Sodium in PDB 7md0: Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3:
2.5.1.48; 4.4.1.1; 4.4.1.8;

The structure of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3, PDB code: 7md0 was solved by A.Nuthanakanti, A.Serganov, A.Kaushik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.66 / 2.12
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	104.791, 104.791, 287.866, 90, 90, 90
R / Rfree (%)	17.1 / 19.8

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3 (pdb code 7md0). 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 Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3, PDB code: 7md0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3


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 Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na403 b:59.7 occ:1.00 O H:HOH686 2.4 58.1 1.0 O H:HOH525 2.6 37.1 1.0 O H:HOH508 2.6 44.6 1.0 O H:HOH734 2.9 56.4 1.0 O H:HOH679 3.2 59.9 1.0 O H:HOH555 4.2 32.7 1.0 O H:GLY186 4.2 36.1 1.0 O H:HOH624 4.2 43.4 1.0 O H:HOH660 4.3 53.9 1.0 O H:ILE187 4.3 33.0 1.0 C H:GLY186 4.5 36.3 1.0 CA H:GLY186 4.6 33.4 1.0 O H:HOH705 4.7 62.6 1.0 OD1 H:ASP188 4.7 33.5 1.0 NZ H:LYS162 4.8 63.5 1.0 O H:LEU183 4.9 38.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3


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 Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na404 b:56.6 occ:1.00 O H:HIS9 2.4 37.8 1.0 O H:GLY11 2.5 38.6 1.0 O H:HOH614 2.6 42.6 1.0 O H:HOH616 3.0 37.4 1.0 O H:HOH648 3.0 53.1 1.0 C H:HIS9 3.3 39.4 1.0 C H:GLY11 3.8 41.0 1.0 CA H:HIS9 3.9 40.4 1.0 C H:GLY10 4.2 41.3 1.0 N H:GLY10 4.2 35.8 1.0 O H:GLY10 4.3 40.0 1.0 N H:GLY11 4.4 42.0 1.0 CA H:GLY10 4.4 37.3 1.0 CA H:HIS12 4.6 43.8 1.0 CB H:HIS9 4.6 33.5 1.0 N H:HIS12 4.6 35.6 1.0 N H:THR13 4.7 36.6 1.0 CA H:GLY11 4.7 38.3 1.0 OG1 H:THR13 4.9 31.3 1.0 O H:ILE8 5.0 33.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3


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 Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na405 b:46.4 occ:0.71 OG1 H:THR315 2.3 41.6 1.0 O H:ILE312 2.5 45.3 1.0 O H:TYR318 2.5 42.3 1.0 O H:HOH701 2.6 58.6 1.0 O H:THR315 2.6 50.9 1.0 C H:THR315 3.5 46.7 1.0 CB H:THR315 3.5 42.9 1.0 C H:ILE312 3.6 51.5 1.0 C H:TYR318 3.7 40.2 1.0 CA H:THR315 3.8 42.2 1.0 O H:HOH665 3.8 47.2 1.0 N H:THR315 3.9 43.7 1.0 CA H:ILE312 4.3 44.5 1.0 N H:TYR318 4.3 38.5 1.0 CA H:TYR318 4.4 39.9 1.0 CG2 H:ILE312 4.5 36.0 1.0 CB H:TYR318 4.5 36.7 1.0 N H:SER316 4.6 39.7 1.0 O H:LYS313 4.7 50.3 1.0 C H:LYS313 4.7 47.9 1.0 N H:LYS313 4.7 49.2 1.0 N H:THR319 4.7 39.2 1.0 CG2 H:THR315 4.7 40.3 1.0 O H:LEU311 4.8 46.9 1.0 CA H:LYS313 4.9 49.9 1.0 CA H:THR319 4.9 34.2 1.0 C H:SER316 5.0 37.2 1.0 CG2 H:ILE331 5.0 36.2 1.0 CA H:SER316 5.0 39.6 1.0

K.Shatalin, A.Nuthanakanti, A.Kaushik, D.Shishov, A.Peselis, I.Shamovsky, B.Pani, M.Lechpammer, N.Vasilyev, E.Shatalina, D.Rebatchouk, A.Mironov, P.Fedichev, A.Serganov, E.Nudler. Inhibitors of Bacterial H 2 S Biogenesis Targeting Antibiotic Resistance and Tolerance. Science V. 372 1169 2021.
ISSN: ESSN 1095-9203
PubMed: 34112687
DOI: 10.1126/SCIENCE.ABD8377