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Magnesium in PDB 8rpk: Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand

Enzymatic activity of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand

All present enzymatic activity of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand:
6.2.1.1;

Protein crystallography data

The structure of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand, PDB code: 8rpk 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) 272.00 / 2.62
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 161.352, 161.352, 814.182, 90, 90, 120
R / Rfree (%) 16.3 / 22.1

Other elements in 8rpk:

The structure of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand (pdb code 8rpk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand, PDB code: 8rpk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8rpk

Go back to Magnesium Binding Sites List in 8rpk
Magnesium binding site 1 out of 4 in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand


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 Without Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:87.0
occ:1.00
 O A:HOH804 2.4 73.8 1.0
O A:HIS554 2.4 79.3 1.0
O A:VAL557 2.7 70.2 1.0
HH22 A:ARG581 2.9 91.4 1.0
O A:VAL552 2.9 74.2 1.0
HA A:PRO555 3.1 79.3 1.0
NH2 A:ARG581 3.4 88.5 1.0
C A:HIS554 3.5 74.8 1.0
H A:VAL557 3.5 74.2 1.0
HE A:ARG581 3.6 101.4 1.0
CA A:PRO555 3.7 79.1 1.0
HH21 A:ARG581 3.7 91.1 1.0
O A:PRO555 3.7 93.4 1.0
C A:PRO555 3.8 82.5 1.0
C A:VAL557 3.8 74.2 1.0
N A:PRO555 4.0 77.5 1.0
N A:VAL557 4.1 73.9 1.0
C A:VAL552 4.1 78.2 1.0
NE A:ARG581 4.2 107.5 1.0
CZ A:ARG581 4.3 99.7 1.0
HB A:VAL557 4.3 72.6 1.0
HG11 A:VAL552 4.5 79.5 1.0
CA A:VAL557 4.5 76.1 1.0
N A:ALA556 4.5 78.0 1.0
C A:SER553 4.5 72.9 1.0
HA A:ALA558 4.5 81.8 1.0
HA A:VAL552 4.6 76.4 1.0
O A:SER553 4.6 76.6 1.0
N A:HIS554 4.6 74.1 1.0
HA A:SER553 4.7 72.3 1.0
CA A:HIS554 4.7 73.4 1.0
HG2 A:ARG581 4.8 87.2 1.0
H A:ALA556 4.8 77.9 1.0
N A:ALA558 4.9 81.1 1.0
C A:ALA556 4.9 75.5 1.0
HG3 A:ARG581 4.9 88.1 1.0
HG12 A:VAL552 4.9 78.6 1.0
CA A:VAL552 5.0 74.7 1.0
CB A:VAL557 5.0 72.8 1.0
N A:SER553 5.0 70.3 1.0
CA A:SER553 5.0 70.8 1.0

Magnesium binding site 2 out of 4 in 8rpk

Go back to Magnesium Binding Sites List in 8rpk
Magnesium binding site 2 out of 4 in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand


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 Without Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:82.3
occ:1.00
 O B:VAL552 2.1 82.7 1.0
O B:HIS554 2.5 80.9 1.0
O B:HOH806 2.5 77.8 1.0
O B:VAL557 2.9 82.0 1.0
C B:VAL552 3.3 72.3 1.0
HH22 B:ARG581 3.6 87.1 1.0
C B:HIS554 3.6 75.5 1.0
HG11 B:VAL552 3.7 74.7 1.0
HA B:SER553 3.8 78.7 1.0
HA B:PRO555 3.9 81.6 1.0
C B:SER553 3.9 76.6 1.0
H B:VAL557 4.0 69.1 1.0
HA B:VAL552 4.1 69.8 1.0
N B:HIS554 4.1 81.1 1.0
C B:VAL557 4.1 77.0 1.0
N B:SER553 4.2 76.6 1.0
CA B:SER553 4.2 77.9 1.0
HG12 B:VAL552 4.2 74.0 1.0
O B:SER553 4.3 77.8 1.0
HE B:ARG581 4.3 90.2 1.0
CA B:VAL552 4.3 69.8 1.0
H B:HIS554 4.4 77.5 1.0
N B:PRO555 4.4 76.3 1.0
HB B:VAL557 4.4 68.0 1.0
CG1 B:VAL552 4.4 74.6 1.0
NH2 B:ARG581 4.4 86.5 1.0
CA B:PRO555 4.4 82.7 1.0
CA B:HIS554 4.5 74.9 1.0
C B:PRO555 4.5 83.2 1.0
O B:PRO555 4.5 84.9 1.0
N B:VAL557 4.6 70.0 1.0
HA B:ALA558 4.8 75.2 1.0
CA B:VAL557 4.8 70.5 1.0
HH21 B:ARG581 4.9 87.7 1.0
NE B:ARG581 4.9 92.2 1.0

Magnesium binding site 3 out of 4 in 8rpk

Go back to Magnesium Binding Sites List in 8rpk
Magnesium binding site 3 out of 4 in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand


