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Magnesium in PDB 2pa4: Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose

Enzymatic activity of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose

All present enzymatic activity of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose:
2.7.7.9;

Protein crystallography data

The structure of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose, PDB code: 2pa4 was solved by H.M.Holden, J.B.Thoden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.400, 47.600, 161.500, 90.00, 102.70, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose (pdb code 2pa4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose, PDB code: 2pa4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2pa4

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Magnesium binding site 1 out of 8 in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg324

b:37.4
occ:1.00
 O A:HOH334 2.0 29.0 1.0
O A:HOH333 2.0 29.9 1.0
O1A A:UPG326 2.1 26.8 1.0
O A:HOH335 2.2 37.2 1.0
O A:HOH332 2.2 34.1 1.0
O A:HOH405 2.3 41.8 1.0
PA A:UPG326 3.5 35.5 1.0
O3A A:UPG326 3.8 33.1 1.0
O A:HOH406 3.8 43.0 1.0
O2B A:UPG326 4.1 33.3 1.0
O A:HOH410 4.1 36.7 1.0
O A:HOH484 4.2 46.2 1.0
OE2 A:GLU238 4.2 39.5 1.0
O5C A:UPG326 4.3 30.9 1.0
O A:HOH452 4.3 44.4 1.0
OE1 A:GLU238 4.4 35.5 1.0
O A:HOH328 4.5 17.7 1.0
O A:HOH327 4.5 23.2 1.0
O A:HOH371 4.5 39.7 1.0
O2A A:UPG326 4.5 32.1 1.0
O A:HOH453 4.6 43.9 1.0
PB A:UPG326 4.7 30.9 1.0
CD A:GLU238 4.8 32.9 1.0
O A:HOH430 4.9 54.0 1.0
C6 A:UPG326 4.9 32.7 1.0
C5 A:UPG326 5.0 29.7 1.0

Magnesium binding site 2 out of 8 in 2pa4

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Magnesium binding site 2 out of 8 in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg325

b:29.3
occ:1.00
 O A:HOH336 2.0 27.8 1.0
O2A A:UPG326 2.0 32.1 1.0
O1B A:UPG326 2.0 32.0 1.0
OD2 A:ASP142 2.1 37.8 1.0
O A:HOH337 2.2 28.7 1.0
O A:HOH363 2.2 27.9 1.0
CG A:ASP142 3.2 18.5 1.0
PA A:UPG326 3.2 35.5 1.0
PB A:UPG326 3.3 30.9 1.0
O3A A:UPG326 3.5 33.1 1.0
OD1 A:ASP142 3.5 32.3 1.0
NZ A:LYS35 3.9 25.8 1.0
O6' A:UPG326 3.9 32.7 1.0
O A:HOH410 4.0 36.7 1.0
O A:HOH451 4.1 33.6 1.0
O5C A:UPG326 4.2 30.9 1.0
O5' A:UPG326 4.2 35.2 1.0
O2B A:UPG326 4.2 33.3 1.0
C5C A:UPG326 4.2 31.4 1.0
O1A A:UPG326 4.2 26.8 1.0
CA A:GLY268 4.3 19.1 1.0
OD1 A:ASP266 4.4 32.7 1.0
O3B A:UPG326 4.4 32.4 1.0
O A:HOH366 4.4 38.8 1.0
CB A:ASP142 4.4 15.2 1.0
C1' A:UPG326 4.7 31.0 1.0
CE A:LYS35 4.7 17.7 1.0
C5' A:UPG326 4.8 30.7 1.0
C6' A:UPG326 4.9 33.5 1.0
N A:GLY268 5.0 16.7 1.0
O A:ASP142 5.0 33.4 1.0

Magnesium binding site 3 out of 8 in 2pa4

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Magnesium binding site 3 out of 8 in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg324

b:38.7
occ:1.00
 O1A B:UPG326 1.9 33.5 1.0
O B:HOH331 2.0 36.6 1.0
O B:HOH332 2.1 40.4 1.0
O B:HOH380 2.1 48.2 1.0
O B:HOH379 2.2 39.2 1.0
O B:HOH333 2.3 41.8 1.0
PA B:UPG326 3.4 33.7 1.0
O3A B:UPG326 3.9 35.5 1.0
O5C B:UPG326 4.1 36.3 1.0
O B:HOH401 4.1 44.5 1.0
OE1 B:GLU238 4.2 42.5 1.0
O B:HOH381 4.3 44.1 1.0
O2B B:UPG326 4.3 33.1 1.0
OE2 B:GLU238 4.3 46.2 1.0
O C:HOH327 4.4 28.5 1.0
O B:HOH327 4.4 18.5 1.0
O B:HOH334 4.4 46.1 1.0
O B:HOH352 4.4 29.1 1.0
O2A B:UPG326 4.4 35.5 1.0
CD B:GLU238 4.7 81.6 1.0
C6 B:UPG326 4.8 32.1 1.0
O B:HOH403 4.8 51.6 1.0
C5 B:UPG326 4.8 33.0 1.0
PB B:UPG326 4.9 36.4 1.0

