0 N A:PRO172 3.9 21.7 1.0 CA A:PRO172 3.9 21.5 1.0 N A:VAL174 3.9 18.6 1.0 CA A:VAL174 4.1 17.4 1.0 C A:PRO172 4.1 21.5 1.0 O A:PRO172 4.1 23.4 1.0 O A:HOH566 4.1 35.7 1.0 O A:LYS170 4.2 22.1 1.0 CB A:ALA176 4.2 19.6 1.0 CA A:TYR171 4.2 22.6 1.0 CB A:VAL174 4.2 17.0 1.0 OD2 A:ASP197 4.2 26.0 1.0 N A:LYS170 4.3 20.8 1.0 O A:GLU195 4.3 21.6 1.0 CA A:LYS170 4.3 22.4 1.0 O A:HOH615 4.3 30.6 1.0 N A:ALA176 4.4 17.9 1.0 CA A:ALA169 4.4 21.6 1.0 NH2 A:ARG247 4.5 23.7 1.0 N A:ILE175 4.5 16.4 1.0 C A:ILE175 4.7 17.8 1.0 N A:SER173 4.8 20.0 1.0 O A:PRO168 4.8 22.9 1.0 CA A:ILE175 4.8 17.0 1.0 CA A:ALA176 4.9 18.5 1.0 CB A:GLU195 4.9 25.4 1.0

A.Toplak, H.J.Rozeboom, E.F.Teixeira De Oliveira, H.J.Wijma, D.J.Janssen, T.Nuijens. From Thiol-Subtilisin to Omniligase: Design and Structure of A Broadly Applicable Peptide Ligase To Be Published.