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Magnesium in PDB 8dbn: Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer

Enzymatic activity of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer

All present enzymatic activity of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer:
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-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer (pdb code 8dbn). 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-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer, PDB code: 8dbn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 8dbn

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Magnesium binding site 1 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:22.4
occ:1.00
 NE2 A:HIS130 2.2 20.7 1.0
O1B A:ATP401 2.3 33.6 1.0
O1A A:ATP401 2.3 29.8 1.0
O1G A:ATP401 2.7 33.3 1.0
CD2 A:HIS130 3.1 20.7 1.0
CE1 A:HIS130 3.2 20.7 1.0
PB A:ATP401 3.3 35.6 1.0
PA A:ATP401 3.5 31.5 1.0
O3A A:ATP401 3.6 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 3.9 21.9 1.0
OD1 A:ASP98 4.1 20.6 1.0
OD2 A:ASP98 4.2 20.6 1.0
ND1 A:HIS130 4.3 20.7 1.0
CG A:HIS130 4.3 20.7 1.0
O3G A:ATP401 4.4 38.7 1.0
CE A:LYS99 4.4 21.9 1.0
O5' A:ATP401 4.5 35.2 1.0
CG A:ASP98 4.5 20.6 1.0
C5' A:ATP401 4.5 29.7 1.0
O2A A:ATP401 4.6 36.2 1.0
O A:ARG96 4.7 21.9 1.0
O2B A:ATP401 4.7 36.8 1.0

Magnesium binding site 2 out of 12 in 8dbn

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Magnesium binding site 2 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:30.0
occ:1.00
 OD2 A:ASP171 2.3 25.8 1.0
O3 A:HSX402 2.4 28.6 1.0
O1 A:HSX402 2.7 33.1 1.0
O2 A:HSX402 3.0 31.1 1.0
CG A:ASP171 3.0 25.8 1.0
OD1 A:ASP171 3.0 25.8 1.0
C3 A:HSX402 3.4 26.7 1.0
C2 A:HSX402 3.5 27.3 1.0
OD1 A:ASP220 3.6 25.8 1.0
C1 A:HSX402 3.6 25.1 1.0
OD1 A:ASP221 3.9 25.3 1.0
OD2 A:ASP220 3.9 25.8 1.0
CG A:ASP220 4.2 25.8 1.0
C4 A:HSX402 4.3 25.2 1.0
O4 A:HSX402 4.3 31.5 1.0
N A:GLY174 4.4 25.3 1.0
CB A:ASP171 4.4 25.8 1.0
O2A A:ATP401 4.5 36.2 1.0
O1G A:ATP401 4.6 33.3 1.0
C A:GLY173 4.6 26.0 1.0
O2G A:ATP401 4.7 42.0 1.0
CA A:GLY173 4.7 26.0 1.0
CE1 A:HIS130 5.0 20.7 1.0
N A:GLY173 5.0 26.0 1.0
CG A:ASP221 5.0 25.3 1.0
CA A:GLY174 5.0 25.3 1.0

Magnesium binding site 3 out of 12 in 8dbn

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Magnesium binding site 3 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:22.4
occ:1.00
 NE2 B:HIS130 2.2 20.7 1.0
O1B B:ATP401 2.3 33.6 1.0
O1A B:ATP401 2.3 29.8 1.0
O1G B:ATP401 2.7 33.3 1.0
CD2 B:HIS130 3.1 20.7 1.0
CE1 B:HIS130 3.1 20.7 1.0
PB B:ATP401 3.3 35.6 1.0
PA B:ATP401 3.5 31.5 1.0
O3A B:ATP401 3.6 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 3.9 21.9 1.0
OD1 B:ASP98 4.1 20.6 1.0
OD2 B:ASP98 4.2 20.6 1.0
ND1 B:HIS130 4.3 20.7 1.0
CG B:HIS130 4.3 20.7 1.0
O3G B:ATP401 4.4 38.7 1.0
CE B:LYS99 4.4 21.9 1.0
O5' B:ATP401 4.5 35.2 1.0
CG B:ASP98 4.5 20.6 1.0
C5' B:ATP401 4.5 29.7 1.0
O2A B:ATP401 4.6 36.2 1.0
O B:ARG96 4.7 21.9 1.0
O2B B:ATP401 4.7 36.8 1.0

