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Magnesium in PDB 2ejw: Homoserine Dehydrogenase From Thermus Thermophilus HB8

Enzymatic activity of Homoserine Dehydrogenase From Thermus Thermophilus HB8

All present enzymatic activity of Homoserine Dehydrogenase From Thermus Thermophilus HB8:
1.1.1.3;

Protein crystallography data

The structure of Homoserine Dehydrogenase From Thermus Thermophilus HB8, PDB code: 2ejw was solved by R.Omi, M.Goto, I.Miyahara, K.Hirotsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.36 / 1.70
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 165.439, 173.603, 97.123, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Homoserine Dehydrogenase From Thermus Thermophilus HB8 (pdb code 2ejw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Homoserine Dehydrogenase From Thermus Thermophilus HB8, PDB code: 2ejw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 2ejw

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Magnesium binding site 1 out of 7 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Homoserine Dehydrogenase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:11.9
occ:1.00
 O A:VAL124 2.3 10.0 1.0
O A:THR128 2.4 10.6 1.0
O A:ALA126 2.4 7.9 1.0
OE2 A:GLU121 2.4 8.6 1.0
O A:GLU121 2.5 9.6 1.0
CD A:GLU121 3.3 9.2 1.0
C A:ALA126 3.5 9.1 1.0
C A:VAL124 3.5 10.1 1.0
C A:GLU121 3.5 8.6 1.0
C A:THR128 3.6 9.9 1.0
CG A:GLU121 3.6 7.6 1.0
C A:MET125 3.7 8.5 1.0
O A:MET125 3.7 8.6 1.0
N A:ALA130 3.9 12.4 1.0
CB A:ALA130 3.9 11.6 1.0
N A:THR128 3.9 9.9 1.0
N A:ALA126 4.0 9.2 1.0
C A:GLY127 4.2 10.8 1.0
CA A:ALA126 4.3 9.2 1.0
CB A:MET125 4.3 11.5 1.0
CA A:MET125 4.3 10.2 1.0
N A:MET125 4.3 9.9 1.0
CA A:GLU121 4.4 7.7 1.0
CA A:THR128 4.4 11.2 1.0
N A:GLY127 4.4 9.1 1.0
N A:ALA122 4.4 9.0 1.0
N A:VAL124 4.5 9.4 1.0
C A:PRO129 4.5 14.1 1.0
CA A:ALA130 4.5 11.1 1.0
CA A:VAL124 4.5 9.4 1.0
OE1 A:GLU121 4.5 10.4 1.0
CA A:GLY127 4.5 9.9 1.0
CA A:ALA122 4.5 9.1 1.0
N A:PRO129 4.5 12.1 1.0
CA A:PRO129 4.5 12.5 1.0
CB A:GLU121 4.5 7.0 1.0
N A:LEU131 4.8 10.2 1.0
O A:GLY127 4.9 9.7 1.0
CB A:VAL124 4.9 10.2 1.0
C A:ALA122 4.9 9.7 1.0
CB A:THR128 5.0 12.2 1.0

Magnesium binding site 2 out of 7 in 2ejw

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Magnesium binding site 2 out of 7 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Homoserine Dehydrogenase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:20.5
occ:1.00
 O A:HOH2807 2.2 15.1 1.0
OD1 A:ASP68 2.2 14.6 1.0
O A:HOH2663 2.3 19.9 1.0
O A:HOH2779 2.4 29.7 1.0
O A:HOH2622 2.4 19.3 1.0
O A:HOH2652 2.4 21.1 1.0
CG A:ASP68 3.2 14.9 1.0
OD2 A:ASP68 3.5 15.1 1.0
O A:HOH2674 4.0 30.4 1.0
O A:HOH2834 4.1 27.3 1.0
O A:HOH2611 4.1 15.8 1.0
O A:HOH2658 4.1 19.3 1.0
O A:HOH2678 4.4 29.8 1.0
CB A:ASP68 4.5 12.9 1.0
O A:HOH2691 4.5 21.8 1.0
O A:HOH2645 4.5 19.2 1.0
O A:HOH2621 4.5 18.2 1.0
O A:ALA3 4.7 16.7 1.0
O A:HOH2825 4.8 30.9 1.0
CA A:ASP68 5.0 12.4 1.0

