Sodium in PDB 7am5: Crystal Structure of Peptiligase Mutant - L217H/M222P/A225N

All present enzymatic activity of Crystal Structure of Peptiligase Mutant - L217H/M222P/A225N:
3.4.21.62;

The structure of Crystal Structure of Peptiligase Mutant - L217H/M222P/A225N, PDB code: 7am5 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)	44.30 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.744, 59.993, 78.358, 90, 90, 90
R / Rfree (%)	23 / 28.7

The binding sites of Sodium atom in the Crystal Structure of Peptiligase Mutant - L217H/M222P/A225N (pdb code 7am5). 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 Peptiligase Mutant - L217H/M222P/A225N, PDB code: 7am5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Peptiligase Mutant - L217H/M222P/A225N


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 Peptiligase Mutant - L217H/M222P/A225N within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:30.7 occ:1.00 O A:HOH446 2.2 20.2 1.0 O A:ALA169 2.2 29.5 1.0 O A:HOH428 2.3 27.9 1.0 O A:VAL174 2.4 28.1 1.0 O A:TYR171 2.6 30.5 1.0 C A:ALA169 3.4 29.6 1.0 C A:TYR171 3.4 31.2 1.0 C A:VAL174 3.5 26.3 1.0 C A:LYS170 3.9 30.6 1.0 N A:TYR171 4.0 30.9 1.0 O A:GLU195 4.0 30.9 1.0 O A:PRO172 4.0 29.2 1.0 OD2 A:ASP197 4.0 30.8 1.0 CB A:ALA176 4.0 23.7 1.0 N A:PRO172 4.1 30.1 1.0 CA A:PRO172 4.1 28.9 1.0 O A:LYS170 4.1 30.5 1.0 C A:PRO172 4.2 28.5 1.0 N A:VAL174 4.2 26.3 1.0 CA A:VAL174 4.2 25.8 1.0 N A:ALA176 4.2 24.8 1.0 N A:LYS170 4.2 30.6 1.0 CA A:LYS170 4.3 31.1 1.0 CB A:VAL174 4.3 26.5 1.0 CA A:TYR171 4.3 31.6 1.0 CA A:ALA169 4.4 31.0 1.0 N A:ILE175 4.5 25.5 1.0 NH2 A:ARG247 4.5 28.0 1.0 CB A:GLU195 4.6 31.2 1.0 C A:ILE175 4.7 25.0 1.0 CA A:ALA176 4.7 23.6 1.0 CA A:ILE175 4.8 25.2 1.0 C A:GLU195 4.9 30.4 1.0 N A:SER173 4.9 27.2 1.0 O A:PRO168 5.0 32.8 1.0 CA A:GLU195 5.0 30.6 1.0 CG A:ASP197 5.0 30.1 1.0 CG1 A:VAL174 5.0 26.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Peptiligase Mutant - L217H/M222P/A225N


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 Peptiligase Mutant - L217H/M222P/A225N within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:28.0 occ:1.00 O A:LEU42 2.3 29.7 1.0 O A:HIS39 2.3 26.8 1.0 O A:SER37 2.3 27.9 1.0 O A:HOH401 2.6 25.3 1.0 O A:HOH420 2.9 14.1 1.0 C A:HIS39 3.3 28.0 1.0 C A:LEU42 3.5 30.9 1.0 C A:SER37 3.5 26.8 1.0 CA A:PRO40 3.8 29.6 1.0 N A:PRO40 4.0 29.3 1.0 O A:PRO40 4.0 30.7 1.0 C A:PRO40 4.0 30.0 1.0 ND2 A:ASN43 4.1 31.1 1.0 N A:LEU42 4.1 30.7 1.0 C A:SER38 4.1 26.5 1.0 N A:HIS39 4.2 26.2 1.0 CA A:LEU42 4.3 31.2 1.0 O A:SER38 4.3 26.4 1.0 CA A:HIS39 4.4 26.1 1.0 N A:SER38 4.4 27.1 1.0 N A:ASN43 4.5 31.5 1.0 CA A:SER37 4.5 27.5 1.0 CA A:SER38 4.5 27.2 1.0 CB A:LEU42 4.6 31.4 1.0 CA A:ASN43 4.7 31.4 1.0 N A:ASP41 4.8 30.8 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.