Magnesium binding site 4 out of 12 in 8dbn

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Magnesium binding site 4 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:30.0
occ:1.00
 OD2 B:ASP171 2.3 25.8 1.0
O3 B:HSX402 2.4 28.6 1.0
O1 B:HSX402 2.7 33.1 1.0
O2 B:HSX402 3.0 31.1 1.0
CG B:ASP171 3.0 25.8 1.0
OD1 B:ASP171 3.0 25.8 1.0
C3 B:HSX402 3.4 26.7 1.0
C2 B:HSX402 3.5 27.3 1.0
OD1 B:ASP220 3.6 25.8 1.0
C1 B:HSX402 3.6 25.1 1.0
OD1 B:ASP221 3.9 25.3 1.0
OD2 B:ASP220 3.9 25.8 1.0
CG B:ASP220 4.2 25.8 1.0
C4 B:HSX402 4.3 25.2 1.0
O4 B:HSX402 4.3 31.5 1.0
N B:GLY174 4.4 25.3 1.0
CB B:ASP171 4.4 25.8 1.0
O2A B:ATP401 4.5 36.2 1.0
O1G B:ATP401 4.6 33.3 1.0
C B:GLY173 4.6 26.0 1.0
O2G B:ATP401 4.7 42.0 1.0
CA B:GLY173 4.7 26.0 1.0
CE1 B:HIS130 5.0 20.7 1.0
N B:GLY173 5.0 26.0 1.0
CG B:ASP221 5.0 25.3 1.0
CA B:GLY174 5.0 25.3 1.0

Magnesium binding site 5 out of 12 in 8dbn

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Magnesium binding site 5 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:22.4
occ:1.00
 NE2 C:HIS130 2.2 20.7 1.0
O1B C:ATP401 2.3 33.6 1.0
O1A C:ATP401 2.3 29.8 1.0
O1G C:ATP401 2.7 33.3 1.0
CD2 C:HIS130 3.1 20.7 1.0
CE1 C:HIS130 3.2 20.7 1.0
PB C:ATP401 3.3 35.6 1.0
PA C:ATP401 3.5 31.5 1.0
O3A C:ATP401 3.6 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 3.9 21.9 1.0
OD1 C:ASP98 4.1 20.6 1.0
OD2 C:ASP98 4.2 20.6 1.0
ND1 C:HIS130 4.3 20.7 1.0
CG C:HIS130 4.3 20.7 1.0
O3G C:ATP401 4.4 38.7 1.0
CE C:LYS99 4.4 21.9 1.0
O5' C:ATP401 4.5 35.2 1.0
CG C:ASP98 4.5 20.6 1.0
C5' C:ATP401 4.5 29.7 1.0
O2A C:ATP401 4.6 36.2 1.0
O C:ARG96 4.7 21.9 1.0
O2B C:ATP401 4.7 36.8 1.0

Magnesium binding site 6 out of 12 in 8dbn

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Magnesium binding site 6 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:30.0
occ:1.00
 OD2 C:ASP171 2.3 25.8 1.0
O3 C:HSX402 2.4 28.6 1.0
O1 C:HSX402 2.7 33.1 1.0
O2 C:HSX402 3.0 31.1 1.0
CG C:ASP171 3.0 25.8 1.0
OD1 C:ASP171 3.0 25.8 1.0
C3 C:HSX402 3.4 26.7 1.0
C2 C:HSX402 3.5 27.3 1.0
OD1 C:ASP220 3.6 25.8 1.0
C1 C:HSX402 3.6 25.1 1.0
OD1 C:ASP221 3.9 25.3 1.0
OD2 C:ASP220 3.9 25.8 1.0
CG C:ASP220 4.2 25.8 1.0
C4 C:HSX402 4.3 25.2 1.0
O4 C:HSX402 4.3 31.5 1.0
N C:GLY174 4.4 25.3 1.0
CB C:ASP171 4.4 25.8 1.0
O2A C:ATP401 4.5 36.2 1.0
O1G C:ATP401 4.6 33.3 1.0
C C:GLY173 4.6 26.0 1.0
O2G C:ATP401 4.7 42.0 1.0
CA C:GLY173 4.7 26.0 1.0
CE1 C:HIS130 5.0 20.7 1.0
N C:GLY173 5.0 26.0 1.0
CG C:ASP221 5.0 25.3 1.0
CA C:GLY174 5.0 25.3 1.0

Magnesium binding site 7 out of 12 in 8dbn

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Magnesium binding site 7 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:22.4
occ:1.00
 NE2 D:HIS130 2.2 20.7 1.0
O1B D:ATP401 2.3 33.6 1.0
O1A D:ATP401 2.3 29.8 1.0
O1G D:ATP401 2.7 33.3 1.0
CD2 D:HIS130 3.1 20.7 1.0
CE1 D:HIS130 3.2 20.7 1.0
PB D:ATP401 3.3 35.6 1.0
PA D:ATP401 3.5 31.5 1.0
O3A D:ATP401 3.6 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 3.9 21.9 1.0
OD1 D:ASP98 4.1 20.6 1.0
OD2 D:ASP98 4.2 20.6 1.0
ND1 D:HIS130 4.3 20.7 1.0
CG D:HIS130 4.3 20.7 1.0
O3G D:ATP401 4.4 38.7 1.0
CE D:LYS99 4.4 21.9 1.0
O5' D:ATP401 4.5 35.2 1.0
CG D:ASP98 4.5 20.6 1.0
C5' D:ATP401 4.5 29.7 1.0
O2A D:ATP401 4.6 36.2 1.0
O D:ARG96 4.7 21.9 1.0
O2B D:ATP401 4.7 36.8 1.0

