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Magnesium in PDB 4xyj: Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275

Enzymatic activity of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275

All present enzymatic activity of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275:
2.7.1.11;

Protein crystallography data

The structure of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275, PDB code: 4xyj was solved by F.Forouhar, B.A.Webb, F.-E.Szu, J.Seetharaman, D.L.Barber, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.69 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 137.199, 159.329, 170.533, 90.00, 104.20, 90.00
R / Rfree (%) 22.1 / 24.6

Other elements in 4xyj:

The structure of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 (pdb code 4xyj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275, PDB code: 4xyj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 4xyj

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Magnesium binding site 1 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:43.1
occ:1.00
 O3G A:ATP801 1.9 54.3 1.0
OD2 A:ASP128 2.0 66.0 1.0
O2B A:ATP801 2.1 46.3 1.0
OD2 A:ASP177 2.8 67.3 1.0
CG A:ASP128 3.1 63.2 1.0
PG A:ATP801 3.2 53.1 1.0
PB A:ATP801 3.3 47.3 1.0
O3B A:ATP801 3.4 49.5 1.0
NE A:ARG219 3.6 89.8 1.0
OD1 A:ASP128 3.6 65.0 1.0
CG A:ASP177 3.6 65.8 1.0
OD1 A:ASP177 3.7 66.3 1.0
CD A:ARG219 4.0 87.8 1.0
O1G A:ATP801 4.1 54.1 1.0
O2A A:ATP801 4.1 47.9 1.0
O1B A:ATP801 4.2 46.5 1.0
N A:ASP128 4.3 57.6 1.0
O2G A:ATP801 4.4 53.9 1.0
CB A:ASP128 4.4 60.8 1.0
O3A A:ATP801 4.4 48.4 1.0
N A:GLY129 4.4 58.7 1.0
OG A:SER173 4.5 60.0 1.0
CZ A:ARG219 4.5 90.3 1.0
NH2 A:ARG219 4.6 89.9 1.0
PA A:ATP801 4.7 47.1 1.0
OD2 A:ASP175 4.8 71.0 1.0
O1A A:ATP801 4.8 48.1 1.0
C A:GLY127 4.8 57.0 1.0
CA A:GLY127 4.9 56.3 1.0
CA A:ASP128 4.9 58.8 1.0
CB A:ASP175 4.9 65.9 1.0
CG A:ASP175 4.9 69.3 1.0
CG A:ARG219 5.0 85.0 1.0

Magnesium binding site 2 out of 15 in 4xyj

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Magnesium binding site 2 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:18.8
occ:1.00
 O2G A:ATP801 2.2 53.9 1.0
O A:GLY34 2.3 57.6 1.0
O A:GLY172 2.9 54.4 1.0
O A:SER32 3.0 57.5 1.0
N A:GLY34 3.2 56.7 1.0
C A:GLY34 3.3 57.3 1.0
C A:GLY33 3.5 56.1 1.0
PG A:ATP801 3.6 53.1 1.0
O1B A:ATP801 3.7 46.5 1.0
CA A:GLY33 3.7 56.2 1.0
CA A:GLY34 3.8 57.1 1.0
N A:GLY127 3.9 55.5 1.0
CB A:SER173 3.9 58.0 1.0
CE A:MET39 3.9 48.0 1.0
C A:GLY172 4.0 54.1 1.0
O3B A:ATP801 4.0 49.5 1.0
CA A:SER173 4.0 56.5 1.0
C A:SER32 4.0 56.8 1.0
CA A:GLY126 4.2 53.3 1.0
O A:GLY33 4.2 56.1 1.0
OG A:SER173 4.3 60.0 1.0
C A:GLY126 4.3 54.5 1.0
N A:GLY33 4.4 56.6 1.0
O1G A:ATP801 4.4 54.1 1.0
N A:SER173 4.5 55.1 1.0
PB A:ATP801 4.5 47.3 1.0
N A:ASP35 4.5 57.5 1.0
CA A:GLY127 4.7 56.3 1.0
O3G A:ATP801 4.8 54.3 1.0
CA A:ASP35 4.9 57.3 1.0