Magnesium binding site 3 out of 7 in 2ejw

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Magnesium binding site 3 out of 7 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Homoserine Dehydrogenase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:15.5
occ:1.00
 OE2 B:GLU114 2.2 14.7 1.0
O B:HOH2517 2.3 11.8 1.0
O B:HOH2504 2.4 14.2 1.0
O B:HOH2509 2.4 12.8 1.0
CD B:GLU114 3.1 15.1 1.0
OE1 B:GLU114 3.4 14.1 1.0
O B:ALA315 4.1 10.6 1.0
O B:HOH2674 4.2 17.6 1.0
CG B:GLU114 4.3 14.1 1.0
O B:PRO316 4.3 17.5 1.0
O B:PRO314 4.3 11.3 1.0
O A:HOH2638 4.4 20.1 1.0
CA B:PRO316 4.4 15.4 1.0
CB B:GLU114 4.4 13.2 1.0
O B:GLU114 4.7 15.1 1.0
CA B:GLU114 4.7 13.4 1.0
C B:PRO316 4.7 16.8 1.0
C B:ALA315 4.8 10.9 1.0
CD B:PRO314 4.9 9.8 1.0
CB B:PRO314 5.0 10.1 1.0
N B:PRO316 5.0 12.8 1.0
C B:PRO314 5.0 10.5 1.0

Magnesium binding site 4 out of 7 in 2ejw

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Magnesium binding site 4 out of 7 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Homoserine Dehydrogenase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2004

b:12.0
occ:1.00
 OE2 B:GLU121 2.4 9.4 1.0
O B:THR128 2.4 9.0 1.0
O B:VAL124 2.4 9.3 1.0
O B:ALA126 2.4 8.2 1.0
O B:GLU121 2.5 8.3 1.0
CD B:GLU121 3.2 12.0 1.0
CG B:GLU121 3.4 8.7 1.0
C B:GLU121 3.5 8.4 1.0
C B:ALA126 3.5 10.1 1.0
C B:THR128 3.5 8.6 1.0
C B:VAL124 3.6 9.9 1.0
O B:MET125 3.7 10.4 1.0
N B:ALA130 3.8 13.4 1.0
C B:MET125 3.8 10.0 1.0
N B:THR128 3.9 9.8 1.0
CB B:ALA130 4.0 12.7 1.0
N B:ALA126 4.1 11.1 1.0
C B:GLY127 4.2 9.7 1.0
CA B:GLU121 4.2 8.2 1.0
CA B:THR128 4.3 10.3 1.0
CA B:ALA126 4.4 10.1 1.0
N B:ALA122 4.4 9.0 1.0
CB B:GLU121 4.4 10.0 1.0
N B:GLY127 4.4 8.9 1.0
OE1 B:GLU121 4.4 9.8 1.0
N B:VAL124 4.4 9.9 1.0
N B:MET125 4.4 9.2 1.0
CA B:MET125 4.4 10.6 1.0
CA B:ALA130 4.5 12.2 1.0
CB B:MET125 4.5 11.7 1.0
CA B:GLY127 4.5 11.3 1.0
CA B:VAL124 4.5 9.1 1.0
N B:PRO129 4.5 10.1 1.0
CA B:ALA122 4.5 9.3 1.0
CA B:PRO129 4.6 11.4 1.0
C B:PRO129 4.7 14.4 1.0
N B:LEU131 4.7 10.8 1.0
O B:GLY127 4.8 10.7 1.0
CB B:VAL124 4.8 8.5 1.0
C B:ALA122 4.9 9.2 1.0
CB B:THR128 4.9 9.1 1.0

Magnesium binding site 5 out of 7 in 2ejw

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Magnesium binding site 5 out of 7 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Homoserine Dehydrogenase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2006

b:11.9
occ:1.00
 O E:ALA126 2.4 9.4 1.0
O E:GLU121 2.4 11.0 1.0
O E:VAL124 2.4 11.9 1.0
OE2 E:GLU121 2.4 12.2 1.0
O E:THR128 2.5 10.9 1.0
CD E:GLU121 3.3 12.3 1.0
C E:GLU121 3.4 11.2 1.0
CG E:GLU121 3.4 9.9 1.0
C E:ALA126 3.5 11.9 1.0
C E:VAL124 3.5 12.6 1.0
O E:MET125 3.7 9.9 1.0
C E:THR128 3.7 12.4 1.0
C E:MET125 3.8 11.6 1.0
CB E:ALA130 3.9 13.4 1.0
N E:ALA130 3.9 14.0 1.0
N E:THR128 4.0 11.5 1.0
N E:ALA126 4.1 12.4 1.0
CA E:GLU121 4.1 9.5 1.0
C E:GLY127 4.3 10.6 1.0
N E:ALA122 4.3 10.4 1.0
CB E:GLU121 4.3 10.0 1.0
CA E:ALA126 4.4 11.4 1.0
N E:VAL124 4.4 10.8 1.0
N E:MET125 4.4 10.8 1.0
CA E:MET125 4.4 12.1 1.0
N E:GLY127 4.4 10.8 1.0
CA E:ALA122 4.5 11.3 1.0
CB E:MET125 4.5 14.4 1.0
CA E:THR128 4.5 12.1 1.0
CA E:VAL124 4.5 11.9 1.0
OE1 E:GLU121 4.5 11.8 1.0
CA E:GLY127 4.5 12.2 1.0
CA E:ALA130 4.6 13.4 1.0
C E:PRO129 4.6 16.0 1.0
N E:PRO129 4.7 12.8 1.0
CA E:PRO129 4.7 14.2 1.0
O E:GLY127 4.8 11.7 1.0
N E:LEU131 4.8 12.5 1.0
CB E:VAL124 4.8 14.2 1.0
C E:ALA122 4.8 11.2 1.0