Magnesium binding site 8 out of 12 in 8dbn

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Magnesium binding site 8 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:30.0
occ:1.00
 OD2 D:ASP171 2.3 25.8 1.0
O3 D:HSX402 2.4 28.6 1.0
O1 D:HSX402 2.7 33.1 1.0
O2 D:HSX402 3.0 31.1 1.0
CG D:ASP171 3.0 25.8 1.0
OD1 D:ASP171 3.0 25.8 1.0
C3 D:HSX402 3.4 26.7 1.0
C2 D:HSX402 3.5 27.3 1.0
OD1 D:ASP220 3.6 25.8 1.0
C1 D:HSX402 3.6 25.1 1.0
OD1 D:ASP221 3.9 25.3 1.0
OD2 D:ASP220 3.9 25.8 1.0
CG D:ASP220 4.2 25.8 1.0
C4 D:HSX402 4.3 25.2 1.0
O4 D:HSX402 4.3 31.5 1.0
N D:GLY174 4.4 25.3 1.0
CB D:ASP171 4.4 25.8 1.0
O2A D:ATP401 4.5 36.2 1.0
O1G D:ATP401 4.6 33.3 1.0
C D:GLY173 4.6 26.0 1.0
O2G D:ATP401 4.7 42.0 1.0
CA D:GLY173 4.7 26.0 1.0
CE1 D:HIS130 5.0 20.7 1.0
N D:GLY173 5.0 26.0 1.0
CG D:ASP221 5.0 25.3 1.0
CA D:GLY174 5.0 25.3 1.0

Magnesium binding site 9 out of 12 in 8dbn

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Magnesium binding site 9 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:22.4
occ:1.00
 NE2 E:HIS130 2.2 20.7 1.0
O1B E:ATP401 2.3 33.6 1.0
O1A E:ATP401 2.3 29.8 1.0
O1G E:ATP401 2.7 33.3 1.0
CD2 E:HIS130 3.1 20.7 1.0
CE1 E:HIS130 3.2 20.7 1.0
PB E:ATP401 3.3 35.6 1.0
PA E:ATP401 3.5 31.5 1.0
O3A E:ATP401 3.6 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 3.9 21.9 1.0
OD1 E:ASP98 4.1 20.6 1.0
OD2 E:ASP98 4.2 20.6 1.0
ND1 E:HIS130 4.3 20.7 1.0
CG E:HIS130 4.3 20.7 1.0
O3G E:ATP401 4.4 38.7 1.0
CE E:LYS99 4.4 21.9 1.0
O5' E:ATP401 4.5 35.2 1.0
CG E:ASP98 4.5 20.6 1.0
C5' E:ATP401 4.5 29.7 1.0
O2A E:ATP401 4.6 36.2 1.0
O E:ARG96 4.7 21.9 1.0
O2B E:ATP401 4.7 36.8 1.0

Magnesium binding site 10 out of 12 in 8dbn

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Magnesium binding site 10 out of 12 in the Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human PRPS1-E307A Engineered Mutation with Phosphate, Atp, and R5P; Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg404

b:30.0
occ:1.00
 OD2 E:ASP171 2.3 25.8 1.0
O3 E:HSX402 2.4 28.6 1.0
O1 E:HSX402 2.7 33.1 1.0
O2 E:HSX402 3.0 31.1 1.0
CG E:ASP171 3.0 25.8 1.0
OD1 E:ASP171 3.0 25.8 1.0
C3 E:HSX402 3.4 26.7 1.0
C2 E:HSX402 3.5 27.3 1.0
OD1 E:ASP220 3.6 25.8 1.0
C1 E:HSX402 3.6 25.1 1.0
OD1 E:ASP221 3.9 25.3 1.0
OD2 E:ASP220 3.9 25.8 1.0
CG E:ASP220 4.2 25.8 1.0
C4 E:HSX402 4.3 25.2 1.0
O4 E:HSX402 4.3 31.5 1.0
N E:GLY174 4.4 25.3 1.0
CB E:ASP171 4.4 25.8 1.0
O2A E:ATP401 4.5 36.2 1.0
O1G E:ATP401 4.6 33.3 1.0
C E:GLY173 4.6 26.0 1.0
O2G E:ATP401 4.7 42.0 1.0
CA E:GLY173 4.7 26.0 1.0
CE1 E:HIS130 5.0 20.7 1.0
N E:GLY173 5.0 26.0 1.0
CG E:ASP221 5.0 25.3 1.0
CA E:GLY174 5.0 25.3 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 00:32:32 2024

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