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Magnesium in PDB 3c1m: Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate

Enzymatic activity of Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate

All present enzymatic activity of Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate:
2.7.2.4;

Protein crystallography data

The structure of Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate, PDB code: 3c1m was solved by X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.408, 104.478, 192.045, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate (pdb code 3c1m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate, PDB code: 3c1m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3c1m

Go back to Magnesium Binding Sites List in 3c1m
Magnesium binding site 1 out of 4 in the Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:32.3
occ:1.00
 O1A A:ANP472 2.0 29.5 1.0
O1G A:ANP472 2.0 32.7 1.0
O A:HOH533 2.0 23.6 1.0
O2B A:ANP472 2.1 27.7 1.0
O A:HOH512 2.1 24.0 1.0
O A:HOH514 2.2 21.9 1.0
PB A:ANP472 3.2 26.3 1.0
PG A:ANP472 3.2 30.5 1.0
PA A:ANP472 3.2 28.0 1.0
N3B A:ANP472 3.5 28.8 1.0
O3A A:ANP472 3.6 28.1 1.0
O2G A:ANP472 3.6 30.8 1.0
O5' A:ANP472 3.9 28.3 1.0
O A:HOH501 4.0 34.0 1.0
O A:HOH638 4.0 43.2 1.0
OD2 A:ASP211 4.1 22.2 1.0
O A:LYS266 4.2 22.0 1.0
OD1 A:ASP471 4.3 37.8 1.0
OD2 A:ASP471 4.3 35.7 1.0
NZ A:LYS6 4.3 19.8 1.0
O A:HOH556 4.3 36.0 1.0
O3G A:ANP472 4.4 31.6 1.0
CA A:GLY208 4.5 21.6 1.0
O2A A:ANP472 4.5 30.5 1.0
O1B A:ANP472 4.6 24.7 1.0
OD1 A:ASP211 4.6 21.9 1.0
CG A:ASP211 4.7 21.8 1.0
CG A:ASP471 4.7 35.8 1.0
O A:GLY208 4.8 21.4 1.0
O A:VAL267 5.0 22.6 1.0

Magnesium binding site 2 out of 4 in 3c1m

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Magnesium binding site 2 out of 4 in the Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate


Mono view


Stereo pair view

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

b:30.0
occ:1.00
 O1G B:ANP473 2.0 35.5 1.0
O B:HOH509 2.1 29.9 1.0
O B:HOH545 2.1 24.9 1.0
O3A B:ANP473 2.1 43.7 1.0
O B:HOH504 2.2 29.5 1.0
O2B B:ANP473 2.6 42.4 1.0
PB B:ANP473 3.0 39.4 1.0
PG B:ANP473 3.2 36.3 1.0
PA B:ANP473 3.5 39.9 1.0
N3B B:ANP473 3.6 38.8 1.0
O2G B:ANP473 3.8 33.8 1.0
O1A B:ANP473 3.9 43.1 1.0
O5' B:ANP473 3.9 40.8 1.0
O B:HOH590 4.0 31.9 1.0
O B:LYS266 4.1 21.2 1.0
O B:HOH517 4.1 40.2 1.0
OD2 B:ASP211 4.2 19.3 1.0
OD2 B:ASP472 4.3 34.4 1.0
O B:HOH614 4.3 33.0 1.0
O B:HOH620 4.3 48.1 1.0
OD1 B:ASP472 4.3 34.2 1.0
O1B B:ANP473 4.3 42.6 1.0
NZ B:LYS6 4.4 13.5 1.0
O3G B:ANP473 4.5 34.9 1.0
O2A B:ANP473 4.5 46.5 1.0
CA B:GLY208 4.6 19.4 1.0
OD1 B:ASP211 4.7 21.3 1.0
CG B:ASP472 4.7 35.1 1.0
CG B:LYS266 4.8 22.9 1.0
CG B:ASP211 4.8 20.2 1.0
O B:GLY208 4.8 19.4 1.0
CE B:LYS266 4.9 24.3 1.0
O B:HOH594 4.9 37.7 1.0

Magnesium binding site 3 out of 4 in 3c1m

Go back to Magnesium Binding Sites List in 3c1m
Magnesium binding site 3 out of 4 in the Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate


