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Sodium in PDB 6qtp: 2.37A Structure of Gepotidacin with S.Aureus Dna Gyrase and Uncleaved Dna

Enzymatic activity of 2.37A Structure of Gepotidacin with S.Aureus Dna Gyrase and Uncleaved Dna

All present enzymatic activity of 2.37A Structure of Gepotidacin with S.Aureus Dna Gyrase and Uncleaved Dna:
5.99.1.3;

Protein crystallography data

The structure of 2.37A Structure of Gepotidacin with S.Aureus Dna Gyrase and Uncleaved Dna, PDB code: 6qtp was solved by B.D.Bax, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.74 / 2.37
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.341, 123.653, 94.099, 90.00, 117.10, 90.00
R / Rfree (%) 18.3 / 22.4

Other elements in 6qtp:

The structure of 2.37A Structure of Gepotidacin with S.Aureus Dna Gyrase and Uncleaved Dna also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.37A Structure of Gepotidacin with S.Aureus Dna Gyrase and Uncleaved Dna (pdb code 6qtp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the 2.37A Structure of Gepotidacin with S.Aureus Dna Gyrase and Uncleaved Dna, PDB code: 6qtp:

Sodium binding site 1 out of 1 in 6qtp

Go back to Sodium Binding Sites List in 6qtp
Sodium binding site 1 out of 1 in the 2.37A Structure of Gepotidacin with S.Aureus Dna Gyrase and Uncleaved Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.37A Structure of Gepotidacin with S.Aureus Dna Gyrase and Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:91.7
occ:1.00
OE1 B:GLU427 3.0 77.6 1.0
OE1 B:GLU428 3.2 73.4 1.0
CD B:GLU428 4.0 72.1 1.0
CD B:GLU427 4.0 77.6 1.0
CB B:GLU428 4.1 69.2 1.0
CG B:GLU428 4.5 70.0 1.0
CG B:GLU427 4.5 76.4 1.0
OE2 B:GLU428 4.8 71.8 1.0
OE2 B:GLU427 4.9 78.5 1.0

Reference:

E.G.Gibson, B.Bax, P.F.Chan, N.Osheroff. Mechanistic and Structural Basis For the Actions of the Antibacterial Gepotidacin Against Staphylococcus Aureus Gyrase. Acs Infect Dis. V. 5 570 2019.
ISSN: ESSN 2373-8227
PubMed: 30757898
DOI: 10.1021/ACSINFECDIS.8B00315
Page generated: Tue Oct 8 12:58:59 2024

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