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Sodium in PDB 7mcy: Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL3

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL3

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL3:
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 with Bound NL3, PDB code: 7mcy 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) 29.71 / 1.72
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.448, 105.448, 287.772, 90, 90, 90
R / Rfree (%) 15.8 / 16.4

Other elements in 7mcy:

The structure of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL3 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL3 (pdb code 7mcy). 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 with Bound NL3, PDB code: 7mcy:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7mcy

Go back to Sodium Binding Sites List in 7mcy
Sodium binding site 1 out of 3 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL3


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 with Bound NL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na404

b:34.6
occ:1.00
 O H:HOH912 2.5 41.5 1.0
O H:HOH566 2.5 22.6 1.0
O H:HOH884 2.5 31.0 1.0
O H:HOH583 2.5 34.0 1.0
O H:HOH946 2.6 48.0 1.0
O H:HOH919 2.7 47.3 1.0
O H:HOH624 4.0 22.0 1.0
O H:HOH620 4.2 26.7 1.0
O H:HOH564 4.2 36.0 1.0
O H:HOH714 4.2 34.6 1.0
O H:HOH832 4.3 44.5 1.0
O H:HOH878 4.3 45.2 1.0
O H:GLY186 4.3 20.4 1.0
O H:ILE187 4.4 19.1 1.0
C H:GLY186 4.6 21.7 1.0
CA H:GLY186 4.7 22.7 1.0
OD1 H:ASP188 4.7 22.5 1.0
O H:HOH796 4.9 43.0 1.0
O H:LEU183 4.9 20.8 1.0

Sodium binding site 2 out of 3 in 7mcy

Go back to Sodium Binding Sites List in 7mcy
Sodium binding site 2 out of 3 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL3


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 with Bound NL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na405

b:36.2
occ:1.00
 O H:HOH820 2.4 38.4 1.0
O H:HOH708 2.4 25.2 1.0
O H:HIS9 2.4 23.7 1.0
O H:GLY11 2.5 24.6 1.0
O H:HOH599 2.6 23.5 1.0
O H:HOH802 2.6 33.7 1.0
C H:HIS9 3.1 23.5 1.0
CA H:HIS9 3.7 20.0 1.0
C H:GLY11 3.7 25.9 1.0
O H:HOH696 3.8 30.4 1.0
O H:GLY10 3.9 24.6 1.0
C H:GLY10 4.0 23.3 1.0
N H:GLY10 4.0 22.2 1.0
N H:GLY11 4.3 22.9 1.0
O H:HOH688 4.3 37.6 1.0
CA H:GLY10 4.4 22.1 1.0
OG1 H:THR13 4.4 21.3 1.0
N H:THR13 4.4 19.3 1.0
O H:HOH639 4.5 41.6 1.0
CA H:HIS12 4.5 21.6 1.0
CB H:HIS9 4.5 19.9 1.0
O H:ILE8 4.5 24.0 1.0
N H:HIS12 4.5 19.2 1.0
CA H:GLY11 4.6 20.4 1.0
N H:HIS9 4.8 19.8 1.0
C H:HIS12 5.0 22.8 1.0

Sodium binding site 3 out of 3 in 7mcy

Go back to Sodium Binding Sites List in 7mcy
Sodium binding site 3 out of 3 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL3


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 with Bound NL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na406

b:42.2
occ:1.00
 O H:HOH518 2.3 35.0 1.0
O H:HOH794 2.4 41.0 1.0
O H:HIS267 2.5 24.9 1.0
O H:VAL270 2.6 26.1 1.0
O H:LEU264 2.7 23.1 1.0
O H:GLN265 3.0 30.6 1.0
C H:GLN265 3.4 32.6 1.0
C H:VAL270 3.5 27.4 1.0
N H:HIS267 3.5 25.7 1.0
C H:HIS267 3.5 28.6 1.0
CB H:VAL270 3.7 25.4 1.0
C H:LEU264 3.8 23.7 1.0
CA H:GLN265 3.8 26.5 1.0
CA H:VAL270 4.0 26.6 1.0
CG1 H:VAL270 4.0 22.4 1.0
CA H:HIS267 4.0 26.1 1.0
C H:ALA266 4.1 26.7 1.0
O H:GLN271 4.2 27.3 1.0
N H:VAL270 4.2 23.3 1.0
N H:ALA266 4.3 28.6 1.0
O H:HOH877 4.3 45.0 1.0
N H:GLN265 4.3 20.7 1.0
O H:HOH882 4.4 41.6 1.0
O H:HOH842 4.5 56.5 1.0
N H:GLN271 4.5 25.2 1.0
CB H:HIS267 4.6 23.4 1.0
N H:PRO268 4.6 27.1 1.0
CA H:ALA266 4.7 28.1 1.0
O H:ALA266 4.8 28.2 1.0
O H:HOH730 4.8 45.0 1.0
CA H:GLN271 4.9 25.4 1.0
CG2 H:VAL270 4.9 21.2 1.0
CA H:PRO268 4.9 29.2 1.0
C H:GLN271 5.0 27.8 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 10:56:17 2025

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