Sodium in PDB 4knk: Crystal Structure of Staphylococcus Aureus Hydrolase Amia

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Hydrolase Amia:
3.2.1.96; 3.5.1.28;

The structure of Crystal Structure of Staphylococcus Aureus Hydrolase Amia, PDB code: 4knk was solved by F.M.Buettner, S.Zoll, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.84 / 1.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.800, 81.680, 68.690, 90.00, 128.84, 90.00
R / Rfree (%)	12.1 / 13.9

The structure of Crystal Structure of Staphylococcus Aureus Hydrolase Amia also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia (pdb code 4knk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia, PDB code: 4knk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia


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 Staphylococcus Aureus Hydrolase Amia within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:14.9 occ:1.00 O A:ASN364 2.3 14.7 1.0 O A:HOH731 2.4 27.3 1.0 O A:SER358 2.4 10.9 1.0 O A:HOH729 2.5 30.3 1.0 OD1 A:ASP357 2.5 17.8 1.0 OD2 A:ASP362 2.5 23.7 1.0 OD1 A:ASP362 2.6 18.1 1.0 CG A:ASP362 3.0 19.9 1.0 C A:SER358 3.4 10.2 1.0 CG A:ASP357 3.5 15.9 1.0 C A:ASN364 3.5 13.8 1.0 OD2 A:ASP357 3.8 18.9 1.0 O A:HOH635 3.9 16.3 1.0 CA A:ALA359 4.1 10.5 1.0 N A:ALA359 4.1 10.4 1.0 N A:SER358 4.2 10.8 1.0 CA A:ASN364 4.4 14.6 1.0 N A:GLY365 4.4 13.3 1.0 CA A:GLY365 4.4 13.3 1.0 CB A:ASN364 4.4 19.2 1.0 N A:ASN364 4.4 13.0 1.0 CA A:SER358 4.4 10.4 1.0 C A:ASP357 4.5 10.2 1.0 CB A:ASP362 4.5 18.6 1.0 ND2 A:ASN364 4.6 28.4 1.0 O A:HOH825 4.6 38.5 1.0 O A:HOH662 4.7 20.7 1.0 CB A:ASP357 4.8 12.4 1.0 O A:ASP357 4.8 10.8 1.0 C A:ALA359 4.9 10.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia


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 Staphylococcus Aureus Hydrolase Amia within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:17.1 occ:1.00 O B:ASN364 2.3 15.2 1.0 O B:HOH707 2.4 30.8 1.0 O B:SER358 2.4 12.4 1.0 OD1 B:ASP357 2.6 19.4 1.0 OD2 B:ASP362 2.6 30.3 1.0 O B:HOH709 2.7 26.4 1.0 OD1 B:ASP362 2.7 22.3 1.0 CG B:ASP362 3.0 25.4 1.0 C B:SER358 3.4 11.7 1.0 CG B:ASP357 3.5 17.2 1.0 C B:ASN364 3.5 13.6 1.0 OD2 B:ASP357 3.8 19.9 1.0 O B:HOH626 3.9 17.7 1.0 CA B:ALA359 4.1 11.0 1.0 N B:ALA359 4.2 10.9 1.0 N B:SER358 4.2 12.5 1.0 CA B:ASN364 4.4 15.4 1.0 CA B:GLY365 4.4 13.6 1.0 N B:GLY365 4.4 13.2 1.0 CB B:ASN364 4.4 19.4 1.0 CA B:SER358 4.4 11.9 1.0 C B:ASP357 4.4 12.1 1.0 N B:ASN364 4.5 14.4 1.0 CB B:ASP362 4.5 23.8 1.0 OD1 B:ASN364 4.6 29.4 1.0 O B:HOH669 4.7 23.7 1.0 O B:ASP357 4.7 11.7 1.0 CB B:ASP357 4.8 13.9 1.0 C B:ALA359 4.9 11.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Staphylococcus Aureus Hydrolase Amia


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Staphylococcus Aureus Hydrolase Amia within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:11.0 occ:1.00 OG1 B:THR305 2.3 9.4 1.0 O B:HOH616 2.3 12.5 1.0 O B:HOH609 2.4 10.9 1.0 O B:HOH607 2.4 11.0 1.0 O B:HOH610 2.4 12.2 1.0 CB B:THR305 3.6 9.6 1.0 CE2 A:TYR243 3.7 11.4 1.0 CG2 B:THR305 3.9 10.9 1.0 OE1 B:GLN348 3.9 12.9 1.0 CD2 A:TYR243 3.9 11.4 1.0 OH B:TYR352 4.0 10.1 1.0 N B:THR305 4.2 8.7 1.0 OE1 B:GLU301 4.3 10.5 1.0 NE2 B:GLN348 4.4 13.8 1.0 OE2 B:GLU301 4.4 10.0 1.0 OD2 B:ASP306 4.4 14.2 1.0 CA B:THR305 4.4 8.5 1.0 CE2 B:TYR351 4.5 10.7 1.0 O B:HOH621 4.5 13.3 1.0 CD B:GLN348 4.5 12.3 1.0 O A:HOH629 4.5 14.7 1.0 CZ B:TYR351 4.7 9.8 1.0 OE1 A:GLU241 4.7 15.0 1.0 CD B:GLU301 4.7 9.5 1.0 OH B:TYR351 4.8 10.3 1.0 CZ B:TYR352 4.8 9.9 1.0 CZ A:TYR243 4.9 11.0 1.0 CE2 B:TYR352 4.9 9.4 1.0 CD2 B:TYR351 4.9 10.7 1.0

F.M.Buettner, S.Zoll, F.Goetz, T.Stehle. High-Resolution Structural Analysis Reveals the Determinants of Peptidoglycan Recognition and Cleavage By Staphylococcus Aureus Amidase To Be Published.