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Magnesium in PDB 8dbj: Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface

Enzymatic activity of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface

All present enzymatic activity of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface:
2.7.6.1;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface (pdb code 8dbj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface, PDB code: 8dbj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in 8dbj

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Magnesium binding site 1 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:19.4
occ:1.00
 O A:HOH502 1.9 18.3 1.0
O A:HOH501 2.0 18.7 1.0
O1A A:ATP401 2.1 29.8 1.0
O1B A:ATP401 2.2 33.6 1.0
NE2 A:HIS130 2.2 16.9 1.0
O1G A:ATP401 2.7 33.3 1.0
CD2 A:HIS130 3.1 16.9 1.0
PB A:ATP401 3.2 35.6 1.0
CE1 A:HIS130 3.2 16.9 1.0
PA A:ATP401 3.2 31.5 1.0
O3A A:ATP401 3.4 26.3 1.0
PG A:ATP401 3.7 52.1 1.0
O3B A:ATP401 3.8 32.1 1.0
NZ A:LYS99 4.0 16.8 1.0
OD1 A:ASP98 4.1 15.5 1.0
O5' A:ATP401 4.2 35.2 1.0
OD2 A:ASP98 4.2 15.5 1.0
CE A:LYS99 4.3 16.8 1.0
C5' A:ATP401 4.3 29.7 1.0
CG A:HIS130 4.3 16.9 1.0
ND1 A:HIS130 4.3 16.9 1.0
O2A A:ATP401 4.4 36.2 1.0
O3G A:ATP401 4.5 38.7 1.0
O2B A:ATP401 4.6 36.8 1.0
CG A:ASP98 4.6 15.5 1.0
O A:ARG96 4.7 17.2 0.2

Magnesium binding site 2 out of 24 in 8dbj

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Magnesium binding site 2 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:27.9
occ:1.00
 OD2 A:ASP171 2.0 34.9 1.0
O3 A:HSX402 2.3 28.6 1.0
O1 A:HSX402 2.8 33.1 1.0
O2 A:HSX402 2.8 31.1 1.0
CG A:ASP171 3.0 34.9 1.0
OD1 A:ASP171 3.3 34.9 1.0
C3 A:HSX402 3.3 26.7 1.0
C2 A:HSX402 3.4 27.3 1.0
C1 A:HSX402 3.6 25.1 1.0
OD1 A:ASP220 3.9 25.8 1.0
OD2 A:ASP220 4.0 25.8 1.0
OD1 A:ASP221 4.2 22.9 1.0
C4 A:HSX402 4.3 25.2 1.0
O2A A:ATP401 4.3 36.2 1.0
O4 A:HSX402 4.4 31.5 1.0
CB A:ASP171 4.4 34.9 1.0
CE1 A:HIS130 4.4 16.9 1.0
CG A:ASP220 4.4 25.8 1.0
O1G A:ATP401 4.4 33.3 1.0
O2G A:ATP401 4.6 42.0 1.0

Magnesium binding site 3 out of 24 in 8dbj

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Magnesium binding site 3 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:19.4
occ:1.00
 O B:HOH502 1.9 18.3 1.0
O B:HOH501 2.0 18.7 1.0
O1A B:ATP401 2.1 29.8 1.0
O1B B:ATP401 2.2 33.6 1.0
NE2 B:HIS130 2.2 16.9 1.0
O1G B:ATP401 2.7 33.3 1.0
CD2 B:HIS130 3.1 16.9 1.0
PB B:ATP401 3.2 35.6 1.0
CE1 B:HIS130 3.2 16.9 1.0
PA B:ATP401 3.2 31.5 1.0
O3A B:ATP401 3.4 26.3 1.0
PG B:ATP401 3.7 52.1 1.0
O3B B:ATP401 3.8 32.1 1.0
NZ B:LYS99 4.0 16.8 1.0
OD1 B:ASP98 4.1 15.5 1.0
O5' B:ATP401 4.2 35.2 1.0
OD2 B:ASP98 4.2 15.5 1.0
CE B:LYS99 4.3 16.8 1.0
C5' B:ATP401 4.3 29.7 1.0
CG B:HIS130 4.3 16.9 1.0
ND1 B:HIS130 4.3 16.9 1.0
O2A B:ATP401 4.4 36.2 1.0
O3G B:ATP401 4.5 38.7 1.0
O2B B:ATP401 4.6 36.8 1.0
CG B:ASP98 4.6 15.5 1.0
O B:ARG96 4.7 17.2 0.2