Mono view


Stereo pair view

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

b:45.0
occ:1.00
 O C:HOH547 2.1 42.6 1.0
O C:HOH520 2.1 34.5 1.0
O1A C:ANP473 2.2 48.0 1.0
O1G C:ANP473 2.3 43.5 1.0
O2B C:ANP473 2.8 46.1 1.0
O3A C:ANP473 3.2 47.5 1.0
PA C:ANP473 3.3 46.1 1.0
PB C:ANP473 3.4 45.5 1.0
PG C:ANP473 3.4 42.1 1.0
N3B C:ANP473 3.7 43.5 1.0
O2G C:ANP473 3.8 41.2 1.0
O C:HOH587 3.9 39.4 1.0
O C:LYS266 3.9 22.4 1.0
O C:HOH591 4.0 36.3 1.0
OD2 C:ASP211 4.0 21.6 1.0
OXT C:ASP472 4.1 39.6 1.0
O5' C:ANP473 4.1 47.2 1.0
O C:ASP472 4.3 39.4 1.0
CA C:GLY208 4.4 23.3 1.0
NZ C:LYS6 4.4 17.6 1.0
O2A C:ANP473 4.6 49.3 1.0
C C:ASP472 4.7 39.5 1.0
CG C:ASP211 4.7 22.1 1.0
O3G C:ANP473 4.7 43.2 1.0
OD1 C:ASP211 4.7 22.6 1.0
O C:GLY208 4.8 23.8 1.0
O1B C:ANP473 4.9 46.3 1.0
CE C:LYS266 4.9 23.3 1.0
CG C:LYS266 4.9 23.0 1.0

Magnesium binding site 4 out of 4 in 3c1m

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Magnesium binding site 4 out of 4 in the Cyrstal Structure of Threonine-Sensitive Aspartokinase From Methanococcus Jannaschii with Mgamp-Pnp and L-Aspartate


Mono view


Stereo pair view

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

b:22.8
occ:1.00
 O1A D:ANP473 2.0 29.1 1.0
O D:HOH537 2.0 18.5 1.0
O D:HOH522 2.1 24.7 1.0
O1G D:ANP473 2.1 30.4 1.0
O D:HOH498 2.1 24.7 1.0
O2B D:ANP473 2.2 27.4 1.0
PG D:ANP473 3.3 29.8 1.0
PB D:ANP473 3.3 28.2 1.0
PA D:ANP473 3.3 28.1 1.0
N3B D:ANP473 3.7 29.1 1.0
O3A D:ANP473 3.7 27.8 1.0
O2G D:ANP473 3.7 30.2 1.0
OD2 D:ASP211 3.9 20.1 1.0
O D:HOH507 4.0 30.4 1.0
O D:HOH541 4.1 35.9 1.0
O5' D:ANP473 4.1 28.6 1.0
OD2 D:ASP472 4.1 30.8 1.0
O D:LYS266 4.2 21.6 1.0
O D:HOH506 4.2 29.0 1.0
OD1 D:ASP472 4.2 33.4 1.0
CA D:GLY208 4.4 19.9 1.0
NZ D:LYS6 4.4 15.6 1.0
O2A D:ANP473 4.5 30.2 1.0
O3G D:ANP473 4.5 27.3 1.0
CG D:ASP472 4.6 30.9 1.0
O D:GLY208 4.6 20.1 1.0
O1B D:ANP473 4.6 28.1 1.0
CG D:ASP211 4.7 20.1 1.0
CE D:LYS266 4.8 25.8 1.0
OD1 D:ASP211 4.8 19.3 1.0
C D:GLY208 4.9 19.7 1.0
O D:HOH553 5.0 39.3 1.0

Reference:

X.Liu, A.G.Pavlovsky, R.E.Viola. The Structural Basis For Allosteric Inhibition of A Threonine-Sensitive Aspartokinase. J.Biol.Chem. V. 283 16216 2008.
ISSN: ISSN 0021-9258
PubMed: 18334478
DOI: 10.1074/JBC.M800760200
Page generated: Wed Aug 14 09:24:47 2024

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