Magnesium binding site 3 out of 15 in 4xyj

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Magnesium binding site 3 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:13.0
occ:1.00
 OD2 B:ASP128 2.3 59.4 1.0
O1G B:ATP801 2.3 41.1 1.0
O1B B:ATP801 2.3 41.5 1.0
O3B B:ATP801 3.0 38.4 1.0
PG B:ATP801 3.1 37.9 1.0
CG B:ASP128 3.1 58.9 1.0
OD1 B:ASP128 3.3 59.0 1.0
PB B:ATP801 3.3 38.7 1.0
NE B:ARG219 3.5 88.4 1.0
OD2 B:ASP177 3.5 63.9 1.0
O3G B:ATP801 3.7 36.2 1.0
O1A B:ATP801 3.9 40.8 1.0
CD B:ARG219 3.9 86.8 1.0
OD1 B:ASP177 4.1 64.7 1.0
CG B:ASP177 4.2 63.0 1.0
OD2 B:ASP175 4.2 68.9 1.0
O3A B:ATP801 4.3 41.8 1.0
PA B:ATP801 4.4 42.6 1.0
N B:GLY129 4.4 57.6 1.0
O2B B:ATP801 4.4 38.5 1.0
CZ B:ARG219 4.4 89.6 1.0
N B:ASP128 4.4 56.8 1.0
O2A B:ATP801 4.4 42.3 1.0
O2G B:ATP801 4.5 38.2 1.0
CB B:ASP128 4.5 57.8 1.0
OG B:SER173 4.7 59.5 1.0
C B:GLY127 4.9 55.6 1.0
CA B:GLY127 5.0 54.5 1.0
CA B:ASP128 5.0 57.4 1.0
CG B:ARG219 5.0 84.7 1.0
NH2 B:ARG219 5.0 90.1 1.0

Magnesium binding site 4 out of 15 in 4xyj

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Magnesium binding site 4 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:13.6
occ:1.00
 O2G B:ATP801 2.3 38.2 1.0
O B:GLY172 2.8 56.3 1.0
O B:GLY34 2.9 54.9 1.0
O B:SER32 2.9 56.6 1.0
O2B B:ATP801 3.0 38.5 1.0
N B:GLY127 3.3 53.0 1.0
N B:GLY34 3.5 53.8 1.0
CA B:GLY126 3.7 52.4 1.0
PG B:ATP801 3.7 37.9 1.0
CB B:SER173 3.7 57.7 1.0
C B:GLY126 3.8 53.0 1.0
CA B:GLY33 3.8 55.6 1.0
C B:GLY33 3.8 54.7 1.0
C B:GLY172 3.8 55.8 1.0
C B:GLY34 3.9 54.2 1.0
C B:SER32 4.0 56.2 1.0
CE B:MET39 4.0 51.4 1.0
CA B:SER173 4.0 56.5 1.0
PB B:ATP801 4.1 38.7 1.0
O3B B:ATP801 4.1 38.4 1.0
CA B:GLY127 4.1 54.5 1.0
OG B:SER173 4.2 59.5 1.0
O1G B:ATP801 4.3 41.1 1.0
CA B:GLY34 4.3 53.5 1.0
N B:SER173 4.4 56.6 1.0
N B:GLY33 4.4 55.9 1.0
O B:GLY33 4.6 55.1 1.0
O B:GLY126 4.7 53.9 1.0
O3G B:ATP801 4.9 36.2 1.0
N B:GLY126 5.0 50.6 1.0
OG B:SER130 5.0 55.0 1.0

Magnesium binding site 5 out of 15 in 4xyj

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Magnesium binding site 5 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:60.2
occ:1.00
 OD2 C:ASP128 2.2 65.7 1.0
O3G C:ATP801 2.2 79.8 1.0
O2B C:ATP801 2.2 82.3 1.0
O3B C:ATP801 2.5 82.5 1.0
PB C:ATP801 2.9 83.6 1.0
PG C:ATP801 2.9 80.0 1.0
CG C:ASP128 3.3 65.1 1.0
OD2 C:ASP177 3.3 80.9 1.0
O2A C:ATP801 3.4 86.9 1.0
NE C:ARG219 3.5 87.1 1.0
OD1 C:ASP128 3.7 65.1 1.0
O3A C:ATP801 3.8 86.0 1.0
O2G C:ATP801 3.9 78.6 1.0
PA C:ATP801 3.9 87.9 1.0
O1A C:ATP801 4.0 88.6 1.0
CG C:ASP177 4.0 81.1 1.0
O1B C:ATP801 4.1 84.3 1.0
O1G C:ATP801 4.1 80.3 1.0
OD1 C:ASP177 4.1 81.1 1.0
N C:GLY129 4.2 61.8 1.0
CD C:ARG219 4.2 85.0 1.0
N C:ASP128 4.2 61.9 1.0
NH2 C:ARG219 4.3 87.7 1.0
CZ C:ARG219 4.3 87.4 1.0
OD2 C:ASP175 4.4 71.3 1.0
OG C:SER173 4.6 63.5 1.0
CB C:ASP128 4.6 63.7 1.0
C C:GLY127 4.6 60.9 1.0
CA C:GLY127 4.6 60.5 1.0
CA C:ASP128 4.8 62.6 1.0
CA C:GLY129 4.9 60.6 1.0