Magnesium binding site 4 out of 24 in 8dbj

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Magnesium binding site 4 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:27.9
occ:1.00
 OD2 B:ASP171 2.0 34.9 1.0
O3 B:HSX402 2.3 28.6 1.0
O1 B:HSX402 2.8 33.1 1.0
O2 B:HSX402 2.8 31.1 1.0
CG B:ASP171 3.0 34.9 1.0
OD1 B:ASP171 3.3 34.9 1.0
C3 B:HSX402 3.3 26.7 1.0
C2 B:HSX402 3.4 27.3 1.0
C1 B:HSX402 3.6 25.1 1.0
OD1 B:ASP220 3.9 25.8 1.0
OD2 B:ASP220 4.0 25.8 1.0
OD1 B:ASP221 4.2 22.9 1.0
C4 B:HSX402 4.3 25.2 1.0
O2A B:ATP401 4.3 36.2 1.0
O4 B:HSX402 4.4 31.5 1.0
CB B:ASP171 4.4 34.9 1.0
CE1 B:HIS130 4.4 16.9 1.0
CG B:ASP220 4.4 25.8 1.0
O1G B:ATP401 4.4 33.3 1.0
O2G B:ATP401 4.6 42.0 1.0

Magnesium binding site 5 out of 24 in 8dbj

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Magnesium binding site 5 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:19.4
occ:1.00
 O C:HOH502 1.9 18.3 1.0
O C:HOH501 2.0 18.7 1.0
O1A C:ATP401 2.1 29.8 1.0
O1B C:ATP401 2.2 33.6 1.0
NE2 C:HIS130 2.2 16.9 1.0
O1G C:ATP401 2.7 33.3 1.0
CD2 C:HIS130 3.1 16.9 1.0
PB C:ATP401 3.2 35.6 1.0
CE1 C:HIS130 3.2 16.9 1.0
PA C:ATP401 3.2 31.5 1.0
O3A C:ATP401 3.4 26.3 1.0
PG C:ATP401 3.7 52.1 1.0
O3B C:ATP401 3.8 32.1 1.0
NZ C:LYS99 4.0 16.8 1.0
OD1 C:ASP98 4.1 15.5 1.0
O5' C:ATP401 4.2 35.2 1.0
OD2 C:ASP98 4.2 15.5 1.0
CE C:LYS99 4.3 16.8 1.0
C5' C:ATP401 4.3 29.7 1.0
CG C:HIS130 4.3 16.9 1.0
ND1 C:HIS130 4.3 16.9 1.0
O2A C:ATP401 4.4 36.2 1.0
O3G C:ATP401 4.5 38.7 1.0
O2B C:ATP401 4.6 36.8 1.0
CG C:ASP98 4.6 15.5 1.0
O C:ARG96 4.7 17.2 0.2

Magnesium binding site 6 out of 24 in 8dbj

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Magnesium binding site 6 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:27.9
occ:1.00
 OD2 C:ASP171 2.0 34.9 1.0
O3 C:HSX402 2.3 28.6 1.0
O1 C:HSX402 2.8 33.1 1.0
O2 C:HSX402 2.8 31.1 1.0
CG C:ASP171 3.0 34.9 1.0
OD1 C:ASP171 3.3 34.9 1.0
C3 C:HSX402 3.3 26.7 1.0
C2 C:HSX402 3.4 27.3 1.0
C1 C:HSX402 3.6 25.1 1.0
OD1 C:ASP220 3.9 25.8 1.0
OD2 C:ASP220 4.0 25.8 1.0
OD1 C:ASP221 4.2 22.9 1.0
C4 C:HSX402 4.3 25.2 1.0
O2A C:ATP401 4.3 36.2 1.0
O4 C:HSX402 4.4 31.5 1.0
CB C:ASP171 4.4 34.9 1.0
CE1 C:HIS130 4.4 16.9 1.0
CG C:ASP220 4.4 25.8 1.0
O1G C:ATP401 4.4 33.3 1.0
O2G C:ATP401 4.6 42.0 1.0

Magnesium binding site 7 out of 24 in 8dbj

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Magnesium binding site 7 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:19.4
occ:1.00
 O D:HOH502 1.9 18.3 1.0
O D:HOH501 2.0 18.7 1.0
O1A D:ATP401 2.1 29.8 1.0
O1B D:ATP401 2.2 33.6 1.0
NE2 D:HIS130 2.2 16.9 1.0
O1G D:ATP401 2.7 33.3 1.0
CD2 D:HIS130 3.1 16.9 1.0
PB D:ATP401 3.2 35.6 1.0
CE1 D:HIS130 3.2 16.9 1.0
PA D:ATP401 3.2 31.5 1.0
O3A D:ATP401 3.4 26.3 1.0
PG D:ATP401 3.7 52.1 1.0
O3B D:ATP401 3.8 32.1 1.0
NZ D:LYS99 4.0 16.8 1.0
OD1 D:ASP98 4.1 15.5 1.0
O5' D:ATP401 4.2 35.2 1.0
OD2 D:ASP98 4.2 15.5 1.0
CE D:LYS99 4.3 16.8 1.0
C5' D:ATP401 4.3 29.7 1.0
CG D:HIS130 4.3 16.9 1.0
ND1 D:HIS130 4.3 16.9 1.0
O2A D:ATP401 4.4 36.2 1.0
O3G D:ATP401 4.5 38.7 1.0
O2B D:ATP401 4.6 36.8 1.0
CG D:ASP98 4.6 15.5 1.0
O D:ARG96 4.7 17.2 0.2