Magnesium binding site 4 out of 8 in 2pa4

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Magnesium binding site 4 out of 8 in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg325

b:30.8
occ:1.00
 OD2 B:ASP142 1.9 27.2 1.0
O B:HOH335 1.9 28.3 1.0
O1B B:UPG326 2.0 35.8 1.0
O B:HOH336 2.1 31.2 1.0
O B:HOH382 2.1 35.8 1.0
O2A B:UPG326 2.2 35.5 1.0
CG B:ASP142 2.9 26.3 1.0
PB B:UPG326 3.3 36.4 1.0
OD1 B:ASP142 3.3 39.9 1.0
PA B:UPG326 3.4 33.7 1.0
O3A B:UPG326 3.5 35.5 1.0
NZ B:LYS35 4.0 26.9 1.0
O6' B:UPG326 4.0 36.7 1.0
C5C B:UPG326 4.2 31.0 1.0
O B:HOH381 4.2 44.1 1.0
OD1 B:ASP266 4.2 38.7 1.0
CB B:ASP142 4.2 27.9 1.0
O5' B:UPG326 4.3 41.1 1.0
O5C B:UPG326 4.3 36.3 1.0
CA B:GLY268 4.4 18.7 1.0
O2B B:UPG326 4.4 33.1 1.0
O3B B:UPG326 4.5 38.3 1.0
O1A B:UPG326 4.6 33.5 1.0
O B:ASP142 4.7 24.7 1.0
CE B:LYS35 4.7 21.5 1.0
O B:HOH399 4.7 37.0 1.0
C1' B:UPG326 4.8 35.0 1.0
C5' B:UPG326 4.9 39.6 1.0
N B:GLY268 5.0 31.3 1.0

Magnesium binding site 5 out of 8 in 2pa4

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Magnesium binding site 5 out of 8 in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg324

b:45.6
occ:1.00
 O C:HOH405 1.7 51.3 1.0
O C:HOH333 2.0 40.5 1.0
O C:HOH407 2.0 39.4 1.0
O1A C:UPG326 2.0 35.1 1.0
O C:HOH332 2.1 35.8 1.0
O C:HOH404 2.3 37.3 1.0
PA C:UPG326 3.4 37.1 1.0
O3A C:UPG326 3.9 39.3 1.0
O5C C:UPG326 4.1 37.3 1.0
O C:HOH334 4.2 46.0 1.0
O2B C:UPG326 4.2 33.6 1.0
O C:HOH337 4.2 45.5 1.0
OE2 C:GLU238 4.3 59.7 1.0
OE1 C:GLU238 4.3 42.0 1.0
O C:HOH406 4.4 35.6 1.0
O C:HOH400 4.4 21.3 1.0
O2A C:UPG326 4.5 37.0 1.0
O C:HOH399 4.6 31.2 1.0
CD C:GLU238 4.7 57.6 1.0
PB C:UPG326 4.7 39.7 1.0
NZ C:LYS202 4.8 29.7 1.0
C6 C:UPG326 4.9 37.5 1.0

Magnesium binding site 6 out of 8 in 2pa4

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Magnesium binding site 6 out of 8 in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg325

