Sodium in PDB 4yaj: Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Apo Form)

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Apo Form), PDB code: 4yaj 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)	83.34 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.808, 111.244, 125.807, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 24.1

The binding sites of Sodium atom in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Apo Form) (pdb code 4yaj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Apo Form), PDB code: 4yaj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Apo Form)


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 (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:54.5 occ:1.00 OE2 A:GLU51 2.5 55.4 1.0 HA A:MET53 3.0 51.4 1.0 H A:GLY54 3.1 50.8 1.0 H A:MET53 3.2 54.8 1.0 HZ3 A:LYS20 3.5 65.1 1.0 N A:GLY54 3.6 42.4 1.0 N A:MET53 3.6 45.7 1.0 CA A:MET53 3.6 42.9 1.0 CD A:GLU51 3.6 52.0 1.0 HZ1 A:LYS20 3.7 65.1 1.0 HZ2 A:LYS20 3.8 65.1 1.0 NZ A:LYS20 3.9 54.3 1.0 C A:MET53 4.0 41.1 1.0 OE1 A:GLU51 4.1 51.3 1.0 HA2 A:GLY54 4.3 49.9 1.0 CA A:GLY54 4.5 41.6 1.0 HA A:LEU52 4.6 52.6 1.0 C A:LEU52 4.7 42.2 1.0 HA3 A:GLY54 4.7 49.9 1.0 CG A:GLU51 4.8 50.1 1.0 HG2 A:GLU51 4.9 60.2 1.0 HG2 A:MET53 4.9 52.3 1.0

Sodium binding site 2 out of 2 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Apo Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:52.7 occ:1.00 OE2 B:GLU22 2.5 62.5 1.0 HH22 B:ARG15 2.6 65.3 1.0 HB3 B:LYS9 2.8 57.0 1.0 O B:LEU6 2.8 39.4 1.0 HD2 B:LYS9 2.8 69.2 1.0 CD B:GLU22 2.9 55.3 1.0 OE1 B:GLU22 3.0 50.4 1.0 HB2 B:ALA10 3.1 55.8 1.0 HH12 B:ARG15 3.2 75.6 1.0 HA B:LEU6 3.2 47.7 1.0 H B:ALA10 3.3 56.5 1.0 NH2 B:ARG15 3.5 54.4 1.0 HD22 B:LEU18 3.6 51.1 1.0 N B:ALA10 3.6 47.1 1.0 CD B:LYS9 3.6 57.6 1.0 CB B:LYS9 3.6 47.5 1.0 C B:LEU6 3.7 38.0 1.0 HD23 B:LEU18 3.7 51.1 1.0 HG2 B:LYS9 3.8 62.5 1.0 HB3 B:LEU6 3.8 46.3 1.0 CA B:LEU6 3.8 39.8 1.0 HD3 B:LYS9 3.8 69.2 1.0 NH1 B:ARG15 3.9 63.0 1.0 CG B:LYS9 3.9 52.1 1.0 HA B:ALA10 3.9 57.4 1.0 CB B:ALA10 3.9 46.5 1.0 HD22 B:LEU6 3.9 46.7 1.0 CD2 B:LEU18 3.9 42.6 1.0 HD23 B:LEU6 4.0 46.7 1.0 HD21 B:LEU18 4.0 51.1 1.0 CA B:ALA10 4.0 47.8 1.0 HH21 B:ARG15 4.0 65.3 1.0 CZ B:ARG15 4.1 66.7 1.0 CG B:GLU22 4.1 46.9 1.0 HG2 B:GLU22 4.2 56.3 1.0 C B:LYS9 4.2 47.7 1.0 HB2 B:LYS9 4.3 57.0 1.0 CB B:LEU6 4.3 38.5 1.0 HB3 B:GLU22 4.3 51.7 1.0 HB3 B:ALA10 4.4 55.8 1.0 CD2 B:LEU6 4.4 38.9 1.0 CA B:LYS9 4.5 45.7 1.0 HB1 B:ALA10 4.6 55.8 1.0 HH11 B:ARG15 4.6 75.6 1.0 HZ3 B:LYS9 4.7 78.4 1.0 H B:LYS9 4.7 49.7 1.0 CB B:GLU22 4.8 43.1 1.0 HG3 B:LYS9 4.8 62.5 1.0 CE B:LYS9 4.8 67.5 1.0 HG3 B:GLU22 4.9 56.3 1.0 N B:LEU7 4.9 37.7 1.0 O B:ASP5 4.9 41.1 1.0 N B:LYS9 5.0 41.4 1.0 HB2 B:GLU22 5.0 51.7 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