Magnesium binding site 8 out of 24 in 8dbj

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Magnesium binding site 8 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg405

b:27.9
occ:1.00
 OD2 D:ASP171 2.0 34.9 1.0
O3 D:HSX402 2.3 28.6 1.0
O1 D:HSX402 2.8 33.1 1.0
O2 D:HSX402 2.8 31.1 1.0
CG D:ASP171 3.0 34.9 1.0
OD1 D:ASP171 3.3 34.9 1.0
C3 D:HSX402 3.3 26.7 1.0
C2 D:HSX402 3.4 27.3 1.0
C1 D:HSX402 3.6 25.1 1.0
OD1 D:ASP220 3.9 25.8 1.0
OD2 D:ASP220 4.0 25.8 1.0
OD1 D:ASP221 4.2 22.9 1.0
C4 D:HSX402 4.3 25.2 1.0
O2A D:ATP401 4.3 36.2 1.0
O4 D:HSX402 4.4 31.5 1.0
CB D:ASP171 4.4 34.9 1.0
CE1 D:HIS130 4.4 16.9 1.0
CG D:ASP220 4.4 25.8 1.0
O1G D:ATP401 4.4 33.3 1.0
O2G D:ATP401 4.6 42.0 1.0

Magnesium binding site 9 out of 24 in 8dbj

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Magnesium binding site 9 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg404

b:19.4
occ:1.00
 O E:HOH502 1.9 18.3 1.0
O E:HOH501 2.0 18.7 1.0
O1A E:ATP401 2.1 29.8 1.0
O1B E:ATP401 2.2 33.6 1.0
NE2 E:HIS130 2.2 16.9 1.0
O1G E:ATP401 2.7 33.3 1.0
CD2 E:HIS130 3.1 16.9 1.0
PB E:ATP401 3.2 35.6 1.0
CE1 E:HIS130 3.2 16.9 1.0
PA E:ATP401 3.2 31.5 1.0
O3A E:ATP401 3.4 26.3 1.0
PG E:ATP401 3.7 52.1 1.0
O3B E:ATP401 3.8 32.1 1.0
NZ E:LYS99 4.0 16.8 1.0
OD1 E:ASP98 4.1 15.5 1.0
O5' E:ATP401 4.2 35.2 1.0
OD2 E:ASP98 4.2 15.5 1.0
CE E:LYS99 4.3 16.8 1.0
C5' E:ATP401 4.3 29.7 1.0
CG E:HIS130 4.3 16.9 1.0
ND1 E:HIS130 4.3 16.9 1.0
O2A E:ATP401 4.4 36.2 1.0
O3G E:ATP401 4.5 38.7 1.0
O2B E:ATP401 4.6 36.8 1.0
CG E:ASP98 4.6 15.5 1.0
O E:ARG96 4.7 17.2 0.2

Magnesium binding site 10 out of 24 in 8dbj

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Magnesium binding site 10 out of 24 in the Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human PRPS1 with Phosphate, Atp, and R5P; Filament Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg405

b:27.9
occ:1.00
 OD2 E:ASP171 2.0 34.9 1.0
O3 E:HSX402 2.3 28.6 1.0
O1 E:HSX402 2.8 33.1 1.0
O2 E:HSX402 2.8 31.1 1.0
CG E:ASP171 3.0 34.9 1.0
OD1 E:ASP171 3.3 34.9 1.0
C3 E:HSX402 3.3 26.7 1.0
C2 E:HSX402 3.4 27.3 1.0
C1 E:HSX402 3.6 25.1 1.0
OD1 E:ASP220 3.9 25.8 1.0
OD2 E:ASP220 4.0 25.8 1.0
OD1 E:ASP221 4.2 22.9 1.0
C4 E:HSX402 4.3 25.2 1.0
O2A E:ATP401 4.3 36.2 1.0
O4 E:HSX402 4.4 31.5 1.0
CB E:ASP171 4.4 34.9 1.0
CE1 E:HIS130 4.4 16.9 1.0
CG E:ASP220 4.4 25.8 1.0
O1G E:ATP401 4.4 33.3 1.0
O2G E:ATP401 4.6 42.0 1.0

Reference:

K.L.Hvorecny, J.M.Kollman. Human PRPS1 Filaments Stabilize Allosteric Sites to Regulate Activity Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-00921-Z
Page generated: Fri Oct 4 00:27:21 2024

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