Atomistry » Sodium » PDB 7m6k-7mq3 » 7md6
Atomistry »
  Sodium »
    PDB 7m6k-7mq3 »
      7md6 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy