Atomistry » Magnesium » PDB 1rtz-1s8f » 1s4e
Atomistry »
  Magnesium »
    PDB 1rtz-1s8f »
      1s4e »

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

Go back to Magnesium Binding Sites List in 1s4e
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

Go back to Magnesium Binding Sites List in 1s4e
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

Go back to Magnesium Binding Sites List in 1s4e
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

Go back to Magnesium Binding Sites List in 1s4e
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

Go back to Magnesium Binding Sites List in 1s4e
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

Go back to Magnesium Binding Sites List in 1s4e
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

Go back to Magnesium Binding Sites List in 1s4e
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

Go back to Magnesium Binding Sites List in 1s4e
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

Go back to Magnesium Binding Sites List in 1s4e
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy