Magnesium in PDB 8w2j: Human Liver Phosphofructokinase-1 Filament in the T-State Conformation

Enzymatic activity of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation

All present enzymatic activity of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation:
2.7.1.11;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation (pdb code 8w2j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation, PDB code: 8w2j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8w2j

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Magnesium binding site 1 out of 8 in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg805

b:102.0
occ:1.00
O3B E:ATP803 2.0 108.1 1.0
O2B E:ATP803 2.1 108.1 1.0
O2G E:ATP803 2.1 108.1 1.0
PB E:ATP803 2.4 108.1 1.0
PG E:ATP803 2.4 108.1 1.0
OD1 E:ASP119 2.6 104.7 1.0
O3A E:ATP803 3.4 108.1 1.0
H E:GLY120 3.4 105.5 1.0
H E:ASP119 3.4 104.7 1.0
O3G E:ATP803 3.4 108.1 1.0
HA3 E:GLY118 3.4 100.0 1.0
O1G E:ATP803 3.6 108.1 1.0
O1B E:ATP803 3.6 108.1 1.0
CG E:ASP119 3.8 104.7 1.0
N E:ASP119 4.0 104.7 1.0
N E:GLY120 4.2 105.5 1.0
CA E:GLY118 4.3 100.0 1.0
OD2 E:ASP119 4.4 104.7 1.0
C E:GLY118 4.5 100.0 1.0
HH21 E:ARG88 4.6 105.2 1.0
HA3 E:GLY120 4.7 105.5 1.0
PA E:ATP803 4.7 108.1 1.0
OD1 E:ASP166 4.8 94.4 1.0
HB2 E:SER164 4.8 88.3 1.0
HA2 E:GLY118 4.8 100.0 1.0
CB E:ASP119 4.8 104.7 1.0
CA E:ASP119 4.8 104.7 1.0
HB3 E:SER164 4.9 88.3 1.0
O2A E:ATP803 4.9 108.1 1.0
CG E:ASP166 5.0 94.4 1.0
H E:GLY118 5.0 100.0 1.0

Magnesium binding site 2 out of 8 in 8w2j

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Magnesium binding site 2 out of 8 in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg805

b:125.9
occ:1.00
O2B F:ATP803 2.0 128.8 1.0
O2G F:ATP803 2.1 128.8 1.0
O3B F:ATP803 2.2 128.8 1.0
OD1 F:ASP119 2.4 127.4 1.0
PG F:ATP803 2.4 128.8 1.0
PB F:ATP803 2.5 128.8 1.0
H F:ASP119 3.0 127.4 1.0
O3G F:ATP803 3.1 128.8 1.0
HA3 F:GLY118 3.1 123.8 1.0
H F:GLY120 3.1 128.5 1.0
O3A F:ATP803 3.4 128.8 1.0
CG F:ASP119 3.5 127.4 1.0
N F:ASP119 3.6 127.4 1.0
O1B F:ATP803 3.7 128.8 1.0
O1G F:ATP803 3.8 128.8 1.0
CA F:GLY118 3.9 123.8 1.0
N F:GLY120 4.0 128.5 1.0
C F:GLY118 4.1 123.8 1.0
OD2 F:ASP119 4.3 127.4 1.0
HA2 F:GLY118 4.4 123.8 1.0
CA F:ASP119 4.5 127.4 1.0
CB F:ASP119 4.5 127.4 1.0
O2A F:ATP803 4.6 128.8 1.0
HA3 F:GLY120 4.6 128.5 1.0
H F:GLY118 4.7 123.8 1.0
PA F:ATP803 4.7 128.8 1.0
HB2 F:SER164 4.7 107.9 1.0
HB3 F:SER164 4.7 107.9 1.0
HB3 F:ASP119 4.8 127.4 1.0
C F:ASP119 4.8 127.4 1.0
H F:SER121 4.8 125.0 1.0
OD1 F:ASP166 4.8 110.5 1.0
HH21 F:ARG88 4.8 126.1 1.0
N F:GLY118 4.9 123.8 1.0
CA F:GLY120 4.9 128.5 1.0
H F:GLY25 5.0 113.6 1.0