Magnesium binding site 6 out of 15 in 4xyj

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Magnesium binding site 6 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:34.6
occ:1.00
 O C:GLY172 2.4 59.5 1.0
O1G C:ATP801 2.4 80.3 1.0
O C:GLY34 2.7 58.8 1.0
O C:SER32 2.9 59.7 1.0
O1B C:ATP801 3.3 84.3 1.0
N C:GLY127 3.5 59.8 1.0
C C:GLY172 3.5 59.4 1.0
CE C:MET39 3.6 56.5 1.0
CA C:GLY126 3.6 57.0 1.0
CB C:SER173 3.7 61.5 1.0
N C:GLY34 3.8 59.1 1.0
C C:GLY126 3.8 58.2 1.0
CA C:SER173 3.8 61.4 1.0
PG C:ATP801 3.9 80.0 1.0
C C:GLY34 3.9 59.2 1.0
C C:GLY33 4.0 58.9 1.0
C C:SER32 4.1 59.8 1.0
CA C:GLY33 4.1 59.4 1.0
N C:SER173 4.1 59.8 1.0
CA C:GLY127 4.3 60.5 1.0
OG C:SER173 4.4 63.5 1.0
CA C:GLY34 4.4 59.4 1.0
PB C:ATP801 4.5 83.6 1.0
O3B C:ATP801 4.6 82.5 1.0
N C:GLY33 4.6 60.3 1.0
CA C:GLY172 4.7 58.6 1.0
O C:GLY126 4.7 56.5 1.0
O C:GLY33 4.8 57.2 1.0
O2G C:ATP801 4.8 78.6 1.0
O3G C:ATP801 4.8 79.8 1.0
N C:GLY126 4.8 56.4 1.0
O C:ILE125 5.0 55.8 1.0
N C:ASP35 5.0 59.6 1.0

Magnesium binding site 7 out of 15 in 4xyj

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Magnesium binding site 7 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:37.3
occ:1.00
 OD2 D:ASP128 2.2 60.1 1.0
O1B D:ATP801 2.2 58.9 1.0
O1G D:ATP801 2.2 58.7 1.0
O3B D:ATP801 2.9 58.3 1.0
PG D:ATP801 3.1 55.9 1.0
PB D:ATP801 3.2 58.6 1.0
CG D:ASP128 3.3 59.9 1.0
NE D:ARG219 3.4 87.6 1.0
OD2 D:ASP177 3.7 76.7 1.0
OD1 D:ASP128 3.8 60.4 1.0
CD D:ARG219 4.0 85.7 1.0
O1A D:ATP801 4.1 65.2 1.0
OD1 D:ASP177 4.1 77.4 1.0
OD2 D:ASP175 4.2 72.2 1.0
O2B D:ATP801 4.2 58.2 1.0
O3G D:ATP801 4.2 55.7 1.0
O2G D:ATP801 4.3 55.6 1.0
O3A D:ATP801 4.3 62.3 1.0
N D:ASP128 4.3 59.1 1.0
CG D:ASP177 4.3 75.7 1.0
CZ D:ARG219 4.4 88.0 1.0
N D:GLY129 4.4 60.7 1.0
NH2 D:ARG219 4.4 87.7 1.0
OG D:SER173 4.5 62.3 1.0
O2A D:ATP801 4.5 65.4 1.0
PA D:ATP801 4.5 64.4 1.0
CB D:ASP128 4.5 59.4 1.0
CA D:GLY127 4.7 58.4 1.0
C D:GLY127 4.8 58.7 1.0
CA D:ASP128 4.9 59.6 1.0
CG D:ARG219 5.0 83.5 1.0

Magnesium binding site 8 out of 15 in 4xyj

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Magnesium binding site 8 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg802

b:39.8
occ:1.00
 OD2 E:ASP128 1.9 64.4 1.0
O1G E:ATP801 2.1 81.8 1.0
O1B E:ATP801 2.1 82.4 1.0
O3B E:ATP801 2.8 83.4 1.0
PG E:ATP801 2.9 81.2 1.0
CG E:ASP128 3.0 63.4 1.0
PB E:ATP801 3.0 83.5 1.0
OD2 E:ASP177 3.1 72.8 1.0
OD1 E:ASP128 3.4 64.1 1.0
OD1 E:ASP177 3.8 75.1 1.0
N E:ASP128 3.8 60.7 1.0
CG E:ASP177 3.8 73.0 1.0
O1A E:ATP801 3.9 85.7 1.0
NE E:ARG219 3.9 88.9 1.0
O3G E:ATP801 4.0 80.7 1.0
O2B E:ATP801 4.0 84.2 1.0
N E:GLY129 4.0 60.4 1.0
O3A E:ATP801 4.1 84.3 1.0
O2G E:ATP801 4.1 79.7 1.0
CB E:ASP128 4.2 61.5 1.0
C E:GLY127 4.3 59.8 1.0
CA E:GLY127 4.3 59.2 1.0
OG E:SER173 4.3 58.2 1.0
OD2 E:ASP175 4.4 70.4 1.0
CD E:ARG219 4.5 86.5 1.0
PA E:ATP801 4.5 85.4 1.0
CA E:ASP128 4.5 60.7 1.0
O2A E:ATP801 4.8 84.4 1.0
C E:ASP128 4.8 60.5 1.0
NH2 E:ARG219 4.8 89.5 1.0
CZ E:ARG219 4.8 89.2 1.0
CA E:GLY129 4.9 60.0 1.0
CB E:SER173 4.9 58.4 1.0

