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Sodium in PDB 7md6: Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1:
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 Y103N Mutant Co-Crystallized with NL1, PDB code: 7md6 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) 29.77 / 2.20
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 104.379, 104.379, 287.729, 90, 90, 90
R / Rfree (%) 17.4 / 20.7

Other elements in 7md6:

The structure of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1 also contains other interesting chemical elements:

Bromine (Br) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1 (pdb code 7md6). 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 Y103N Mutant Co-Crystallized with NL1, PDB code: 7md6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7md6

Go back to Sodium Binding Sites List in 7md6
Sodium binding site 1 out of 2 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1


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 Y103N Mutant Co-Crystallized with NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na409

b:55.1
occ:1.00
 O H:HOH677 2.5 55.0 1.0
O H:HOH552 2.5 41.4 1.0
O H:HOH510 2.6 39.8 1.0
O H:HOH672 2.7 48.6 1.0
O H:HOH679 2.7 56.2 1.0
O H:HOH681 2.8 49.2 1.0
O H:HOH557 4.2 44.0 1.0
O H:HOH563 4.2 36.4 1.0
O H:GLY186 4.2 41.0 1.0
O H:ILE187 4.3 34.9 1.0
O H:HOH665 4.5 59.4 1.0
C H:GLY186 4.5 40.6 1.0
CA H:GLY186 4.6 34.6 1.0
OD1 H:ASP188 4.8 37.4 1.0
O H:LEU183 4.9 40.0 1.0

Sodium binding site 2 out of 2 in 7md6

Go back to Sodium Binding Sites List in 7md6
Sodium binding site 2 out of 2 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1


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 Y103N Mutant Co-Crystallized with NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na410

b:72.3
occ:1.00
 O H:HOH659 2.7 56.0 1.0
O H:HOH614 2.7 35.8 1.0
O H:HOH623 3.1 61.8 1.0
OD2 H:ASP292 3.7 64.6 1.0
OD1 H:ASN181 4.0 35.7 1.0
O H:TYR179 4.4 39.3 1.0
CG H:ASP292 4.5 54.8 1.0
O H:GLN290 4.5 35.4 1.0
N H:ASN181 4.6 30.9 1.0
OD1 H:ASP292 4.8 58.2 1.0
CG H:ASN181 4.9 36.0 1.0
CB H:ASN181 5.0 30.7 1.0
CA H:GLN180 5.0 32.1 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: Tue Oct 8 17:56:37 2024

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