Magnesium binding site 3 out of 8 in 8w2j

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Magnesium binding site 3 out of 8 in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg805

b:67.7
occ:1.00
OD1 G:ASP119 2.0 72.8 1.0
O2B G:ATP803 2.1 73.6 1.0
O2G G:ATP803 2.1 73.6 1.0
PG G:ATP803 3.2 73.6 1.0
CG G:ASP119 3.2 72.8 1.0
PB G:ATP803 3.2 73.6 1.0
H G:ASP119 3.3 72.8 1.0
O3B G:ATP803 3.5 73.6 1.0
H G:GLY120 3.6 73.1 1.0
OD2 G:ASP119 3.8 72.8 1.0
O1G G:ATP803 3.9 73.6 1.0
HA3 G:GLY118 3.9 68.6 1.0
N G:ASP119 4.0 72.8 1.0
O2A G:ATP803 4.1 73.6 1.0
O3A G:ATP803 4.2 73.6 1.0
O1B G:ATP803 4.2 73.6 1.0
O3G G:ATP803 4.3 73.6 1.0
CB G:ASP119 4.4 72.8 1.0
HB3 G:ASP168 4.4 70.8 1.0
N G:GLY120 4.4 73.1 1.0
HB3 G:ASP119 4.5 72.8 1.0
HB2 G:ASP166 4.6 62.6 1.0
HD2 G:HIS211 4.6 68.1 1.0
OD1 G:ASP166 4.7 62.6 1.0
CA G:ASP119 4.7 72.8 1.0
CG G:ASP166 4.7 62.6 1.0
CA G:GLY118 4.7 68.6 1.0
PA G:ATP803 4.8 73.6 1.0
C G:GLY118 4.8 68.6 1.0
OD2 G:ASP166 4.9 62.6 1.0
HB2 G:SER164 4.9 58.9 1.0
OD2 G:ASP168 5.0 70.8 1.0
HB2 G:ASP168 5.0 70.8 1.0

Magnesium binding site 4 out of 8 in 8w2j

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Magnesium binding site 4 out of 8 in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg805

b:78.2
occ:1.00
O2B H:ATP803 2.0 85.5 1.0
O2G H:ATP803 2.2 85.5 1.0
O1G H:ATP803 2.2 85.5 1.0
PG H:ATP803 2.4 85.5 1.0
PB H:ATP803 2.7 85.5 1.0
O3B H:ATP803 2.8 85.5 1.0
OD1 H:ASP119 3.0 82.5 1.0
O3A H:ATP803 3.6 85.5 1.0
HA3 H:GLY118 3.6 78.6 1.0
H H:ASP119 3.8 82.5 1.0
O3G H:ATP803 3.8 85.5 1.0
O1B H:ATP803 3.9 85.5 1.0
H H:GLY120 4.0 83.8 1.0
CG H:ASP119 4.2 82.5 1.0
OD1 H:ASP166 4.3 72.0 1.0
N H:ASP119 4.4 82.5 1.0
HH21 H:ARG88 4.4 83.0 1.0
CG H:ASP166 4.5 72.0 1.0
CA H:GLY118 4.5 78.6 1.0
OD2 H:ASP166 4.6 72.0 1.0
HB2 H:SER164 4.8 67.8 1.0
OD2 H:ASP119 4.8 82.5 1.0
N H:GLY120 4.8 83.8 1.0
HB2 H:ASP166 4.9 72.0 1.0
PA H:ATP803 4.9 85.5 1.0
C H:GLY118 4.9 78.6 1.0
HA2 H:GLY118 4.9 78.6 1.0
H H:GLY25 5.0 72.6 1.0
O2A H:ATP803 5.0 85.5 1.0

