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Magnesium in PDB 1s4e: Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium

Enzymatic activity of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium

All present enzymatic activity of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium:
2.7.1.6;

Protein crystallography data

The structure of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium, PDB code: 1s4e was solved by A.Hartley, S.E.Glynn, V.Barynin, P.J.Baker, S.E.Sedelnikova, C.Verhees, D.De Geus, J.Van Der Oost, D.J.Timson, R.J.Reece, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.974, 355.672, 165.613, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 27

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium (pdb code 1s4e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium, PDB code: 1s4e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 1s4e

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Magnesium binding site 1 out of 9 in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:47.0
occ:1.00
 O2A A:ADP400 2.2 51.3 1.0
OG A:SER107 2.2 70.0 1.0
O1B A:ADP400 2.3 56.3 1.0
O3B A:ADP400 2.8 58.9 1.0
PB A:ADP400 3.0 59.1 1.0
PA A:ADP400 3.3 51.8 1.0
CB A:SER107 3.3 66.8 1.0
O3A A:ADP400 3.4 56.1 1.0
O1A A:ADP400 4.1 51.0 1.0
OG A:SER105 4.1 58.3 1.0
CA A:SER105 4.2 58.6 1.0
O2B A:ADP400 4.5 59.0 1.0
N A:SER107 4.5 66.1 1.0
OD2 A:ASP151 4.5 55.2 1.0
CA A:SER107 4.5 67.2 1.0
OE2 A:GLU139 4.6 71.2 1.0
O5' A:ADP400 4.6 52.8 1.0
CB A:SER105 4.6 56.9 1.0
C A:SER105 4.9 59.8 1.0

Magnesium binding site 2 out of 9 in 1s4e

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Magnesium binding site 2 out of 9 in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1600

b:55.9
occ:1.00
 O1B B:ADP1400 2.2 65.8 1.0
OG B:SER107 2.2 96.3 1.0
O2A B:ADP1400 2.2 63.3 1.0
O3B B:ADP1400 2.7 68.6 1.0
PB B:ADP1400 2.8 70.2 1.0
CB B:SER107 3.2 92.9 1.0
PA B:ADP1400 3.3 68.6 1.0
O3A B:ADP1400 3.4 66.7 1.0
OG B:SER105 3.8 81.5 1.0
CA B:SER105 3.8 86.5 1.0
N B:SER107 4.1 96.3 1.0
O2B B:ADP1400 4.2 70.6 1.0
CB B:SER105 4.3 82.2 1.0
CA B:SER107 4.3 95.8 1.0
O1A B:ADP1400 4.3 64.0 1.0
C B:SER105 4.5 90.0 1.0
O5' B:ADP1400 4.5 68.8 1.0
OE2 B:GLU139 4.7 87.2 1.0
N B:SER106 4.7 94.2 1.0
N B:SER105 4.7 87.1 1.0
OD2 B:ASP151 4.8 69.1 1.0
C5' B:ADP1400 4.9 67.2 1.0

Magnesium binding site 3 out of 9 in 1s4e

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Magnesium binding site 3 out of 9 in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2600

b:51.2
occ:1.00
 O2A C:ADP2400 2.1 58.9 1.0
OG C:SER107 2.2 81.5 1.0
O1B C:ADP2400 2.2 59.5 1.0
CB C:SER107 3.3 76.8 1.0
PA C:ADP2400 3.3 60.3 1.0
PB C:ADP2400 3.3 62.1 1.0
O3B C:ADP2400 3.7 60.5 1.0
O3A C:ADP2400 3.8 59.5 1.0
O1A C:ADP2400 3.9 60.8 1.0
CA C:SER105 4.3 76.1 1.0
OD2 C:ASP151 4.4 66.2 1.0
N C:SER107 4.4 78.7 1.0
CA C:SER107 4.5 77.7 1.0
O5' C:ADP2400 4.6 59.8 1.0
OG C:SER105 4.7 72.2 1.0
O2B C:ADP2400 4.7 63.6 1.0
CB C:SER105 4.7 73.2 1.0

Magnesium binding site 4 out of 9 in 1s4e

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Magnesium binding site 4 out of 9 in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3600

b:44.7
occ:1.00
 O2A D:ADP3400 2.1 48.6 1.0
OG D:SER107 2.2 62.8 1.0
O1B D:ADP3400 2.2 52.0 1.0
O3B D:ADP3400 3.2 54.4 1.0
PB D:ADP3400 3.3 51.4 1.0
CB D:SER107 3.4 58.5 1.0
PA D:ADP3400 3.5 49.9 1.0
O3A D:ADP3400 4.0 51.0 1.0
OG D:SER105 4.1 54.3 1.0
OD2 D:ASP151 4.2 55.0 1.0
CA D:SER105 4.3 56.1 1.0
O1A D:ADP3400 4.3 51.1 1.0
OE2 D:GLU139 4.4 63.9 1.0
O2B D:ADP3400 4.6 53.4 1.0
N D:SER107 4.6 57.8 1.0
CA D:SER107 4.6 57.9 1.0
O5' D:ADP3400 4.6 50.9 1.0
CB D:SER105 4.7 54.4 1.0
N D:SER105 5.0 57.7 1.0