b:34.1
occ:1.00
 OD2 C:ASP142 1.9 31.8 1.0
O1B C:UPG326 1.9 36.5 1.0
O C:HOH336 2.0 31.9 1.0
O2A C:UPG326 2.1 37.0 1.0
O C:HOH409 2.1 32.6 1.0
O C:HOH408 2.2 34.2 1.0
CG C:ASP142 2.9 16.9 1.0
OD1 C:ASP142 3.1 37.7 1.0
PB C:UPG326 3.2 39.7 1.0
PA C:UPG326 3.3 37.1 1.0
O3A C:UPG326 3.4 39.3 1.0
O6' C:UPG326 3.8 34.6 1.0
NZ C:LYS35 3.9 35.8 1.0
CB C:ASP142 4.2 22.6 1.0
OD1 C:ASP266 4.2 36.9 1.0
O C:HOH335 4.2 39.8 1.0
C5C C:UPG326 4.3 34.9 1.0
O5C C:UPG326 4.3 37.3 1.0
O2B C:UPG326 4.3 33.6 1.0
CA C:GLY268 4.3 20.0 1.0
O3B C:UPG326 4.4 35.9 1.0
O5' C:UPG326 4.4 35.5 1.0
O1A C:UPG326 4.4 35.1 1.0
O C:HOH334 4.5 46.0 1.0
O C:ASP142 4.7 33.0 1.0
C1' C:UPG326 4.7 36.6 1.0
CE C:LYS35 4.8 22.7 1.0
C5' C:UPG326 4.9 34.5 1.0
C6' C:UPG326 5.0 31.5 1.0
CG C:ASP266 5.0 36.2 1.0
N C:GLY268 5.0 26.1 1.0

Magnesium binding site 7 out of 8 in 2pa4

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Magnesium binding site 7 out of 8 in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg324

b:38.9
occ:1.00
 O D:HOH332 2.0 37.2 1.0
O D:HOH333 2.0 35.2 1.0
O1A D:UPG326 2.1 31.4 1.0
O D:HOH339 2.1 49.9 1.0
O D:HOH350 2.2 38.0 1.0
O D:HOH351 2.2 38.5 1.0
PA D:UPG326 3.5 32.7 1.0
O3A D:UPG326 4.1 35.5 1.0
OE1 D:GLU238 4.1 32.8 1.0
O D:HOH390 4.2 57.0 1.0
O2B D:UPG326 4.2 30.7 1.0
OE2 D:GLU238 4.2 35.7 1.0
O D:HOH327 4.3 28.4 1.0
O5C D:UPG326 4.3 30.3 1.0
O D:HOH420 4.3 45.5 1.0
O D:HOH328 4.4 22.3 1.0
CD D:GLU238 4.6 33.8 1.0
O2A D:UPG326 4.6 29.1 1.0
O D:HOH334 4.7 55.6 1.0
C6 D:UPG326 4.8 34.2 1.0
C5 D:UPG326 4.9 32.6 1.0
PB D:UPG326 4.9 34.1 1.0

Magnesium binding site 8 out of 8 in 2pa4

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Magnesium binding site 8 out of 8 in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Udp-Glucose Pyrophosphorylase From Corynebacteria Glutamicum in Complex with Magnesium and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg325

b:34.1
occ:1.00
 O D:HOH335 2.0 35.1 1.0
OD2 D:ASP142 2.0 23.7 1.0
O2A D:UPG326 2.0 29.1 1.0
O1B D:UPG326 2.1 36.2 1.0
O D:HOH349 2.1 34.2 1.0
O D:HOH336 2.2 33.4 1.0
CG D:ASP142 3.1 22.4 1.0
PB D:UPG326 3.3 34.1 1.0
PA D:UPG326 3.3 32.7 1.0
OD1 D:ASP142 3.4 32.0 1.0
O3A D:UPG326 3.5 35.5 1.0
NZ D:LYS35 3.6 28.3 1.0
O D:HOH393 3.9 41.5 1.0
O6' D:UPG326 4.1 41.2 1.0
OD1 D:ASP266 4.2 30.3 1.0
C5C D:UPG326 4.2 30.2 1.0
O5C D:UPG326 4.2 30.3 1.0
CA D:GLY268 4.2 23.2 1.0
O2B D:UPG326 4.3 30.7 1.0
O D:HOH392 4.3 48.6 1.0
CB D:ASP142 4.3 17.6 1.0
O1A D:UPG326 4.4 31.4 1.0
O3B D:UPG326 4.4 35.8 1.0
O5' D:UPG326 4.4 39.0 1.0
CE D:LYS35 4.7 19.7 1.0
C1' D:UPG326 4.8 37.6 1.0
N D:GLY268 4.9 23.6 1.0
O D:ASP142 4.9 38.1 1.0
C5' D:UPG326 5.0 38.5 1.0

Reference:

J.B.Thoden, H.M.Holden. Active Site Geometry of Glucose-1-Phosphate Uridylyltransferase. Protein Sci. V. 16 1379 2007.
ISSN: ISSN 0961-8368
PubMed: 17567737
DOI: 10.1110/PS.072864707
Page generated: Mon Dec 14 07:34:21 2020

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