Magnesium in PDB 4y8v: Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site, PDB code: 4y8v 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)	49.21 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.470, 110.990, 126.720, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.6

The binding sites of Magnesium atom in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site (pdb code 4y8v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site, PDB code: 4y8v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site


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 Additional Adp Bound to Phosphate Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:47.7 occ:1.00 O3B C:ADP602 2.3 54.1 1.0 O A:HOH911 2.5 35.5 1.0 H8 C:ADP602 2.9 87.6 1.0 OD2 A:ASP351 3.1 38.8 1.0 H A:GLY308 3.1 32.5 1.0 PB C:ADP602 3.7 65.6 1.0 HA A:THR353 3.8 34.5 1.0 N A:GLY308 3.9 27.1 1.0 C8 C:ADP602 3.9 73.0 1.0 HA2 A:GLY307 4.0 37.4 1.0 O1B C:ADP602 4.0 38.8 1.0 O2A C:ADP602 4.0 60.2 1.0 CG A:ASP351 4.1 32.1 1.0 H1' C:ADP602 4.2 90.3 1.0 HA3 A:GLY308 4.2 35.9 1.0 O A:HOH905 4.2 40.5 1.0 OD1 A:ASP351 4.2 26.5 1.0 H A:GLY354 4.3 31.0 1.0 CA A:GLY308 4.6 29.9 1.0 O3A C:ADP602 4.6 60.6 1.0 HB A:THR353 4.6 34.9 1.0 N7 C:ADP602 4.7 76.2 1.0 O2B C:ADP602 4.7 43.6 1.0 CA A:THR353 4.8 28.7 1.0 CA A:GLY307 4.8 31.2 1.0 C A:GLY307 4.8 28.0 1.0 HG22 A:THR353 4.9 37.8 1.0 N9 C:ADP602 4.9 72.5 1.0 HA2 A:GLY308 4.9 35.9 1.0 H4' C:ADP602 4.9 82.6 1.0 C1' C:ADP602 4.9 75.2 1.0 N A:GLY354 5.0 25.9 1.0 PA C:ADP602 5.0 70.5 1.0

Magnesium binding site 2 out of 4 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site


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 Additional Adp Bound to Phosphate Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:56.3 occ:1.00 O2B B:ADP300 2.0 69.0 1.0 O1A B:ADP300 2.2 64.1 1.0 PB B:ADP300 3.5 76.5 1.0 H5'1 B:ADP300 3.5 78.8 1.0 O3' B:ADP300 3.5 56.1 1.0 PA B:ADP300 3.6 73.6 1.0 O B:HOH438 3.6 58.5 1.0 OD2 B:ASP224 3.6 53.7 1.0 O3A B:ADP300 3.8 67.4 1.0 O B:HOH444 4.0 65.6 1.0 H3' B:ADP300 4.1 69.9 1.0 O1B B:ADP300 4.2 66.8 1.0 HH22 B:ARG226 4.3 79.5 1.0 C5' B:ADP300 4.3 65.6 1.0 C3' B:ADP300 4.3 58.3 1.0 HH21 B:ARG226 4.3 79.5 1.0 HD3 B:PRO212 4.3 40.2 1.0 O5' B:ADP300 4.4 68.3 1.0 O B:ASN211 4.4 31.0 1.0 O3B B:ADP300 4.5 74.3 1.0 O2A B:ADP300 4.6 63.2 1.0 HB3 B:ASP224 4.6 49.9 1.0 NH2 B:ARG226 4.6 66.2 1.0 CG B:ASP224 4.7 49.6 1.0 C4' B:ADP300 4.8 62.1 1.0 HB2 B:ASP224 4.8 49.9 1.0 HD2 B:PRO212 4.9 40.2 1.0 HG B:SER70 4.9 85.0 1.0 CB B:ASP224 5.0 41.6 1.0