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 Without Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:87.0
occ:1.00
 O C:HOH805 1.9 68.5 1.0
O C:HOH802 2.1 72.3 1.0
O C:HOH810 2.3 72.9 1.0
O C:VAL557 2.4 72.0 1.0
O C:VAL552 2.4 61.4 1.0
O C:HIS554 2.4 65.6 1.0
HH22 C:ARG581 3.0 94.9 1.0
H C:VAL557 3.5 69.7 1.0
C C:VAL557 3.5 72.3 1.0
C C:VAL552 3.5 69.3 1.0
C C:HIS554 3.6 63.7 1.0
HB C:VAL557 3.6 68.9 1.0
HE C:ARG581 3.7 88.4 1.0
NH2 C:ARG581 3.8 98.2 1.0
HA C:PRO555 3.9 72.2 1.0
N C:VAL557 4.0 68.5 1.0
HA C:VAL552 4.0 72.8 1.0
HG11 C:VAL552 4.1 72.0 1.0
N C:HIS554 4.1 73.6 1.0
HA C:SER553 4.2 69.3 1.0
CA C:VAL557 4.2 67.3 1.0
H C:HIS554 4.2 71.6 1.0
HA C:ALA558 4.2 76.4 1.0
HG12 C:VAL552 4.3 71.9 1.0
C C:PRO555 4.3 77.0 1.0
HH21 C:ARG581 4.3 95.9 1.0
C C:SER553 4.3 72.2 1.0
CA C:PRO555 4.4 71.6 1.0
NE C:ARG581 4.4 88.1 1.0
CB C:VAL557 4.4 68.0 1.0
CA C:VAL552 4.4 74.5 1.0
N C:PRO555 4.4 68.5 1.0
N C:SER553 4.4 67.9 1.0
CA C:SER553 4.5 67.9 1.0
O C:PRO555 4.5 80.5 1.0
CA C:HIS554 4.5 68.0 1.0
CZ C:ARG581 4.5 90.9 1.0
CG1 C:VAL552 4.6 71.6 1.0
N C:ALA558 4.6 77.4 1.0
N C:ALA556 4.6 77.2 1.0
HG12 C:VAL557 4.6 72.1 1.0
H C:ALA556 4.7 76.0 1.0
CA C:ALA558 4.9 75.4 1.0
C C:ALA556 4.9 76.4 1.0
HG2 C:ARG581 4.9 86.6 1.0
O C:LEU551 4.9 72.1 1.0
O C:SER553 4.9 79.6 1.0

Magnesium binding site 4 out of 4 in 8rpk

Go back to Magnesium Binding Sites List in 8rpk
Magnesium binding site 4 out of 4 in the Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Amp-Forming Acetyl-Coa Synthetase From Chloroflexota Bacterium Without Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:72.4
occ:1.00
 O D:VAL552 2.3 83.8 1.0
O D:HOH801 2.4 77.3 1.0
O D:HIS554 2.8 64.7 1.0
HH22 D:ARG581 2.9 80.5 1.0
O D:VAL557 3.0 67.3 1.0
C D:VAL552 3.5 62.3 1.0
NH2 D:ARG581 3.5 84.5 1.0
HA D:SER553 3.7 64.1 1.0
HH21 D:ARG581 3.8 80.7 1.0
C D:HIS554 3.8 61.1 1.0
HA D:PRO555 3.9 68.0 1.0
HG11 D:VAL552 3.9 70.5 1.0
HE D:ARG581 4.0 73.9 1.0
C D:SER553 4.0 61.8 1.0
H D:VAL557 4.2 63.6 1.0
C D:VAL557 4.2 63.1 1.0
CA D:SER553 4.2 63.2 1.0
O D:SER553 4.2 64.3 1.0
N D:SER553 4.3 65.5 1.0
HG12 D:VAL552 4.3 69.9 1.0
HA D:VAL552 4.3 64.5 1.0
N D:HIS554 4.4 64.1 1.0
HB D:VAL557 4.4 63.1 1.0
CA D:PRO555 4.5 67.0 1.0
CZ D:ARG581 4.5 74.6 1.0
CA D:VAL552 4.5 65.1 1.0
N D:PRO555 4.5 66.8 1.0
CG1 D:VAL552 4.5 70.0 1.0
HA D:ALA558 4.6 66.6 1.0
NE D:ARG581 4.6 74.7 1.0
C D:PRO555 4.7 73.0 1.0
O D:PRO555 4.7 76.9 1.0
H D:HIS554 4.7 62.3 1.0
N D:VAL557 4.8 63.7 1.0
CA D:HIS554 4.8 61.5 1.0
CA D:VAL557 5.0 62.0 1.0

Reference:

C.Qin, G.J.Palm. 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 Structural Biology 2024.
Page generated: Fri Oct 4 17:45:29 2024

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