Magnesium in PDB 8rpl: Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp

All present enzymatic activity of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp:
6.2.1.1;

The structure of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp, PDB code: 8rpl was solved by K.Striska, G.J.Palm, M.Lammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.30 / 2.37
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	161.909, 161.909, 817.234, 90, 90, 120
R / Rfree (%)	16.1 / 20.1

The structure of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp (pdb code 8rpl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp, PDB code: 8rpl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:69.4 occ:1.00 O A:HOH858 1.9 79.8 1.0 O A:VAL552 2.4 58.8 1.0 O A:HIS554 2.5 68.4 1.0 O A:HOH856 2.6 72.2 1.0 O A:VAL557 2.6 68.9 1.0 O A:HOH813 2.7 74.2 1.0 HH22 A:ARG581 3.0 87.8 1.0 C A:HIS554 3.5 67.4 1.0 HA A:PRO555 3.6 71.1 1.0 C A:VAL552 3.6 59.9 1.0 H A:VAL557 3.7 62.5 1.0 C A:VAL557 3.8 64.7 1.0 HG11 A:VAL552 3.9 63.5 1.0 NH2 A:ARG581 3.9 90.0 1.0 HB A:VAL557 4.0 60.3 1.0 HA A:VAL552 4.1 62.6 1.0 N A:HIS554 4.1 64.1 1.0 CA A:PRO555 4.1 70.0 1.0 N A:PRO555 4.2 71.2 1.0 C A:SER553 4.2 66.5 1.0 C A:PRO555 4.2 70.3 1.0 H A:HIS554 4.2 63.9 1.0 HH21 A:ARG581 4.2 88.5 1.0 N A:VAL557 4.2 63.8 1.0 O A:PRO555 4.3 79.3 1.0 CA A:VAL552 4.4 62.0 1.0 HE A:ARG581 4.4 88.3 1.0 CA A:HIS554 4.4 63.5 1.0 O A:SER553 4.5 80.6 1.0 CA A:VAL557 4.5 62.8 1.0 HA A:ALA558 4.5 64.4 1.0 N A:SER553 4.5 62.4 1.0 HA A:SER553 4.5 66.2 1.0 CG1 A:VAL552 4.7 62.2 1.0 CA A:SER553 4.7 66.2 1.0 CB A:VAL557 4.7 60.9 1.0 HG12 A:VAL552 4.7 62.1 1.0 N A:ALA558 4.8 67.3 1.0 N A:ALA556 4.9 66.8 1.0 CZ A:ARG581 4.9 87.4 1.0 HG12 A:VAL557 4.9 60.6 1.0 NE A:ARG581 5.0 92.0 1.0

Magnesium binding site 2 out of 3 in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:83.2 occ:1.00 O B:HOH815 1.6 81.9 1.0 O B:VAL552 2.4 77.9 1.0 O B:HOH819 2.4 96.9 1.0 O B:HIS554 2.6 77.1 1.0 O B:VAL557 3.0 81.8 1.0 C B:HIS554 3.5 76.1 1.0 C B:VAL552 3.6 72.4 1.0 HA B:PRO555 3.7 82.2 1.0 HH22 B:ARG581 3.9 109.4 1.0 HG11 B:VAL552 3.9 76.2 1.0 C B:SER553 3.9 82.0 1.0 HE B:ARG581 4.0 105.4 1.0 N B:HIS554 4.0 79.5 1.0 H B:VAL557 4.0 74.0 1.0 O B:SER553 4.1 85.0 1.0 HA B:VAL552 4.1 76.3 1.0 C B:VAL557 4.1 77.0 1.0 HB B:VAL557 4.2 73.5 1.0 HA B:SER553 4.2 81.3 1.0 H B:HIS554 4.2 79.5 1.0 N B:PRO555 4.3 81.9 1.0 CA B:PRO555 4.3 80.9 1.0 N B:SER553 4.4 79.7 1.0 CA B:SER553 4.4 80.3 1.0 CA B:HIS554 4.4 80.9 1.0 CA B:VAL552 4.5 75.3 1.0 HG12 B:VAL552 4.5 75.0 1.0 C B:PRO555 4.6 82.5 1.0 N B:VAL557 4.6 74.5 1.0 NH2 B:ARG581 4.6 111.9 1.0 CG1 B:VAL552 4.6 73.5 1.0 NE B:ARG581 4.8 108.2 1.0 O B:PRO555 4.8 90.3 1.0 CA B:VAL557 4.8 74.8 1.0 HA B:ALA558 4.8 80.2 1.0 CB B:VAL557 4.9 73.5 1.0

Magnesium binding site 3 out of 3 in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium with Bound Acetyl Amp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:70.8 occ:1.00 O C:HOH839 2.1 73.1 1.0 O C:VAL552 2.4 66.5 1.0 O C:VAL557 2.6 64.9 1.0 O C:HOH823 2.6 66.5 1.0 O C:HIS554 2.7 71.9 1.0 O C:HOH804 3.0 75.8 1.0 HH22 C:ARG581 3.3 79.7 1.0 C C:VAL552 3.6 65.2 1.0 HA C:PRO555 3.6 73.3 1.0 HG11 C:VAL552 3.7 67.2 1.0 C C:HIS554 3.7 66.9 1.0 C C:VAL557 3.8 61.6 1.0 H C:VAL557 3.8 59.1 1.0 HB C:VAL557 3.9 60.1 1.0 HE C:ARG581 4.0 77.1 1.0 HA C:VAL552 4.1 64.4 1.0 NH2 C:ARG581 4.1 81.2 1.0 CA C:PRO555 4.2 72.6 1.0 C C:SER553 4.3 73.1 1.0 HG12 C:VAL552 4.3 66.5 1.0 HA C:SER553 4.3 72.9 1.0 N C:VAL557 4.3 57.8 1.0 HA C:ALA558 4.3 62.8 1.0 N C:HIS554 4.4 66.9 1.0 N C:PRO555 4.4 72.6 1.0 CA C:VAL552 4.4 63.6 1.0 C C:PRO555 4.4 72.2 1.0 CG1 C:VAL552 4.4 66.2 1.0 CA C:VAL557 4.5 62.0 1.0 O C:SER553 4.5 77.8 1.0 O C:PRO555 4.5 69.3 1.0 N C:SER553 4.5 69.9 1.0 CA C:SER553 4.6 71.5 1.0 HH21 C:ARG581 4.6 80.6 1.0 CB C:VAL557 4.7 59.8 1.0 H C:HIS554 4.7 66.6 1.0 NE C:ARG581 4.7 78.7 1.0 CA C:HIS554 4.7 63.7 1.0 HG12 C:VAL557 4.8 61.6 1.0 N C:ALA558 4.8 60.6 1.0 CZ C:ARG581 4.9 80.1 1.0

C.Qin, M.Lammers. The Amp-Forming Acetyl-Coa-Synthetase Is Regulated By Lysine Acetylation and Has An Intrinsic Phosphotransacetylase Activity to Adjust Its Activity to the Cellular Acetyl-Phosphate Level Nature Comm 2024.