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Magnesium in PDB 7ns5: Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)

Enzymatic activity of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)

All present enzymatic activity of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1):
3.1.3.11;

Protein crystallography data

The structure of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1), PDB code: 7ns5 was solved by D.Sherpa, J.Chrustowicz, J.R.Prabu, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.22 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.018, 133.794, 171.49, 90, 90, 90
R / Rfree (%) 20.8 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1) (pdb code 7ns5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1), PDB code: 7ns5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7ns5

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Magnesium binding site 1 out of 8 in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:45.3
occ:1.00
 OE1 A:GLU292 2.0 36.7 1.0
OD2 A:ASP128 2.0 44.1 1.0
O A:HOH510 2.1 39.0 1.0
O2 A:PO4401 2.1 61.3 0.6
OD1 A:ASP131 2.1 41.0 1.0
OE1 A:GLU108 2.4 48.5 1.0
CD A:GLU292 3.0 38.7 1.0
O1 A:PO4401 3.1 62.4 0.6
CG A:ASP128 3.1 43.2 1.0
CG A:ASP131 3.2 43.2 1.0
OE2 A:GLU292 3.3 46.5 1.0
CD A:GLU108 3.3 52.8 1.0
P A:PO4401 3.4 64.9 0.6
OE2 A:GLU108 3.6 58.0 1.0
CB A:ASP131 3.7 40.7 1.0
CB A:ASP128 3.8 36.9 1.0
MG A:MG403 3.9 48.9 0.6
O A:HOH568 3.9 39.1 1.0
OD1 A:ASP128 4.0 44.1 1.0
CA A:ASP131 4.1 43.8 1.0
O3 A:PO4401 4.2 63.4 0.6
OD2 A:ASP131 4.2 38.3 1.0
CG A:GLU292 4.3 35.5 1.0
O4 A:PO4401 4.5 61.4 0.6
CG A:GLU108 4.6 46.4 1.0

Magnesium binding site 2 out of 8 in 7ns5

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Magnesium binding site 2 out of 8 in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:48.9
occ:0.63
 O1 A:PO4401 2.1 62.4 0.6
OD1 A:ASP128 2.1 44.1 1.0
O A:HOH502 2.1 68.2 1.0
O A:ILE130 2.2 43.6 1.0
OD2 A:ASP128 2.6 44.1 1.0
CG A:ASP128 2.6 43.2 1.0
OE2 A:GLU108 2.8 58.0 1.0
C A:ILE130 3.2 41.3 1.0
P A:PO4401 3.4 64.9 0.6
CD A:GLU108 3.5 52.8 1.0
N A:ASP131 3.8 38.2 1.0
O2 A:PO4401 3.8 61.3 0.6
CA A:ASP131 3.9 43.8 1.0
OE1 A:GLU108 3.9 48.5 1.0
O3 A:PO4401 3.9 63.4 0.6
MG A:MG402 3.9 45.3 1.0
CB A:ASP128 4.2 36.9 1.0
N A:ILE130 4.2 36.1 1.0
OG A:SER133 4.2 56.5 1.0
CA A:ILE130 4.3 38.0 1.0
OE2 A:GLU109 4.3 71.4 1.0
O4 A:PO4401 4.4 61.4 0.6
CG A:GLU108 4.5 46.4 1.0
CB A:GLU108 4.5 45.7 1.0
CB A:ASP131 4.7 40.7 1.0
CA A:ASP128 4.7 36.7 1.0
C A:ASP128 4.8 37.2 1.0
N A:PRO129 4.9 38.0 1.0
OD1 A:ASP131 4.9 41.0 1.0
CB A:ILE130 4.9 42.4 1.0
CD A:GLU109 4.9 71.4 1.0
CD A:PRO129 5.0 38.9 1.0
CG A:GLU109 5.0 67.3 1.0
C A:ASP131 5.0 42.7 1.0

Magnesium binding site 3 out of 8 in 7ns5

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Magnesium binding site 3 out of 8 in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:53.5
occ:1.00
 OD2 D:ASP128 1.9 55.7 1.0
O2 D:PO4401 2.1 60.6 0.6
O D:HOH510 2.1 55.7 1.0
OE2 D:GLU292 2.1 54.7 1.0
OD1 D:ASP131 2.1 48.2 1.0
OE1 D:GLU108 2.1 59.2 1.0
CG D:ASP128 2.9 53.2 1.0
CD D:GLU292 3.0 55.5 1.0
CD D:GLU108 3.2 63.8 1.0
CG D:ASP131 3.2 47.6 1.0
OE1 D:GLU292 3.4 52.4 1.0
O1 D:PO4401 3.4 59.2 0.6
P D:PO4401 3.5 64.0 0.6
OE2 D:GLU108 3.6 69.3 1.0
OD1 D:ASP128 3.7 55.4 1.0
CB D:ASP131 3.8 45.9 1.0
CB D:ASP128 3.9 51.8 1.0
CA D:ASP131 4.1 48.8 1.0
MG D:MG403 4.1 59.0 0.7
CG D:GLU292 4.3 51.4 1.0
OD2 D:ASP131 4.3 47.9 1.0
O4 D:PO4401 4.4 60.6 0.6
O3 D:PO4401 4.4 66.9 0.6
CG D:GLU108 4.5 61.5 1.0
N D:ASP131 5.0 45.0 1.0