Magnesium binding site 3 out of 4 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:36.4 occ:1.00 O A:HOH746 2.1 32.5 1.0 O C:HOH727 2.1 31.5 1.0 O C:HOH728 2.2 27.6 1.0 O C:HOH730 2.3 38.3 1.0 O1B A:ADP600 2.3 34.4 1.0 O C:HOH729 2.3 35.3 1.0 OD2 C:ASP351 3.3 36.6 1.0 H C:GLY308 3.3 28.2 1.0 HA C:THR353 3.5 35.2 1.0 PB A:ADP600 3.6 35.4 1.0 H8 A:ADP600 3.9 53.6 1.0 H C:GLY354 3.9 40.7 1.0 HA2 C:GLY307 3.9 33.4 1.0 O1A A:ADP600 4.0 33.6 1.0 N C:GLY308 4.1 23.5 1.0 CG C:ASP351 4.1 29.5 1.0 O3A A:ADP600 4.1 40.4 1.0 OD1 C:ASP351 4.1 28.2 1.0 O3B A:ADP600 4.2 28.6 1.0 HA3 C:GLY308 4.4 31.2 1.0 HB C:THR353 4.4 42.8 1.0 CA C:THR353 4.4 29.4 1.0 N7 A:ADP600 4.5 43.9 1.0 C8 A:ADP600 4.6 44.6 1.0 N C:GLY354 4.6 33.9 1.0 O A:HOH904 4.6 38.1 1.0 PA A:ADP600 4.7 41.8 1.0 HG22 C:THR353 4.7 43.2 1.0 CA C:GLY308 4.7 26.0 1.0 CA C:GLY307 4.8 27.8 1.0 O2B A:ADP600 4.8 31.9 1.0 C C:GLY307 4.9 25.0 1.0 CB C:THR353 4.9 35.7 1.0 H C:THR353 4.9 36.0 1.0

Magnesium binding site 4 out of 4 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Adp and Additional Adp Bound to Phosphate Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:54.8 occ:1.00 O2B D:ADP300 2.3 55.1 1.0 O2A D:ADP300 2.4 51.9 1.0 O D:ASN211 3.2 39.5 1.0 HD3 D:PRO212 3.3 44.7 1.0 OD2 D:ASP224 3.4 47.4 1.0 PB D:ADP300 3.8 60.1 1.0 HH21 D:ARG226 3.8 79.2 1.0 O3' D:ADP300 3.8 49.3 1.0 PA D:ADP300 3.8 49.6 1.0 HB3 D:ASP224 3.9 41.2 1.0 HD2 D:PRO212 3.9 44.7 1.0 CD D:PRO212 4.0 37.2 1.0 C D:ASN211 4.1 34.2 1.0 O3A D:ADP300 4.2 63.5 1.0 H3' D:ADP300 4.2 57.7 1.0 H5'1 D:ADP300 4.3 64.2 1.0 CG D:ASP224 4.3 47.0 1.0 HB2 D:ASP224 4.3 41.2 1.0 NH2 D:ARG226 4.3 66.0 1.0 CB D:ASP224 4.4 34.3 1.0 O D:HOH439 4.4 51.0 1.0 N D:PRO212 4.5 31.6 1.0 HE D:ARG226 4.6 74.2 1.0 C3' D:ADP300 4.6 48.1 1.0 O1A D:ADP300 4.6 46.0 1.0 HH22 D:ARG226 4.7 79.2 1.0 O3B D:ADP300 4.7 67.5 1.0 O1B D:ADP300 4.7 61.5 1.0 HZ3 D:LYS69 4.8 69.1 1.0 O D:HOH426 4.8 42.1 1.0 O5' D:ADP300 4.9 50.5 1.0 HB3 D:ASN211 4.9 38.7 1.0 OD1 D:ASN211 4.9 31.8 1.0 CG D:ASN211 4.9 32.4 1.0 C5' D:ADP300 5.0 53.5 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