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Magnesium in PDB 2hmf: Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate

Enzymatic activity of Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate

All present enzymatic activity of Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate:
2.7.2.4;

Protein crystallography data

The structure of Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate, PDB code: 2hmf was solved by C.R.Faehnle, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.741, 104.508, 192.920, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 27.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate (pdb code 2hmf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate, PDB code: 2hmf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2hmf

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Magnesium binding site 1 out of 4 in the Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg471

b:43.2
occ:1.00
 O1A A:ADP472 2.1 30.5 1.0
O3B A:ADP472 2.3 29.0 1.0
OD1 A:ASP502 3.4 46.4 1.0
PB A:ADP472 3.5 26.2 1.0
PA A:ADP472 3.5 29.1 1.0
CA A:GLY208 3.9 34.3 1.0
CG A:ASP502 3.9 44.2 1.0
O2B A:ADP472 3.9 27.2 1.0
O3A A:ADP472 3.9 25.3 1.0
OD2 A:ASP502 4.1 44.2 1.0
OD2 A:ASP211 4.3 34.0 1.0
O A:GLY208 4.4 34.6 1.0
O A:LYS266 4.5 37.8 1.0
O5' A:ADP472 4.5 28.7 1.0
C A:GLY208 4.5 34.4 1.0
NZ A:LYS6 4.6 37.4 1.0
O2A A:ADP472 4.6 30.7 1.0
CE A:LYS266 4.6 39.9 1.0
O1B A:ADP472 4.8 24.9 1.0
CG A:ASP211 4.9 34.7 1.0
OD1 A:ASP211 4.9 34.1 1.0
CB A:ASP502 4.9 43.0 1.0
N A:GLY208 4.9 34.1 1.0

Magnesium binding site 2 out of 4 in 2hmf

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Magnesium binding site 2 out of 4 in the Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg471

b:31.5
occ:1.00
 O3B B:ADP472 2.1 34.6 1.0
O1A B:ADP472 2.2 36.1 1.0
O B:HOH504 2.6 27.9 1.0
PB B:ADP472 3.4 34.1 1.0
OD1 B:ASP501 3.5 44.0 1.0
PA B:ADP472 3.6 36.0 1.0
O3A B:ADP472 3.9 35.7 1.0
O B:HOH522 3.9 34.1 1.0
O2B B:ADP472 4.0 33.5 1.0
CA B:GLY208 4.0 34.3 1.0
OD2 B:ASP211 4.1 34.1 1.0
O B:LYS266 4.3 37.9 1.0
O B:GLY208 4.3 34.5 1.0
CG B:ASP501 4.4 42.2 1.0
O5' B:ADP472 4.4 36.3 1.0
NZ B:LYS6 4.4 37.6 1.0
OD2 B:ASP501 4.5 41.4 1.0
C B:GLY208 4.6 34.3 1.0
OD1 B:ASP211 4.6 33.9 1.0
CG B:ASP211 4.6 34.7 1.0
O1B B:ADP472 4.6 33.8 1.0
O2A B:ADP472 4.7 34.5 1.0
CE B:LYS266 4.8 39.8 1.0

Magnesium binding site 3 out of 4 in 2hmf

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Magnesium binding site 3 out of 4 in the Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg471

b:47.1
occ:1.00
 O1A C:ADP472 2.0 40.6 1.0
O3B C:ADP472 2.3 40.3 1.0
PA C:ADP472 3.5 39.6 1.0
PB C:ADP472 3.7 39.4 1.0
O C:LYS266 3.8 37.9 1.0
OD2 C:ASP211 4.0 34.0 1.0
CA C:GLY208 4.0 34.4 1.0
O3A C:ADP472 4.0 39.1 1.0
O5' C:ADP472 4.3 41.2 1.0
O C:GLY208 4.4 34.5 1.0
OD2 C:ASP503 4.5 38.2 1.0
OD1 C:ASP503 4.5 38.9 1.0
O2B C:ADP472 4.5 38.7 1.0
CE C:LYS266 4.5 39.8 1.0
O2A C:ADP472 4.5 39.7 1.0
CG C:ASP211 4.6 34.9 1.0
C C:GLY208 4.7 34.4 1.0
NZ C:LYS6 4.7 37.6 1.0
CG C:LYS266 4.7 38.5 1.0
OD1 C:ASP211 4.7 34.3 1.0
O1B C:ADP472 4.7 39.3 1.0
CG C:ASP503 4.8 37.0 1.0
C C:LYS266 4.9 37.8 1.0
CD C:LYS266 5.0 39.4 1.0

Magnesium binding site 4 out of 4 in 2hmf

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Magnesium binding site 4 out of 4 in the Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Threonine Sensitive Aspartokinase From Methanococcus Jannaschii Complexed with Mg-Adp and Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg471

b:32.4
occ:1.00
 O3B D:ADP472 2.1 25.2 1.0
O1A D:ADP472 2.1 29.6 1.0
O D:HOH516 2.6 31.4 1.0
PB D:ADP472 3.4 26.0 1.0
PA D:ADP472 3.5 28.1 1.0
O3A D:ADP472 3.8 24.9 1.0
O2B D:ADP472 4.0 26.5 1.0
O D:LYS266 4.1 37.8 1.0
OD2 D:ASP211 4.1 33.8 1.0
CA D:GLY208 4.1 34.3 1.0
O5' D:ADP472 4.1 28.0 1.0
OD1 D:ASP504 4.3 28.1 1.0
NZ D:LYS6 4.5 37.5 1.0
O D:GLY208 4.5 34.5 1.0
O1B D:ADP472 4.6 25.9 1.0
OD2 D:ASP504 4.6 30.2 1.0
CG D:ASP211 4.7 34.6 1.0
CE D:LYS266 4.7 39.9 1.0
OD1 D:ASP211 4.7 34.0 1.0
O2A D:ADP472 4.7 28.1 1.0
C D:GLY208 4.8 34.3 1.0
CG D:ASP504 4.8 29.1 1.0
CG D:LYS266 5.0 38.5 1.0

Reference:

C.R.Faehnle, X.Liu, A.Pavlovsky, R.E.Viola. The Initial Step in the Archaeal Aspartate Biosynthetic Pathway Catalyzed By A Monofunctional Aspartokinase. Acta Crystallogr.,Sect.F V. 62 962 2006.
ISSN: ESSN 1744-3091
PubMed: 17012784
DOI: 10.1107/S1744309106038279
Page generated: Sun Aug 10 11:24:27 2025

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