Magnesium binding site 4 out of 8 in 7ns5

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Magnesium binding site 4 out of 8 in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:59.0
occ:0.66
 O1 D:PO4401 2.0 59.2 0.6
OD1 D:ASP128 2.1 55.4 1.0
O D:ILE130 2.1 51.7 1.0
O D:HOH501 2.1 70.9 1.0
CG D:ASP128 3.0 53.2 1.0
OE2 D:GLU108 3.1 69.3 1.0
C D:ILE130 3.1 46.9 1.0
OE1 D:GLU109 3.2 81.7 1.0
OD2 D:ASP128 3.2 55.7 1.0
P D:PO4401 3.5 64.0 0.6
CD D:GLU108 3.6 63.8 1.0
O2 D:PO4401 3.6 60.6 0.6
N D:ASP131 3.8 45.0 1.0
OE1 D:GLU108 3.9 59.2 1.0
CA D:ASP131 4.0 48.8 1.0
MG D:MG402 4.1 53.5 1.0
N D:ILE130 4.1 46.4 1.0
CD D:GLU109 4.2 84.1 1.0
CA D:ILE130 4.2 45.5 1.0
O3 D:PO4401 4.2 66.9 0.6
CB D:ASP128 4.4 51.8 1.0
O4 D:PO4401 4.4 60.6 0.6
CB D:GLU108 4.5 62.2 1.0
CG D:GLU108 4.5 61.5 1.0
CG D:GLU109 4.7 80.7 1.0
CB D:ILE130 4.8 43.9 1.0
CA D:ASP128 4.8 51.3 1.0
CB D:SER133 4.8 51.2 1.0
CD D:PRO129 4.8 50.6 1.0
C D:ASP128 4.8 49.4 1.0
N D:PRO129 4.8 48.9 1.0
CB D:ASP131 4.9 45.9 1.0

Magnesium binding site 5 out of 8 in 7ns5

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Magnesium binding site 5 out of 8 in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:44.6
occ:1.00
 OD2 B:ASP128 2.0 43.8 1.0
OE2 B:GLU292 2.1 44.5 1.0
O2 B:PO4401 2.1 37.9 0.6
O B:HOH512 2.1 44.3 1.0
OD1 B:ASP131 2.1 40.8 1.0
OE1 B:GLU108 2.1 48.8 1.0
CD B:GLU108 3.0 50.0 1.0
CD B:GLU292 3.0 41.6 1.0
CG B:ASP128 3.1 42.3 1.0
O3 B:PO4401 3.2 46.8 0.6
CG B:ASP131 3.2 40.4 1.0
OE2 B:GLU108 3.3 56.6 1.0
OE1 B:GLU292 3.3 40.1 1.0
P B:PO4401 3.3 45.7 0.6
CB B:ASP131 3.8 37.6 1.0
CB B:ASP128 3.9 39.4 1.0
MG B:MG403 3.9 46.0 0.6
O4 B:PO4401 4.0 42.0 0.6
OD1 B:ASP128 4.0 43.4 1.0
CA B:ASP131 4.2 40.5 1.0
OD2 B:ASP131 4.3 39.1 1.0
CG B:GLU108 4.4 46.6 1.0
CG B:GLU292 4.4 38.7 1.0
O1 B:PO4401 4.5 49.5 0.6
CG B:ARG288 4.8 43.9 1.0

Magnesium binding site 6 out of 8 in 7ns5

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Magnesium binding site 6 out of 8 in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:46.0
occ:0.56
 O3 B:PO4401 2.1 46.8 0.6
O B:HOH506 2.1 68.3 1.0
O B:ILE130 2.1 41.4 1.0
OD1 B:ASP128 2.2 43.4 1.0
OE2 B:GLU108 2.7 56.6 1.0
OD2 B:ASP128 2.7 43.8 1.0
CG B:ASP128 2.7 42.3 1.0
C B:ILE130 3.1 39.6 1.0
P B:PO4401 3.4 45.7 0.6
O2 B:PO4401 3.5 37.9 0.6
CD B:GLU108 3.5 50.0 1.0
OE1 B:GLU109 3.7 61.5 1.0
N B:ASP131 3.8 35.3 1.0
CA B:ASP131 3.8 40.5 1.0
MG B:MG402 3.9 44.6 1.0
O1 B:PO4401 3.9 49.5 0.6
OE1 B:GLU108 4.0 48.8 1.0
OG B:SER133 4.2 50.0 1.0
OE2 B:GLU109 4.2 67.9 1.0
N B:ILE130 4.2 37.8 1.0
CB B:ASP128 4.2 39.4 1.0
CA B:ILE130 4.2 37.3 1.0
CD B:GLU109 4.4 64.1 1.0
CG B:GLU108 4.5 46.6 1.0
CB B:GLU108 4.6 45.3 1.0
O4 B:PO4401 4.6 42.0 0.6
CB B:ASP131 4.6 37.6 1.0
OD1 B:ASP131 4.8 40.8 1.0
CA B:ASP128 4.8 38.1 1.0
CB B:ILE130 4.8 39.1 1.0
C B:ASP128 4.9 36.9 1.0
C B:ASP131 4.9 38.8 1.0
CB B:SER133 5.0 43.2 1.0