Magnesium binding site 6 out of 7 in 2ejw

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Magnesium binding site 6 out of 7 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Homoserine Dehydrogenase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2007

b:28.3
occ:1.00
 O F:HOH2776 2.2 29.5 1.0
O E:HOH2639 2.3 26.6 1.0
O F:HOH2729 2.4 21.8 1.0
O E:HOH2700 2.4 25.0 1.0
OE1 E:GLU24 2.4 28.5 1.0
O E:HOH2652 2.5 25.3 1.0
CD E:GLU24 3.2 27.2 1.0
CG E:GLU24 3.7 23.5 1.0
OE2 F:GLU141 3.9 20.6 1.0
OE1 F:GLU141 4.0 20.6 1.0
O F:HOH2778 4.1 26.9 1.0
O E:GLU24 4.1 18.4 1.0
OE2 E:GLU24 4.1 28.7 1.0
CD F:GLU141 4.4 20.2 1.0
CD2 F:LEU322 4.9 28.5 1.0
C E:GLU24 4.9 19.5 1.0

Magnesium binding site 7 out of 7 in 2ejw

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Magnesium binding site 7 out of 7 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Homoserine Dehydrogenase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2005

b:12.0
occ:1.00
 O F:ALA126 2.3 12.9 1.0
OE2 F:GLU121 2.3 10.5 1.0
O F:VAL124 2.3 10.9 1.0
O F:THR128 2.4 10.8 1.0
O F:GLU121 2.4 10.0 1.0
CD F:GLU121 3.2 9.4 1.0
CG F:GLU121 3.4 10.2 1.0
C F:GLU121 3.4 9.9 1.0
C F:ALA126 3.5 12.2 1.0
C F:VAL124 3.5 11.1 1.0
C F:THR128 3.6 11.2 1.0
O F:MET125 3.7 10.5 1.0
C F:MET125 3.8 11.2 1.0
N F:ALA130 3.9 13.4 1.0
CB F:ALA130 3.9 14.0 1.0
N F:THR128 4.0 10.3 1.0
N F:ALA126 4.0 11.9 1.0
CA F:GLU121 4.2 9.2 1.0
C F:GLY127 4.3 10.8 1.0
CA F:ALA126 4.3 12.5 1.0
N F:ALA122 4.3 10.2 1.0
CA F:MET125 4.3 12.2 1.0
CB F:GLU121 4.4 9.5 1.0
CB F:MET125 4.4 12.9 1.0
N F:MET125 4.4 10.8 1.0
CA F:THR128 4.4 11.1 1.0
OE1 F:GLU121 4.4 12.3 1.0
N F:GLY127 4.4 10.4 1.0
N F:VAL124 4.4 9.6 1.0
CA F:ALA122 4.5 10.2 1.0
CA F:VAL124 4.5 10.7 1.0
CA F:ALA130 4.5 13.3 1.0
CA F:GLY127 4.5 10.8 1.0
C F:PRO129 4.6 15.7 1.0
N F:PRO129 4.6 11.9 1.0
CA F:PRO129 4.6 13.4 1.0
N F:LEU131 4.8 11.7 1.0
CB F:VAL124 4.8 10.5 1.0
C F:ALA122 4.8 11.0 1.0
O F:GLY127 4.9 12.0 1.0
CB F:THR128 5.0 10.4 1.0

Reference:

R.Omi, M.Goto, I.Miyahara, K.Hirotsu. Crystal Structure of Homoserine Dehydrogenase From Thermus Thermophilus HB8 To Be Published.
Page generated: Tue Aug 13 22:47:58 2024

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