Magnesium binding site 9 out of 15 in 4xyj

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Magnesium binding site 9 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg803

b:40.7
occ:1.00
 O2G E:ATP801 2.3 79.7 1.0
O2B E:ATP801 2.7 84.2 1.0
O E:GLY172 2.8 57.8 1.0
O E:GLY34 2.9 58.7 1.0
O E:SER32 3.0 58.8 1.0
N E:GLY127 3.4 57.5 1.0
N E:GLY34 3.5 60.1 1.0
CB E:SER173 3.6 58.4 1.0
PG E:ATP801 3.7 81.2 1.0
CA E:GLY33 3.8 59.1 1.0
C E:GLY172 3.8 57.6 1.0
C E:GLY33 3.8 59.3 1.0
CA E:GLY126 3.8 56.5 1.0
C E:GLY126 3.9 56.8 1.0
C E:GLY34 3.9 58.7 1.0
CA E:SER173 3.9 59.5 1.0
PB E:ATP801 3.9 83.5 1.0
CE E:MET39 4.1 50.9 1.0
C E:SER32 4.1 58.8 1.0
OG E:SER173 4.1 58.2 1.0
CA E:GLY127 4.1 59.2 1.0
CA E:GLY34 4.2 59.4 1.0
O3B E:ATP801 4.3 83.4 1.0
N E:SER173 4.3 58.7 1.0
O1G E:ATP801 4.3 81.8 1.0
N E:GLY33 4.4 58.5 1.0
O E:GLY33 4.7 59.2 1.0
O1B E:ATP801 4.8 82.4 1.0
O E:GLY126 4.8 57.1 1.0
O3G E:ATP801 4.8 80.7 1.0

Magnesium binding site 10 out of 15 in 4xyj

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Magnesium binding site 10 out of 15 in the Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Human Phosphofructokinase-1 in Complex with Atp and Mg, Northeast Structural Genomics Consortium Target HR9275 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg802

b:54.1
occ:1.00
 OD2 F:ASP128 2.1 64.1 1.0
O2B F:ATP801 2.1 47.2 1.0
O3G F:ATP801 2.2 49.7 1.0
OD2 F:ASP177 2.8 69.1 1.0
CG F:ASP128 3.0 62.5 1.0
OD1 F:ASP128 3.3 63.8 1.0
PB F:ATP801 3.3 48.1 1.0
O3B F:ATP801 3.4 48.7 1.0
NE F:ARG219 3.4 87.3 1.0
PG F:ATP801 3.4 46.4 1.0
CG F:ASP177 3.7 69.5 1.0
CD F:ARG219 3.9 85.5 1.0
OD1 F:ASP177 3.9 71.2 1.0
OD2 F:ASP175 4.1 70.7 1.0
O2A F:ATP801 4.2 51.5 1.0
O1B F:ATP801 4.2 46.0 1.0
O1G F:ATP801 4.3 48.4 1.0
CZ F:ARG219 4.3 88.0 1.0
N F:ASP128 4.4 60.7 1.0
O3A F:ATP801 4.4 49.7 1.0
N F:GLY129 4.4 58.2 1.0
CB F:ASP128 4.4 60.3 1.0
O2G F:ATP801 4.5 48.4 1.0
OG F:SER173 4.6 59.4 1.0
PA F:ATP801 4.7 52.9 1.0
O1A F:ATP801 4.8 51.4 1.0
NH2 F:ARG219 4.8 87.8 1.0
CG F:ARG219 4.9 84.0 1.0
CA F:ASP128 4.9 59.9 1.0
C F:GLY127 4.9 59.5 1.0
CG F:ASP175 5.0 69.6 1.0
CB F:ASP177 5.0 68.5 1.0
CA F:GLY127 5.0 57.9 1.0

Reference:

B.A.Webb, F.Forouhar, F.-E.Szu, J.Seetharaman, L.Tong, D.L.Barber. Structures of Human Phosphofructokinase-1 and Atomic Basis of Cancer-Associated Mutations To Be Published.
Page generated: Tue Aug 20 16:03:32 2024

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