Magnesium in PDB 4ybz: Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and with Phosphorylated Phosphohistidine Segment (Site I Orientation)

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and with Phosphorylated Phosphohistidine Segment (Site I Orientation), PDB code: 4ybz 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)	83.03 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.303, 109.879, 126.776, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.3

The binding sites of Magnesium atom in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and with Phosphorylated Phosphohistidine Segment (Site I Orientation) (pdb code 4ybz). 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 Adp and with Phosphorylated Phosphohistidine Segment (Site I Orientation), PDB code: 4ybz:
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 Adp and with Phosphorylated Phosphohistidine Segment (Site I Orientation)


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 Adp and with Phosphorylated Phosphohistidine Segment (Site I Orientation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:49.5 occ:1.00 O3P A:NEP254 2.3 31.9 1.0 OD2 C:ASP351 3.0 37.4 1.0 HD2 A:NEP254 3.2 47.0 1.0 HA C:THR353 3.2 38.3 1.0 H C:GLY308 3.4 37.3 1.0 OD1 C:ASP351 3.7 31.2 1.0 CG C:ASP351 3.7 33.6 1.0 P A:NEP254 3.8 33.7 1.0 O A:HOH777 3.8 45.0 1.0 H C:GLY354 3.8 40.6 1.0 HA2 C:GLY307 4.0 40.3 1.0 CD2 A:NEP254 4.1 39.1 1.0 N C:GLY308 4.1 31.1 1.0 CA C:THR353 4.2 31.9 1.0 NE2 A:NEP254 4.4 43.6 1.0 HB C:THR353 4.4 41.4 1.0 O1P A:NEP254 4.4 37.9 1.0 HA3 C:GLY308 4.4 42.4 1.0 N C:GLY354 4.5 33.9 1.0 O C:ASN306 4.6 34.4 1.0 H C:THR353 4.6 40.8 1.0 O A:HOH798 4.6 43.3 1.0 O A:HOH680 4.6 41.6 1.0 HG22 C:THR353 4.7 44.0 1.0 O2P A:NEP254 4.7 39.2 1.0 CB C:THR353 4.8 34.5 1.0 CA C:GLY308 4.8 35.3 1.0 C C:THR353 4.8 31.9 1.0 CA C:GLY307 4.9 33.5 1.0 HB2 A:ALA162 4.9 39.8 1.0 N C:THR353 5.0 34.0 1.0 C C:GLY307 5.0 30.5 1.0

Magnesium binding site 2 out of 2 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and with Phosphorylated Phosphohistidine Segment (Site I Orientation)


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 Adp and with Phosphorylated Phosphohistidine Segment (Site I Orientation) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:46.7 occ:1.00 O A:HOH793 2.0 38.2 1.0 O1P C:NEP254 2.1 37.7 1.0 O A:HOH685 2.3 39.5 1.0 O C:HOH715 2.3 44.3 1.0 O A:HOH686 2.5 39.7 1.0 P C:NEP254 3.1 34.9 1.0 O3P C:NEP254 3.3 43.6 1.0 HD2 C:NEP254 3.4 47.8 1.0 H A:GLY308 3.7 42.3 1.0 H A:GLY354 3.9 40.4 1.0 NE2 C:NEP254 3.9 39.2 1.0 CD2 C:NEP254 4.0 39.8 1.0 HA A:THR353 4.1 40.9 1.0 OD2 A:ASP351 4.2 39.4 1.0 O2P C:NEP254 4.3 33.0 1.0 HA2 A:GLY307 4.4 44.0 1.0 HB2 C:ALA162 4.4 40.1 1.0 O C:HOH769 4.5 37.8 1.0 N A:GLY308 4.5 35.2 1.0 N A:GLY354 4.7 33.7 1.0 HA3 A:GLY308 4.7 48.5 1.0 H C:ALA162 4.7 38.0 1.0 OD1 A:ASP351 4.9 35.6 1.0 HB3 C:ALA162 4.9 40.1 1.0 HB A:THR353 4.9 46.5 1.0 CG A:ASP351 4.9 40.0 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