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Sodium in PDB 5npk: 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna

Enzymatic activity of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

Protein crystallography data

The structure of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna, PDB code: 5npk was solved by B.D.Bax, P.F.Chan, R.A.Stavenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.442, 120.680, 168.899, 90.00, 90.05, 90.00
R / Rfree (%) 15.4 / 18.3

Other elements in 5npk:

The structure of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna also contains other interesting chemical elements:

Manganese (Mn) 5 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna (pdb code 5npk). 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 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna, PDB code: 5npk:

Sodium binding site 1 out of 1 in 5npk

Go back to Sodium Binding Sites List in 5npk
Sodium binding site 1 out of 1 in the 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.98A Structure of THIOPHENE1 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Na1507

b:47.5
occ:1.00
O b:HOH2074 2.2 63.5 1.0
O b:GLN1328 2.4 36.5 1.0
O b:THR1325 2.5 45.0 1.0
O b:TYR1322 2.5 45.4 1.0
O b:HOH1991 2.7 54.7 1.0
C b:GLN1328 3.5 40.0 1.0
C b:THR1325 3.6 47.3 1.0
O b:LYS1323 3.6 57.1 1.0
C b:TYR1322 3.7 46.5 1.0
C b:LYS1323 3.9 51.9 1.0
N b:THR1325 4.0 51.9 1.0
N b:GLN1328 4.0 40.0 1.0
O b:HOH2043 4.1 62.8 1.0
CB b:GLN1328 4.1 43.1 1.0
CA b:GLN1328 4.1 39.0 1.0
CA b:LYS1323 4.3 52.3 1.0
N b:LYS1323 4.4 50.1 1.0
N b:PRO1326 4.4 48.1 1.0
CA b:THR1325 4.4 48.4 1.0
N b:GLN1324 4.4 54.1 1.0
CA b:PRO1326 4.5 43.6 1.0
N b:THR1329 4.6 37.7 1.0
O b:LEU1321 4.7 48.7 1.0
CA b:TYR1322 4.7 46.5 1.0
C b:GLN1324 4.7 55.0 1.0
C b:PRO1326 4.8 42.4 1.0
N b:LEU1327 4.8 39.4 1.0
CA b:GLN1324 4.8 54.6 1.0
CA b:THR1329 4.9 39.2 1.0
CG b:GLN1328 4.9 40.7 1.0

Reference:

P.F.Chan, T.Germe, B.D.Bax, J.Huang, R.K.Thalji, E.Bacque, A.Checchia, D.Chen, H.Cui, X.Ding, K.Ingraham, L.Mccloskey, K.Raha, V.Srikannathasan, A.Maxwell, R.A.Stavenger. Thiophene Antibacterials That Allosterically Stabilize Dna-Cleavage Complexes with Dna Gyrase. Proc. Natl. Acad. Sci. V. 114 E4492 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28507124
DOI: 10.1073/PNAS.1700721114
Page generated: Tue Dec 15 11:21:49 2020

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