Sodium in PDB 8ciy: Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin.

The structure of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin., PDB code: 8ciy was solved by C.Fu, Y.Liu, C.Walt, C.Bader, S.Rasheed, P.Lukat, M.Neuber, W.Blankenfeldt, O.Kalinina, R.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 1.54
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	83.907, 150.723, 71.502, 90, 90, 90
R / Rfree (%)	17.1 / 20

The structure of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin. also contains other interesting chemical elements:

Calcium	(Ca)	6 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Sodium atom in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin. (pdb code 8ciy). 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 Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin., PDB code: 8ciy:

Sodium binding site 1 out of 1 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:35.7 occ:1.00 O A:HOH598 2.1 42.2 1.0 O A:ASN295 2.3 18.9 0.7 O A:HOH619 2.4 20.0 1.0 O A:ASN295 2.4 19.6 0.3 O A:HOH702 2.7 24.8 1.0 OD1 A:ASN295 2.8 32.3 0.7 O A:HOH804 3.1 22.3 1.0 H A:ASN295 3.2 19.8 0.7 H A:ASN295 3.2 20.4 0.3 C A:ASN295 3.3 18.9 0.3 C A:ASN295 3.3 18.9 0.7 HB2 A:ASN295 3.3 22.2 0.3 HB2 A:ASN275 3.6 22.8 1.0 H A:ASN275 3.7 22.3 1.0 HA A:ASN296 3.8 22.2 1.0 CG A:ASN295 3.8 32.6 0.7 N A:ASN295 3.9 17.0 0.3 N A:ASN295 3.9 16.5 0.7 CA A:ASN295 3.9 18.2 0.3 CB A:ASN295 4.0 18.5 0.3 O A:HOH769 4.1 23.3 1.0 CA A:ASN295 4.1 20.5 0.7 N A:ASN296 4.2 19.1 1.0 O A:GLY280 4.3 20.2 1.0 CB A:ASN295 4.4 21.0 0.7 HA A:SER274 4.4 21.1 1.0 HB3 A:ASN295 4.4 22.2 0.3 CA A:ASN296 4.4 18.5 1.0 N A:ASN275 4.5 18.6 1.0 CB A:ASN275 4.5 19.0 1.0 HB2 A:ASN295 4.6 25.2 0.7 HB3 A:ASN275 4.6 22.8 1.0 HD22 A:ASN275 4.7 31.0 1.0 ND2 A:ASN295 4.8 41.2 0.7 HA A:ASN295 4.9 21.8 0.3 HD21 A:ASN295 4.9 49.4 0.7 H A:ASN296 4.9 23.0 0.3 H A:ASN296 4.9 23.0 0.7 HA A:ASN295 5.0 24.7 0.7 H A:GLY280 5.0 23.5 1.0 HA A:ALA294 5.0 19.7 1.0

C.Fu, Y.Liu, C.Walt, S.Rasheed, C.Bader, P.Lukat, M.Neuber, J.Haeckl, W.Blankenfeldt, O.Kalinina, R.Muller. Elucidation of Unusual Biosynthesis and Dnan-Targeting Mode of Action of Potent Anti-Tuberculosis Antibiotics Mycoplanecins Nat Commun 2023.
ISSN: ESSN 2041-1723