Sodium in PDB 5hbr: Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Coenzyme A

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Coenzyme A, PDB code: 5hbr 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)	81.17 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.118, 110.710, 126.027, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.2

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

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Coenzyme A (pdb code 5hbr). 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 Phosphate and Coenzyme A, PDB code: 5hbr:

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


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 Phosphate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:62.7 occ:1.00 O3 C:PO4503 2.4 54.2 1.0 OD2 A:ASP351 2.9 58.1 1.0 H A:GLY308 3.0 50.1 1.0 HA2 A:GLY307 3.5 60.2 1.0 HA A:THR353 3.6 53.7 1.0 HD2 C:HIS254 3.7 99.0 1.0 N A:GLY308 3.7 41.8 1.0 CG A:ASP351 3.8 48.4 1.0 P C:PO4503 3.8 54.0 1.0 OD1 A:ASP351 3.8 46.6 1.0 H A:GLY354 4.1 50.9 1.0 HA3 A:GLY308 4.2 54.8 1.0 CD2 C:HIS254 4.2 82.5 1.0 O1 C:PO4503 4.3 66.3 1.0 O4 C:PO4503 4.4 60.2 1.0 CA A:GLY307 4.4 50.2 1.0 CA A:GLY308 4.5 45.6 1.0 C A:GLY307 4.5 44.2 1.0 CA A:THR353 4.6 44.8 1.0 NE2 C:HIS254 4.6 77.3 1.0 N A:GLY354 4.7 42.4 1.0 HA2 A:GLY308 4.8 54.8 1.0 H A:THR353 4.8 51.1 1.0 HB A:THR353 4.9 59.7 1.0 O2 C:PO4503 4.9 55.2 1.0 HG22 A:THR353 4.9 61.1 1.0 HA3 A:GLY307 5.0 60.2 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