Sodium in PDB 4xym: Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+, PDB code: 4xym was solved by R.H.-J.Weisse, A.J.Scheidig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.02 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.560, 114.416, 127.040, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.7

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ also contains other interesting chemical elements:

Mercury	(Hg)	8 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ (pdb code 4xym). 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 Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+, PDB code: 4xym:

Sodium binding site 1 out of 1 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:48.4 occ:1.00 OD2 D:ASP190 2.4 44.3 1.0 O D:HOH442 2.6 37.9 1.0 HD2 D:ARG194 2.6 41.4 1.0 HD3 D:PRO33 2.8 47.3 1.0 HA D:ILE32 2.9 42.0 1.0 O D:GLY31 2.9 34.1 1.0 HE D:ARG194 3.0 45.1 1.0 HA D:ALA191 3.0 35.5 1.0 CD D:ARG194 3.4 34.5 1.0 NE D:ARG194 3.4 37.6 1.0 CG D:ASP190 3.4 39.8 1.0 HB2 D:ALA191 3.5 34.5 1.0 HG12 D:ILE32 3.5 39.4 1.0 HB3 D:ASP190 3.5 44.4 1.0 N D:ALA191 3.6 29.9 1.0 CA D:ALA191 3.7 29.5 1.0 CD D:PRO33 3.7 39.4 1.0 HD3 D:ARG194 3.8 41.4 1.0 C D:ASP190 3.8 31.4 1.0 H D:ALA191 3.8 35.8 1.0 CA D:ILE32 3.8 35.0 1.0 C D:GLY31 3.8 31.4 1.0 HD2 D:PRO33 3.9 47.3 1.0 CB D:ASP190 4.0 37.0 1.0 O D:ASP190 4.1 28.7 1.0 CB D:ALA191 4.1 28.8 1.0 N D:ILE32 4.2 32.9 1.0 HG23 D:ILE32 4.3 37.4 1.0 CG1 D:ILE32 4.3 32.8 1.0 HG13 D:ILE32 4.4 39.4 1.0 OD1 D:ASP190 4.4 46.0 1.0 HB2 D:ARG194 4.4 33.4 1.0 HD11 D:ILE220 4.4 46.5 1.0 HG3 D:PRO33 4.5 50.8 1.0 HB1 D:ALA191 4.5 34.5 1.0 CZ D:ARG194 4.5 38.5 1.0 O D:ALA187 4.5 29.5 1.0 CA D:ASP190 4.6 33.2 1.0 CG D:ARG194 4.6 35.3 1.0 CB D:ILE32 4.6 32.7 1.0 CG D:PRO33 4.6 42.3 1.0 HG3 D:ARG194 4.6 42.4 1.0 N D:PRO33 4.7 32.8 1.0 HH21 D:ARG194 4.8 48.7 1.0 HG2 D:PRO33 4.8 50.8 1.0 C D:ILE32 4.8 34.5 1.0 HB2 D:ASP190 4.8 44.4 1.0 HB3 D:ALA191 4.8 34.5 1.0 HA3 D:GLY31 4.9 39.4 1.0 CG2 D:ILE32 4.9 31.2 1.0 H D:ILE32 5.0 39.5 1.0

R.H.Weie, A.Faust, M.Schmidt, P.Schonheit, A.J.Scheidig. Structure of Ndp-Forming Acetyl-Coa Synthetase ACD1 Reveals A Large Rearrangement For Phosphoryl Transfer. Proc.Natl.Acad.Sci.Usa V. 113 E519 2016.
ISSN: ESSN 1091-6490
PubMed: 26787904
DOI: 10.1073/PNAS.1518614113