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Sodium in PDB 7mdb: Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2:
2.5.1.48; 4.4.1.1; 4.4.1.8;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2, PDB code: 7mdb 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) 29.69 / 1.80
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.119, 105.119, 287.79, 90, 90, 90
R / Rfree (%) 17 / 18.9

Other elements in 7mdb:

The structure of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2 also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Bromine (Br) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2 (pdb code 7mdb). 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 Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2, PDB code: 7mdb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7mdb

Go back to Sodium Binding Sites List in 7mdb
Sodium binding site 1 out of 2 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2


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 Y103A Mutant Co-Crystallized with NL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na408

b:44.7
occ:1.00
 O H:HOH832 2.5 48.8 1.0
O H:HOH847 2.5 51.0 1.0
O H:HOH544 2.6 28.6 1.0
O H:HOH812 2.6 35.0 1.0
O H:HOH837 2.6 51.1 1.0
O H:HOH517 2.7 38.9 1.0
O H:HOH656 4.0 29.3 1.0
O H:HOH652 4.1 35.6 1.0
O H:HOH527 4.2 40.0 1.0
O H:HOH630 4.3 44.1 1.0
O H:GLY186 4.3 27.0 1.0
O H:ILE187 4.4 27.8 1.0
O H:HOH775 4.4 52.4 1.0
O H:HOH826 4.4 55.4 1.0
O H:HOH776 4.6 54.4 1.0
C H:GLY186 4.6 31.8 1.0
CA H:GLY186 4.7 31.1 1.0
OD1 H:ASP188 4.8 29.9 1.0
O H:LEU183 4.9 32.1 1.0

Sodium binding site 2 out of 2 in 7mdb

Go back to Sodium Binding Sites List in 7mdb
Sodium binding site 2 out of 2 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2


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 Y103A Mutant Co-Crystallized with NL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na409

b:47.5
occ:0.65
 O1 H:CAC405 2.3 46.2 0.7
O H:HOH524 2.5 41.3 1.0
O H:HOH620 2.7 28.5 1.0
O H:THR123 2.9 28.1 1.0
O H:HOH573 3.2 50.9 1.0
C H:THR123 3.8 30.3 1.0
AS H:CAC405 3.9 54.5 0.5
N H:THR125 3.9 29.2 1.0
ND2 H:ASN283 4.0 28.1 1.0
CA H:HIS124 4.0 29.6 1.0
CB H:ASP153 4.1 30.0 1.0
OD1 H:ASN283 4.1 29.4 1.0
CG2 H:THR125 4.2 31.7 1.0
N H:HIS124 4.3 30.1 1.0
OG1 H:THR125 4.4 35.0 1.0
CG H:ASN283 4.4 29.1 1.0
C1 H:CAC405 4.4 55.8 0.7
C2 H:CAC405 4.5 42.2 0.8
C H:HIS124 4.5 30.6 1.0
OD2 H:ASP153 4.8 44.8 1.0
O H:THR122 4.8 30.1 1.0
CB H:THR125 4.8 32.8 1.0
N H:ASP153 4.8 26.9 1.0
CA H:THR123 4.8 27.6 1.0
CG2 H:VAL286 4.9 29.5 1.0
CA H:THR125 4.9 31.0 1.0
CG H:ASP153 5.0 34.7 1.0

Reference:

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
Page generated: Mon Aug 18 10:57:12 2025

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