Magnesium binding site 7 out of 8 in 7ns5

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Magnesium binding site 7 out of 8 in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:53.0
occ:1.00
 OD2 C:ASP128 2.0 51.2 1.0
O1 C:PO4401 2.1 50.0 0.6
O C:HOH514 2.1 53.4 1.0
OD1 C:ASP131 2.1 47.1 1.0
OE1 C:GLU108 2.1 55.5 1.0
OE2 C:GLU292 2.1 57.6 1.0
CG C:ASP128 3.1 50.8 1.0
CD C:GLU292 3.1 52.2 1.0
CD C:GLU108 3.1 59.3 1.0
CG C:ASP131 3.2 45.1 1.0
O3 C:PO4401 3.3 53.0 0.6
OE1 C:GLU292 3.4 49.9 1.0
P C:PO4401 3.5 52.5 0.6
OE2 C:GLU108 3.6 68.6 1.0
CB C:ASP131 3.8 46.0 1.0
CB C:ASP128 3.9 48.0 1.0
OD1 C:ASP128 3.9 52.8 1.0
MG C:MG403 4.0 54.3 0.6
CA C:ASP131 4.1 43.5 1.0
O4 C:PO4401 4.2 48.4 0.6
OD2 C:ASP131 4.3 44.4 1.0
CG C:GLU108 4.4 59.1 1.0
CG C:GLU292 4.5 48.2 1.0
O2 C:PO4401 4.6 55.9 0.6
N C:ASP131 5.0 40.9 1.0

Magnesium binding site 8 out of 8 in 7ns5

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Magnesium binding site 8 out of 8 in the Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Yeast FBP1 (Fructose-1,6-Bisphosphatase 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:54.3
occ:0.64
 O3 C:PO4401 2.0 53.0 0.6
O C:HOH501 2.1 65.3 1.0
O C:ILE130 2.1 48.1 1.0
OD1 C:ASP128 2.1 52.8 1.0
OE2 C:GLU108 2.1 68.6 1.0
CG C:ASP128 2.9 50.8 1.0
OD2 C:ASP128 2.9 51.2 1.0
C C:ILE130 3.2 45.0 1.0
CD C:GLU108 3.2 59.3 1.0
OE2 C:GLU109 3.3 85.1 1.0
P C:PO4401 3.4 52.5 0.6
O1 C:PO4401 3.5 50.0 0.6
N C:ASP131 3.8 40.9 1.0
OE1 C:GLU108 3.8 55.5 1.0
CA C:ASP131 4.0 43.5 1.0
OG C:SER133 4.0 51.0 1.0
MG C:MG402 4.0 53.0 1.0
N C:ILE130 4.2 42.2 1.0
O2 C:PO4401 4.2 55.9 0.6
CA C:ILE130 4.3 41.4 1.0
CB C:ASP128 4.3 48.0 1.0
O4 C:PO4401 4.3 48.4 0.6
CG C:GLU108 4.3 59.1 1.0
CD C:GLU109 4.4 86.7 1.0
CB C:GLU108 4.5 56.9 1.0
CG C:GLU109 4.8 81.4 1.0
CA C:ASP128 4.8 45.6 1.0
CB C:ASP131 4.9 46.0 1.0
N C:PRO129 4.9 45.6 1.0
CB C:ILE130 4.9 44.8 1.0
CD C:PRO129 4.9 47.9 1.0
C C:ASP128 4.9 45.1 1.0

Reference:

D.Sherpa, J.Chrustowicz, S.Qiao, C.R.Langlois, L.A.Hehl, K.V.Gottemukkala, F.M.Hansen, O.Karayel, J.R.Prabu, M.Mann, A.F.Alpi, B.A.Schulman. Gid E3 Ligase Supramolecular Chelate Assembly Configures Multipronged Ubiquitin Targeting of An Oligomeric Metabolic Enzyme Mol.Cell 2021.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2021.03.025
Page generated: Thu Oct 3 02:13:11 2024

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