Magnesium 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:

Sodium

(Na)

1 atom

The binding sites of Magnesium 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 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 Coenzyme A, PDB code: 5hbr:
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 Coenzyme A


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 Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:44.2 occ:1.00 O4 A:PO4502 1.9 51.0 1.0 NE2 A:HIS254 2.0 63.6 1.0 O A:HOH601 2.1 50.1 1.0 O A:HOH736 2.1 58.5 1.0 O A:HOH737 2.7 55.3 1.0 CD2 A:HIS254 2.9 66.6 1.0 OE1 A:GLU213 2.9 58.7 1.0 HD2 A:HIS254 3.0 79.9 1.0 CE1 A:HIS254 3.1 59.0 1.0 P A:PO4502 3.3 46.6 1.0 HE1 A:HIS254 3.3 70.8 1.0 HA A:SER160 3.4 43.8 1.0 OE2 A:GLU213 3.5 73.2 1.0 CD A:GLU213 3.6 62.5 1.0 O2 A:PO4502 3.8 51.9 1.0 CG A:HIS254 4.0 73.3 1.0 ND1 A:HIS254 4.1 65.0 1.0 O A:GLN159 4.2 40.5 1.0 H A:GLY161 4.2 42.8 1.0 O1 A:PO4502 4.2 54.4 1.0 O3 A:PO4502 4.3 49.3 1.0 HB2 A:SER160 4.3 45.8 1.0 HG A:SER160 4.3 50.5 1.0 CA A:SER160 4.3 36.5 1.0 O A:HOH704 4.3 53.0 1.0 HG22 A:THR255 4.5 0.3 1.0 HA3 C:GLY308 4.6 54.8 1.0 H C:GLY309 4.6 52.2 1.0 CB A:SER160 4.7 38.2 1.0 HG2 A:GLN159 4.7 56.8 1.0 C A:GLN159 4.9 38.2 1.0 OG A:SER160 4.9 42.1 1.0 N A:GLY161 4.9 35.6 1.0 N A:SER160 5.0 34.4 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 Coenzyme A


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 Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:59.6 occ:1.00 O C:HOH602 2.0 56.5 1.0 O1 A:PO4502 2.0 54.4 1.0 O C:HOH610 2.1 53.1 1.0 O C:HOH697 2.2 57.7 1.0 O A:HOH704 2.3 53.0 1.0 O A:HOH651 2.4 49.1 1.0 H C:GLY308 3.1 47.4 1.0 HE1 A:HIS254 3.2 70.8 1.0 P A:PO4502 3.4 46.6 1.0 HA C:THR353 3.6 59.6 1.0 OD2 C:ASP351 3.6 52.1 1.0 H C:GLY354 3.8 58.6 1.0 HA2 C:GLY307 3.8 52.5 1.0 N C:GLY308 3.9 39.5 1.0 O3 A:PO4502 3.9 49.3 1.0 O4 A:PO4502 4.0 51.0 1.0 CE1 A:HIS254 4.2 59.0 1.0 HA3 C:GLY308 4.2 54.8 1.0 OD1 C:ASP351 4.2 49.8 1.0 CG C:ASP351 4.3 49.5 1.0 N C:GLY354 4.4 48.8 1.0 CA C:THR353 4.5 49.7 1.0 CA C:GLY308 4.6 45.7 1.0 O2 A:PO4502 4.6 51.9 1.0 O C:ASN306 4.6 45.7 1.0 O A:HOH733 4.7 50.9 1.0 CA C:GLY307 4.7 43.8 1.0 HB C:THR353 4.7 66.6 1.0 C C:GLY307 4.7 44.7 1.0 HA3 C:GLY354 4.9 53.5 1.0 HB2 A:ALA162 4.9 48.7 1.0 C C:THR353 4.9 44.6 1.0 HA2 C:GLY308 5.0 54.8 1.0 HG22 C:THR353 5.0 67.0 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