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Sodium in PDB 7mcq: Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form:
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, Aoaa-Bound Enzyme in Dimeric Form, PDB code: 7mcq 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) 29.76 / 2.84
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 104.354, 104.354, 287.362, 90, 90, 90
R / Rfree (%) 17.7 / 20.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form (pdb code 7mcq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form, PDB code: 7mcq:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7mcq

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Sodium binding site 1 out of 4 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form


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, Aoaa-Bound Enzyme in Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:73.6
occ:1.00
 NZ A:LYS162 4.0 72.5 1.0
O A:GLY186 4.2 44.3 1.0
OD1 A:ASP188 4.4 39.2 1.0
O A:ILE187 4.5 42.2 1.0
C A:GLY186 4.6 45.6 1.0
CA A:GLY186 4.6 39.7 1.0
CE A:LYS162 4.7 53.4 1.0

Sodium binding site 2 out of 4 in 7mcq

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Sodium binding site 2 out of 4 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form


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, Aoaa-Bound Enzyme in Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:65.8
occ:1.00
 O A:HIS9 2.6 37.1 1.0
O A:GLY11 2.9 49.6 1.0
C A:HIS9 3.7 39.3 1.0
C A:GLY11 4.1 43.2 1.0
CA A:HIS9 4.3 38.1 1.0
N A:GLY11 4.6 35.2 1.0
C A:GLY10 4.6 41.0 1.0
CB A:HIS9 4.7 34.9 1.0
N A:GLY10 4.7 38.4 1.0
CA A:GLY10 4.9 37.2 1.0
O A:GLY10 4.9 45.4 1.0
N A:HIS12 5.0 36.4 1.0
CA A:GLY11 5.0 36.3 1.0
CA A:HIS12 5.0 36.1 1.0

Sodium binding site 3 out of 4 in 7mcq

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Sodium binding site 3 out of 4 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form


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, Aoaa-Bound Enzyme in Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na402

b:76.5
occ:1.00
 O H:GLY186 4.4 47.9 1.0
O H:ILE187 4.5 45.4 1.0
CA H:GLY186 4.6 37.9 1.0
C H:GLY186 4.6 43.4 1.0
O H:LEU183 4.8 43.7 1.0
OD1 H:ASP188 4.8 50.9 1.0

Sodium binding site 4 out of 4 in 7mcq

Go back to Sodium Binding Sites List in 7mcq
Sodium binding site 4 out of 4 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na403

b:73.6
occ:1.00
 O H:HIS9 2.8 45.0 1.0
O H:GLY11 3.0 49.8 1.0
C H:HIS9 4.0 40.9 1.0
C H:GLY11 4.1 39.6 1.0
O H:HOH518 4.5 53.7 1.0
N H:GLY11 4.6 39.7 1.0
CA H:HIS9 4.7 38.0 1.0
C H:GLY10 4.8 38.0 1.0
CA H:HIS12 4.9 47.6 1.0
N H:HIS12 4.9 38.0 1.0
N H:GLY10 4.9 38.8 1.0
CA H:GLY10 5.0 39.1 1.0
CB H:HIS9 5.0 34.8 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: Tue Oct 8 17:55:39 2024

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