Magnesium 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:

Sodium

(Na)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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 B:Mg301 b:70.4 occ:1.00 O1A B:ADP300 2.3 0.0 1.0 O3B B:ADP300 2.3 92.7 1.0 O3' B:ADP300 3.4 94.9 1.0 H5'2 B:ADP300 3.4 0.8 1.0 PA B:ADP300 3.6 0.5 1.0 PB B:ADP300 3.7 0.5 1.0 O3A B:ADP300 4.0 0.9 1.0 H3' B:ADP300 4.1 0.7 1.0 C3' B:ADP300 4.2 99.8 1.0 C5' B:ADP300 4.3 98.2 1.0 OD2 B:ASP224 4.3 69.2 1.0 O1B B:ADP300 4.3 95.4 1.0 O5' B:ADP300 4.4 96.4 1.0 HD3 B:PRO212 4.5 60.6 1.0 O2A B:ADP300 4.6 84.8 1.0 C4' B:ADP300 4.7 0.4 1.0 O2B B:ADP300 4.9 0.1 1.0 H4' B:ADP300 4.9 0.1 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 D:Mg301 b:70.2 occ:1.00 O2B D:ADP300 2.4 68.8 1.0 O2A D:ADP300 2.5 67.8 1.0 HH21 D:ARG226 3.1 99.4 1.0 OD2 D:ASP224 3.4 69.2 1.0 O D:ASN211 3.4 53.4 1.0 HD3 D:PRO212 3.7 60.5 1.0 PB D:ADP300 3.8 75.2 1.0 PA D:ADP300 3.9 69.0 1.0 NH2 D:ARG226 3.9 82.8 1.0 HE D:ARG226 3.9 98.3 1.0 HB3 D:ASP224 4.0 64.4 1.0 O3' D:ADP300 4.1 68.5 1.0 O3A D:ADP300 4.1 78.4 1.0 H5'1 D:ADP300 4.2 82.7 1.0 HH22 D:ARG226 4.3 99.4 1.0 CG D:ASP224 4.4 68.2 1.0 H3' D:ADP300 4.4 80.0 1.0 C D:ASN211 4.4 50.7 1.0 CD D:PRO212 4.4 50.4 1.0 HD2 D:PRO212 4.5 60.5 1.0 O D:HOH413 4.5 48.2 1.0 CB D:ASP224 4.5 53.6 1.0 HB2 D:ASP224 4.6 64.4 1.0 NE D:ARG226 4.6 81.9 1.0 O1A D:ADP300 4.6 65.7 1.0 CZ D:ARG226 4.7 81.4 1.0 O3B D:ADP300 4.7 80.1 1.0 O1B D:ADP300 4.8 76.1 1.0 HB3 D:ASN211 4.8 63.0 1.0 C3' D:ADP300 4.8 66.7 1.0 N D:PRO212 4.9 46.7 1.0 CG D:ASN211 4.9 46.2 1.0 O5' D:ADP300 4.9 68.8 1.0 C5' D:ADP300 5.0 68.9 1.0 ND2 D:ASN211 5.0 51.2 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