Sodium in PDB 4yb8: Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Adp

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Adp, PDB code: 4yb8 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)	83.04 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.071, 110.615, 125.709, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.1

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Adp 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 Adp (pdb code 4yb8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Adp, PDB code: 4yb8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:53.0 occ:1.00 O A:LYS327 2.4 44.6 1.0 HB2 A:SER326 2.8 60.5 1.0 HG A:SER326 2.9 61.3 1.0 OG A:SER326 3.0 51.0 1.0 HH11 A:ARG300 3.0 72.8 1.0 NH1 A:ARG300 3.2 60.6 1.0 HE A:ARG300 3.3 71.1 1.0 CB A:SER326 3.3 50.4 1.0 N A:LYS327 3.4 44.3 1.0 H A:LYS327 3.4 53.2 1.0 C A:LYS327 3.4 41.5 1.0 CZ A:ARG300 3.5 62.5 1.0 HB3 A:LYS327 3.5 62.2 1.0 NE A:ARG300 3.5 59.2 1.0 O A:HOH664 3.5 51.6 1.0 HH12 A:ARG300 3.6 72.8 1.0 C A:SER326 3.6 48.8 1.0 CA A:LYS327 3.8 47.3 1.0 O A:SER326 4.1 44.2 1.0 CA A:SER326 4.1 45.1 1.0 CB A:LYS327 4.1 51.9 1.0 HB3 A:SER326 4.1 60.5 1.0 NH2 A:ARG300 4.3 59.1 1.0 CD A:ARG300 4.5 54.6 1.0 HD3 A:ARG300 4.5 65.5 1.0 HD2 A:ARG300 4.5 65.5 1.0 HB2 A:LYS327 4.6 62.2 1.0 N A:PRO328 4.6 43.0 1.0 HH22 A:ARG300 4.6 70.9 1.0 HA A:SER326 4.7 54.1 1.0 HA A:LYS327 4.7 56.7 1.0 HA A:PRO328 4.8 56.8 1.0 HH21 A:ARG300 4.8 70.9 1.0 O A:PRO328 4.9 44.9 1.0 C A:PRO328 4.9 49.1 1.0 HE3 A:LYS327 5.0 83.0 1.0 H A:SER326 5.0 51.7 1.0 CA A:PRO328 5.0 47.3 1.0

Sodium binding site 2 out of 3 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Adp


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 in Complex with Phosphate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:56.0 occ:1.00 O3 A:PO4502 2.2 53.0 1.0 NE2 A:HIS254 2.3 68.9 1.0 O A:HOH720 2.4 53.3 1.0 OE2 A:GLU213 2.6 63.2 1.0 CD2 A:HIS254 3.1 77.2 1.0 OE1 A:GLU213 3.1 66.7 1.0 HD2 A:HIS254 3.1 92.6 1.0 CD A:GLU213 3.3 64.0 1.0 HA A:SER160 3.3 41.9 1.0 CE1 A:HIS254 3.4 64.5 1.0 P A:PO4502 3.4 47.2 1.0 O4 A:PO4502 3.6 48.3 1.0 HE1 A:HIS254 3.6 77.3 1.0 HB2 A:SER160 3.8 46.5 1.0 O1 A:PO4502 4.2 53.4 1.0 CA A:SER160 4.2 34.9 1.0 O A:GLN159 4.2 34.4 1.0 HG22 A:THR255 4.2 0.8 1.0 CG A:HIS254 4.3 80.4 1.0 H A:GLY161 4.3 38.3 1.0 HG A:SER160 4.3 43.8 1.0 CB A:SER160 4.4 38.8 1.0 ND1 A:HIS254 4.4 72.0 1.0 HA3 C:GLY308 4.5 50.9 1.0 O2 A:PO4502 4.5 42.8 1.0 H C:GLY309 4.6 49.8 1.0 HG23 A:THR255 4.6 0.8 1.0 HG2 A:GLN159 4.6 46.0 1.0 O A:HOH719 4.7 56.4 1.0 CG A:GLU213 4.8 56.8 1.0 N C:GLY309 4.8 41.5 1.0 CG2 A:THR255 4.8 94.0 1.0 C A:GLN159 4.8 35.9 1.0 OG A:SER160 4.8 36.5 1.0 N A:SER160 4.9 34.4 1.0 N A:GLY161 5.0 31.9 1.0 HA2 C:GLY309 5.0 46.7 1.0

Sodium binding site 3 out of 3 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Phosphate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:61.0 occ:1.00 O C:HOH683 2.2 51.3 1.0 O1 A:PO4502 2.3 53.4 1.0 O A:HOH719 2.4 56.4 1.0 HE1 A:HIS254 2.9 77.3 1.0 O A:HOH718 3.0 55.0 1.0 OD2 C:ASP351 3.1 48.6 1.0 H C:GLY308 3.2 43.9 1.0 P A:PO4502 3.7 47.2 1.0 CE1 A:HIS254 3.8 64.5 1.0 HA C:THR353 3.8 55.2 1.0 N C:GLY308 3.9 36.6 1.0 HA2 C:GLY307 4.0 51.0 1.0 CG C:ASP351 4.0 45.0 1.0 OD1 C:ASP351 4.0 41.9 1.0 O3 A:PO4502 4.1 53.0 1.0 HA3 C:GLY308 4.1 50.9 1.0 O2 A:PO4502 4.2 42.8 1.0 H C:GLY354 4.2 54.6 1.0 CA C:GLY308 4.5 42.4 1.0 ND1 A:HIS254 4.6 72.0 1.0 NE2 A:HIS254 4.7 68.9 1.0 CA C:THR353 4.8 46.0 1.0 HB C:THR353 4.8 54.8 1.0 CA C:GLY307 4.8 42.5 1.0 O4 A:PO4502 4.8 48.3 1.0 C C:GLY307 4.9 37.9 1.0 N C:GLY354 4.9 45.5 1.0 HA2 C:GLY308 4.9 50.9 1.0 HG22 C:THR353 5.0 62.5 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