Magnesium binding site 5 out of 9 in 1s4e

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Magnesium binding site 5 out of 9 in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg4600

b:47.1
occ:1.00
 O2A E:ADP4400 2.1 49.6 1.0
OG E:SER107 2.2 64.2 1.0
O1B E:ADP4400 2.3 55.6 1.0
O3B E:ADP4400 2.8 56.8 1.0
PB E:ADP4400 3.1 55.8 1.0
CB E:SER107 3.4 56.6 1.0
PA E:ADP4400 3.4 50.6 1.0
O3A E:ADP4400 3.8 52.8 1.0
CA E:SER105 4.1 57.6 1.0
OG E:SER105 4.2 57.1 1.0
OD2 E:ASP151 4.3 67.9 1.0
O1A E:ADP4400 4.4 49.9 1.0
O5' E:ADP4400 4.5 53.5 1.0
N E:SER107 4.5 54.1 1.0
O2B E:ADP4400 4.6 57.0 1.0
CA E:SER107 4.6 54.5 1.0
OE2 E:GLU139 4.6 66.8 1.0
CB E:SER105 4.6 59.4 1.0
N E:SER105 4.8 58.8 1.0
C E:SER105 4.9 55.6 1.0

Magnesium binding site 6 out of 9 in 1s4e

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Magnesium binding site 6 out of 9 in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg5600

b:32.5
occ:1.00
 O2A F:ADP5400 2.1 32.8 1.0
OG F:SER107 2.2 44.9 1.0
O1B F:ADP5400 2.4 35.7 1.0
O3B F:ADP5400 3.0 31.5 1.0
PB F:ADP5400 3.1 30.5 1.0
PA F:ADP5400 3.2 31.1 1.0
O3A F:ADP5400 3.5 35.8 1.0
CB F:SER107 3.6 39.8 1.0
O1A F:ADP5400 4.0 30.6 1.0
O5' F:ADP5400 4.5 33.4 1.0
O2B F:ADP5400 4.6 38.0 1.0
OE2 F:GLU139 4.6 54.6 1.0
CA F:SER105 4.7 39.5 1.0
N F:SER107 4.8 37.9 1.0
CA F:SER107 4.8 37.9 1.0
OD2 F:ASP151 4.8 48.6 1.0
OG F:SER105 5.0 39.8 1.0

Magnesium binding site 7 out of 9 in 1s4e

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Magnesium binding site 7 out of 9 in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg6600

b:60.6
occ:1.00
 O1B G:ADP6400 2.2 73.1 1.0
OG G:SER107 2.2 0.9 1.0
O2A G:ADP6400 2.2 67.8 1.0
CB G:SER107 2.9 0.6 1.0
PB G:ADP6400 3.2 76.2 1.0
PA G:ADP6400 3.4 74.5 1.0
O3A G:ADP6400 3.5 72.6 1.0
O3B G:ADP6400 3.5 72.7 1.0
OG G:SER105 3.7 0.3 1.0
CA G:SER107 4.0 0.6 1.0
N G:SER107 4.0 0.7 1.0
O5' G:ADP6400 4.2 70.2 1.0
O2B G:ADP6400 4.5 72.8 1.0
O1A G:ADP6400 4.6 69.8 1.0
CB G:SER105 4.6 0.9 1.0
OD2 G:ASP151 4.8 0.3 1.0
C5' G:ADP6400 4.8 70.2 1.0

Magnesium binding site 8 out of 9 in 1s4e

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Magnesium binding site 8 out of 9 in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg7600

b:44.1
occ:1.00
 O2A H:ADP7400 2.1 42.9 1.0
OG H:SER107 2.2 49.2 1.0
O1B H:ADP7400 2.3 47.2 1.0
O3B H:ADP7400 2.7 45.6 1.0
PB H:ADP7400 2.9 45.2 1.0
PA H:ADP7400 3.1 41.8 1.0
O3A H:ADP7400 3.2 44.3 1.0
CB H:SER107 3.4 43.5 1.0
O5' H:ADP7400 4.0 46.4 1.0
O1A H:ADP7400 4.3 40.4 1.0
O2B H:ADP7400 4.3 47.4 1.0
N H:SER107 4.4 42.6 1.0
CA H:SER105 4.4 47.9 1.0
CA H:SER107 4.5 43.0 1.0
OE2 H:GLU139 4.6 57.6 1.0
OG H:SER105 4.6 51.7 1.0
OD2 H:ASP151 4.9 48.4 1.0
C H:SER105 5.0 46.0 1.0

Magnesium binding site 9 out of 9 in 1s4e

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Magnesium binding site 9 out of 9 in the Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pyrococcus Furiosus Galactokinase in Complex with Galactose, Adp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg8600

b:35.5
occ:1.00
 O2A I:ADP8400 2.1 34.2 1.0
OG I:SER107 2.3 39.8 1.0
O1B I:ADP8400 2.4 35.2 1.0
O3B I:ADP8400 2.7 37.9 1.0
PB I:ADP8400 2.9 31.3 1.0
PA I:ADP8400 3.2 32.9 1.0
O3A I:ADP8400 3.3 36.3 1.0
CB I:SER107 3.6 34.5 1.0
O1A I:ADP8400 3.9 34.8 1.0
O2B I:ADP8400 4.4 38.0 1.0
CA I:SER105 4.4 34.4 1.0
OD2 I:ASP151 4.5 38.4 1.0
O5' I:ADP8400 4.5 35.6 1.0
N I:SER107 4.6 32.3 1.0
OG I:SER105 4.7 34.8 1.0
CA I:SER107 4.7 32.9 1.0
OE2 I:GLU139 5.0 53.1 1.0
CB I:SER105 5.0 34.6 1.0

Reference:

A.Hartley, S.E.Glynn, V.Barynin, P.J.Baker, S.E.Sedelnikova, C.Verhees, D.De Geus, J.Van Der Oost, D.J.Timson, R.J.Reece, D.W.Rice. Substrate Specificity and Mechanism From the Structure of Pyrococcus Furiosus Galactokinase J.Mol.Biol. V. 337 387 2004.
ISSN: ISSN 0022-2836
PubMed: 15003454
DOI: 10.1016/J.JMB.2004.01.043
Page generated: Tue Aug 13 13:15:17 2024

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