Magnesium binding site 5 out of 8 in 8w2j

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Magnesium binding site 5 out of 8 in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:78.7
occ:1.00
O2B A:ATP803 2.0 86.2 1.0
O1G A:ATP803 2.2 86.2 1.0
O2G A:ATP803 2.2 86.2 1.0
PG A:ATP803 2.4 86.2 1.0
PB A:ATP803 2.7 86.2 1.0
O3B A:ATP803 2.8 86.2 1.0
OD1 A:ASP119 3.0 83.6 1.0
O3A A:ATP803 3.5 86.2 1.0
HA3 A:GLY118 3.6 79.2 1.0
H A:ASP119 3.8 83.6 1.0
O3G A:ATP803 3.8 86.2 1.0
O1B A:ATP803 3.9 86.2 1.0
H A:GLY120 4.0 84.7 1.0
CG A:ASP119 4.2 83.6 1.0
OD1 A:ASP166 4.3 72.3 1.0
N A:ASP119 4.4 83.6 1.0
CG A:ASP166 4.5 72.3 1.0
HH21 A:ARG88 4.5 84.0 1.0
CA A:GLY118 4.5 79.2 1.0
OD2 A:ASP166 4.5 72.3 1.0
HB2 A:SER164 4.8 68.4 1.0
N A:GLY120 4.8 84.7 1.0
OD2 A:ASP119 4.9 83.6 1.0
HB2 A:ASP166 4.9 72.3 1.0
PA A:ATP803 4.9 86.2 1.0
C A:GLY118 4.9 79.2 1.0
HA2 A:GLY118 4.9 79.2 1.0
H A:GLY25 5.0 72.6 1.0
O2A A:ATP803 5.0 86.2 1.0

Magnesium binding site 6 out of 8 in 8w2j

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Magnesium binding site 6 out of 8 in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg805

b:71.1
occ:1.00
OD1 B:ASP119 2.0 73.1 1.0
O2B B:ATP803 2.1 74.0 1.0
O2G B:ATP803 2.1 74.0 1.0
PG B:ATP803 3.2 74.0 1.0
CG B:ASP119 3.2 73.1 1.0
PB B:ATP803 3.2 74.0 1.0
H B:ASP119 3.3 73.1 1.0
O3B B:ATP803 3.5 74.0 1.0
H B:GLY120 3.6 73.5 1.0
OD2 B:ASP119 3.8 73.1 1.0
HA3 B:GLY118 3.9 68.6 1.0
O1G B:ATP803 3.9 74.0 1.0
N B:ASP119 4.0 73.1 1.0
O2A B:ATP803 4.0 74.0 1.0
O3A B:ATP803 4.2 74.0 1.0
O1B B:ATP803 4.2 74.0 1.0
O3G B:ATP803 4.3 74.0 1.0
CB B:ASP119 4.4 73.1 1.0
HB3 B:ASP168 4.4 70.6 1.0
N B:GLY120 4.4 73.5 1.0
HB3 B:ASP119 4.5 73.1 1.0
HB2 B:ASP166 4.6 62.2 1.0
HD2 B:HIS211 4.6 68.0 1.0
CA B:ASP119 4.7 73.1 1.0
OD1 B:ASP166 4.7 62.2 1.0
CG B:ASP166 4.7 62.2 1.0
CA B:GLY118 4.7 68.6 1.0
PA B:ATP803 4.8 74.0 1.0
C B:GLY118 4.8 68.6 1.0
OD2 B:ASP166 4.9 62.2 1.0
HB2 B:SER164 4.9 58.7 1.0
HB2 B:ASP168 5.0 70.6 1.0

