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Magnesium in PDB 8dbk: Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops

Enzymatic activity of Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops

All present enzymatic activity of Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops:
2.7.6.1;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops (pdb code 8dbk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops, PDB code: 8dbk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 8dbk

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Magnesium binding site 1 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:20.7
occ:1.00
 O A:HOH501 1.9 20.0 1.0
O1A A:ATP401 2.0 29.8 1.0
O A:HOH502 2.1 19.7 1.0
NE2 A:HIS130 2.1 18.4 1.0
O1B A:ATP401 2.2 33.6 1.0
O1G A:ATP401 2.6 33.3 1.0
CD2 A:HIS130 3.0 18.4 1.0
CE1 A:HIS130 3.1 18.4 1.0
PA A:ATP401 3.1 31.5 1.0
PB A:ATP401 3.2 35.6 1.0
O3A A:ATP401 3.3 26.3 1.0
PG A:ATP401 3.7 52.1 1.0
O3B A:ATP401 3.7 32.1 1.0
O5' A:ATP401 4.2 35.2 1.0
ND1 A:HIS130 4.2 18.4 1.0
CG A:HIS130 4.2 18.4 1.0
OD1 A:ASP98 4.2 20.0 1.0
O2A A:ATP401 4.3 36.2 1.0
CE A:LYS99 4.3 21.3 1.0
C5' A:ATP401 4.3 29.7 1.0
NZ A:LYS99 4.3 21.3 1.0
OD2 A:ASP98 4.4 20.0 1.0
O3G A:ATP401 4.4 38.7 1.0
O2B A:ATP401 4.6 36.8 1.0
CG A:ASP98 4.7 20.0 1.0
O A:ARG96 4.8 22.1 0.2
O2G A:ATP401 4.9 42.0 1.0

Magnesium binding site 2 out of 12 in 8dbk

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Magnesium binding site 2 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:28.3
occ:1.00
 OD2 A:ASP171 2.2 33.7 1.0
O3 A:HSX402 2.7 28.6 1.0
O1 A:HSX402 3.1 33.1 1.0
O2 A:HSX402 3.1 31.1 1.0
CG A:ASP171 3.3 33.7 1.0
OD1 A:ASP171 3.7 33.7 1.0
C3 A:HSX402 3.7 26.7 1.0
C2 A:HSX402 3.8 27.3 1.0
C1 A:HSX402 4.0 25.1 1.0
O2G A:ATP401 4.2 42.0 1.0
OD1 A:ASP220 4.3 26.5 1.0
O1G A:ATP401 4.3 33.3 1.0
O2A A:ATP401 4.3 36.2 1.0
OD2 A:ASP220 4.4 26.5 1.0
OD1 A:ASP221 4.4 24.7 1.0
CE1 A:HIS130 4.5 18.4 1.0
CB A:ASP171 4.6 33.7 1.0
C4 A:HSX402 4.7 25.2 1.0
O4 A:HSX402 4.7 31.5 1.0
CG A:ASP220 4.8 26.5 1.0
PG A:ATP401 4.9 52.1 1.0
CA A:GLY173 5.0 33.4 1.0
C A:GLY173 5.0 33.4 1.0

Magnesium binding site 3 out of 12 in 8dbk

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Magnesium binding site 3 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:21.0
occ:1.00
 O B:HOH502 1.9 18.6 1.0
O B:HOH501 2.0 19.1 1.0
O3B B:PRP401 2.2 56.0 1.0
NE2 B:HIS130 2.2 16.8 1.0
O1A B:PRP401 2.3 50.0 1.0
O1P B:AMP402 2.5 20.0 1.0
CE1 B:HIS130 3.0 16.8 1.0
CD2 B:HIS130 3.3 16.8 1.0
PB B:PRP401 3.4 60.1 1.0
PA B:PRP401 3.5 50.3 1.0
O3A B:PRP401 3.6 49.5 1.0
P B:AMP402 3.7 20.0 1.0
C5' B:AMP402 3.8 20.0 1.0
O5' B:AMP402 3.9 20.0 1.0
O1B B:PRP401 4.1 53.3 1.0
ND1 B:HIS130 4.2 16.8 1.0
O3P B:AMP402 4.3 20.0 1.0
CG B:HIS130 4.4 16.8 1.0
OD1 B:ASP98 4.4 20.0 1.0
O1 B:PRP401 4.5 53.6 1.0
O2A B:PRP401 4.6 51.4 1.0
O2B B:PRP401 4.6 50.9 1.0
O B:ARG96 4.6 17.0 0.2
OD2 B:ASP98 4.8 20.0 1.0
C1 B:PRP401 4.9 50.3 1.0
CG B:ASP98 5.0 20.0 1.0

Magnesium binding site 4 out of 12 in 8dbk

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Magnesium binding site 4 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:25.1
occ:1.00
 O1B B:PRP401 1.8 53.3 1.0
O2 B:PRP401 1.8 52.1 1.0
OD2 B:ASP171 2.3 27.8 1.0
OD1 B:ASP171 2.5 27.8 1.0
CG B:ASP171 2.7 27.8 1.0
PB B:PRP401 3.1 60.1 1.0
C2 B:PRP401 3.2 49.1 1.0
O1 B:PRP401 3.3 53.6 1.0
O3 B:PRP401 3.5 52.8 1.0
O3A B:PRP401 3.7 49.5 1.0
OD1 B:ASP220 3.7 23.2 1.0
C1 B:PRP401 3.8 50.3 1.0
O2B B:PRP401 3.8 50.9 1.0
OD1 B:ASP221 3.8 21.3 1.0
C3 B:PRP401 3.9 51.3 1.0
CB B:ASP171 4.1 27.8 1.0
OD2 B:ASP220 4.1 23.2 1.0
PA B:PRP401 4.2 50.3 1.0
CE1 B:HIS130 4.2 16.8 1.0
N B:GLY174 4.3 26.8 1.0
O3B B:PRP401 4.3 56.0 1.0
CA B:GLY173 4.3 26.8 1.0
CG B:ASP220 4.3 23.2 1.0
C B:GLY173 4.5 26.8 1.0
N B:GLY173 4.5 26.8 1.0
NZ B:LYS194 4.7 34.0 1.0
CG B:ASP221 4.7 21.3 1.0
ND1 B:HIS130 4.7 16.8 1.0
O1A B:PRP401 4.8 50.0 1.0
C4 B:PRP401 4.9 47.9 1.0
O4 B:PRP401 5.0 54.8 1.0

Magnesium binding site 5 out of 12 in 8dbk

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Magnesium binding site 5 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops 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 12 in 8dbk

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Magnesium binding site 6 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops 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 12 in 8dbk

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Magnesium binding site 7 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops 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 12 in 8dbk

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Magnesium binding site 8 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops 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 12 in 8dbk

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Magnesium binding site 9 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops 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 12 in 8dbk

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Magnesium binding site 10 out of 12 in the Human PRPS1 with Phosphate, Atp, and R5P; Hexamer with Resolved Catalytic Loops


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; Hexamer with Resolved Catalytic Loops 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 00:27:43 2024

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