Magnesium binding site 7 out of 8 in 8w2j

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Magnesium binding site 7 out of 8 in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg805

b:127.2
occ:1.00
O2B C:ATP803 2.0 128.9 1.0
O2G C:ATP803 2.1 128.9 1.0
O3B C:ATP803 2.2 128.9 1.0
OD1 C:ASP119 2.4 127.8 1.0
PG C:ATP803 2.4 128.9 1.0
PB C:ATP803 2.5 128.9 1.0
H C:ASP119 3.1 127.8 1.0
O3G C:ATP803 3.1 128.9 1.0
HA3 C:GLY118 3.1 124.1 1.0
H C:GLY120 3.2 128.6 1.0
O3A C:ATP803 3.4 128.9 1.0
CG C:ASP119 3.6 127.8 1.0
N C:ASP119 3.6 127.8 1.0
O1B C:ATP803 3.7 128.9 1.0
O1G C:ATP803 3.7 128.9 1.0
CA C:GLY118 4.0 124.1 1.0
N C:GLY120 4.0 128.6 1.0
C C:GLY118 4.2 124.1 1.0
OD2 C:ASP119 4.3 127.8 1.0
HA2 C:GLY118 4.5 124.1 1.0
CA C:ASP119 4.5 127.8 1.0
CB C:ASP119 4.6 127.8 1.0
O2A C:ATP803 4.6 128.9 1.0
PA C:ATP803 4.6 128.9 1.0
HA3 C:GLY120 4.7 128.6 1.0
HB2 C:SER164 4.7 107.8 1.0
H C:GLY118 4.7 124.1 1.0
HH21 C:ARG88 4.7 125.9 1.0
HB3 C:SER164 4.7 107.8 1.0
OD1 C:ASP166 4.8 110.4 1.0
HB3 C:ASP119 4.8 127.8 1.0
H C:SER121 4.8 125.5 1.0
C C:ASP119 4.8 127.8 1.0
N C:GLY118 4.9 124.1 1.0
CA C:GLY120 5.0 128.6 1.0
H C:GLY25 5.0 113.3 1.0

Magnesium binding site 8 out of 8 in 8w2j

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Magnesium binding site 8 out of 8 in the Human Liver Phosphofructokinase-1 Filament in the T-State Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Liver Phosphofructokinase-1 Filament in the T-State Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg805

b:102.7
occ:1.00
O3B D:ATP803 2.0 109.0 1.0
O2B D:ATP803 2.1 109.0 1.0
O2G D:ATP803 2.1 109.0 1.0
PB D:ATP803 2.4 109.0 1.0
PG D:ATP803 2.4 109.0 1.0
OD1 D:ASP119 2.6 104.8 1.0
O3A D:ATP803 3.4 109.0 1.0
H D:GLY120 3.4 106.1 1.0
O3G D:ATP803 3.4 109.0 1.0
H D:ASP119 3.4 104.8 1.0
HA3 D:GLY118 3.5 100.3 1.0
O1G D:ATP803 3.6 109.0 1.0
O1B D:ATP803 3.6 109.0 1.0
CG D:ASP119 3.7 104.8 1.0
N D:ASP119 4.0 104.8 1.0
N D:GLY120 4.2 106.1 1.0
CA D:GLY118 4.3 100.3 1.0
OD2 D:ASP119 4.4 104.8 1.0
C D:GLY118 4.6 100.3 1.0
HH21 D:ARG88 4.6 106.2 1.0
HA3 D:GLY120 4.7 106.1 1.0
PA D:ATP803 4.7 109.0 1.0
HB2 D:SER164 4.8 88.7 1.0
OD1 D:ASP166 4.8 94.8 1.0
CB D:ASP119 4.8 104.8 1.0
CA D:ASP119 4.8 104.8 1.0
HA2 D:GLY118 4.8 100.3 1.0
HB3 D:SER164 4.9 88.7 1.0
O2A D:ATP803 4.9 109.0 1.0

Reference:

E.M.Lynch, H.Hansen, L.Salay, M.Cooper, S.Timr, J.M.Kollman, B.A.Webb. Structural Basis For Allosteric Regulation of Human Phosphofructokinase-1 Nat Commun V. 15 7323 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-51808-6
Page generated: Fri Oct 4 22:17:15 2024

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